WorldWideScience

Sample records for atom molecular mechanics

  1. 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...

  2. 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.

  3. MATCH: an atom-typing toolset for molecular mechanics force fields.

    Science.gov (United States)

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

    2012-01-15

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

  4. Molecular mechanics on bonding and non-bonding interactions in (atom@C60)

    Institute of Scientific and Technical Information of China (English)

    朱传宝; 徐志谨; 严继民

    1997-01-01

    The interactions between the embedded atom X (X=Li,Na,K,Rb,Cs; F,Cl,Br,I) and C60cage in the endohedral-form complexes (X@C60) are calculated and discussed according to molecular mechanics from the point of view of the bonding and non-bonding.It is found from the computational results that for atoms with radii larger than Li’s,their locations with the minimum interaction in (X@C60) are at the cage center,while atom Li has an off-center location with the minimum interaction deviation of-0.05 nm,and the cage-environment in C60 can be regarded as sphero-symmetry in the region with radius r of ~0.2 nm.It is shown that the interaction between X and C60 cage is of non-bonding characteristic,and this non-bonding interaction is not purely electrostatic.The repulsion and dispersion in non-bonding interactions should not be neglected,which make important contribution to the location with minimum interaction of X,at center or off center.Some rules about the variations of interactions with atomic radii have been ob

  5. 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.

  6. Atomic and molecular supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.

    1997-12-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  7. 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...

  8. Atomic & Molecular Interactions

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & 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.

  9. The mechanical robustness of atomic-layer- and molecular-layer-deposited coatings on polymer substrates

    Science.gov (United States)

    Miller, David C.; Foster, Ross R.; Zhang, Yadong; Jen, Shih-Hui; Bertrand, Jacob A.; Lu, Zhixing; Seghete, Dragos; O'Patchen, Jennifer L.; Yang, Ronggui; Lee, Yung-Cheng; George, Steven M.; Dunn, Martin L.

    2009-05-01

    The mechanical robustness of atomic layer deposited alumina and recently developed molecular layer deposited aluminum alkoxide ("alucone") films, as well as laminated composite films composed of both materials, was characterized using mechanical tensile tests along with a recently developed fluorescent tag to visualize channel cracks in the transparent films. All coatings were deposited on polyethylene naphthalate substrates and demonstrated a similar evolution of damage morphology according to applied strain, including channel crack initiation, crack propagation at the critical strain, crack densification up to saturation, and transverse crack formation associated with buckling and delamination. From measurements of crack density versus applied tensile strain coupled with a fracture mechanics model, the mode I fracture toughness of alumina and alucone films was determined to be KIC=1.89±0.10 and 0.17±0.02 MPa m0.5, respectively. From measurements of the saturated crack density, the critical interfacial shear stress was estimated to be τc=39.5±8.3 and 66.6±6.1 MPa, respectively. The toughness of nanometer-scale alumina was comparable to that of alumina thin films grown using other techniques, whereas alucone was quite brittle. The use of alucone as a spacer layer between alumina films was not found to increase the critical strain at fracture for the composite films. This performance is attributed to the low toughness of alucone. The experimental results were supported by companion simulations using fracture mechanics formalism for multilayer films. To aid future development, the modeling method was used to study the increase in the toughness and elastic modulus of the spacer layer required to render improved critical strain at fracture. These results may be applied to a broad variety of multilayer material systems composed of ceramic and spacer layers to yield robust coatings for use in chemical barrier and other applications.

  10. 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.

  11. Reaction of Np atom with H₂O in the gas phase: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-01

    The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.

  12. 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

    2007-12-01

    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.

  13. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    Science.gov (United States)

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

  14. Atomic and Molecular Processes

    Science.gov (United States)

    1980-06-25

    The topics investigated experimentally and theoretically by the Pittsburgh Atomic Sciences Institute with applications to high power laser development and atmospheric IR backgrounds are enumerated. Reports containing the detailed scientific progress in these studies are cited. Finally, a list of the journal articles describing the results of the programs, with full references, is given.

  15. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-06

    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  16. 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

  17. Atomic mechanics of solids

    CERN Document Server

    MacPherson, A K

    1990-01-01

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

  18. Generation of molecular diffuse-band stimulated radiation through multiple excitation mechanism in potassium molecule-atom system

    Institute of Scientific and Technical Information of China (English)

    贾锁堂; 秦莉娟; 钱祖良; 王祖赓; 王钢; 周国生

    1997-01-01

    Population reduction effect generated in two-photon resonant excitation process of potassium atoms in a potassium molecule-atom system is theoretically investigated The obtained result is compared with the relevant experimental ones in the process of two-photon resonant excitation of potassium molecules and in the process of two-photon mixed excitation of potassium molecule-atoms.

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-21

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

  1. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Bederson, Benjamin

    1993-01-01

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

  2. 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

  3. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    Science.gov (United States)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

  4. 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)

  5. Molecular Mechanisms of Preeclampsia

    OpenAIRE

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

    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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Berman, Paul R; Arimondo, Ennio

    2006-01-01

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

  11. 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.

  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 adsorption on Rh(111)

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    Science.gov (United States)

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

    2011-10-01

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

  15. Molecular photons interfaced with alkali atoms.

    Science.gov (United States)

    Siyushev, Petr; Stein, Guilherme; Wrachtrup, Jörg; Gerhardt, Ilja

    2014-05-01

    Future quantum communication will rely on the integration of single-photon sources, quantum memories and systems with strong single-photon nonlinearities. Two key parameters are crucial for the single-photon source: a high photon flux with a very small bandwidth, and a spectral match to other components of the system. Atoms or ions may act as single-photon sources--owing to their narrowband emission and their intrinsic spectral match to other atomic systems--and can serve as quantum nonlinear elements. Unfortunately, their emission rates are still limited, even for highly efficient cavity designs. Single solid-state emitters such as single organic dye molecules are significantly brighter and allow for narrowband photons; they have shown potential in a variety of quantum optical experiments but have yet to be interfaced with other components such as stationary memory qubits. Here we describe the optical interaction between Fourier-limited photons from a single organic molecule and atomic alkali vapours, which can constitute an efficient quantum memory. Single-photon emission rates reach up to several hundred thousand counts per second and show a high spectral brightness of 30,000 detectable photons per second per megahertz of bandwidth. The molecular emission is robust and we demonstrate perfect tuning to the spectral transitions of the sodium D line and efficient filtering, even for emitters at ambient conditions. In addition, we achieve storage of molecular photons originating from a single dibenzanthanthrene molecule in atomic sodium vapour. Given the large set of molecular emission lines matching to atomic transitions, our results enable the combination of almost ideal single-photon sources with various atomic vapours, such that experiments with giant single-photon nonlinearities, mediated, for example, by Rydberg atoms, become feasible.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-01-01

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

  18. 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

  19. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

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

  20. Theory of atomic additivity in molecular hyperpolizabilities

    Science.gov (United States)

    Baird, James K.

    1987-01-01

    Hyperpolarizability is a function of frequency. This is called dispersion. Because of the Kramers-Kronig relations, researchers expect that a material that is dispersing light is also absorbing it. Where there is both dispersion and absorption, the molecular polarizabilities are complex functions of the frequency. This led researchers to consider atomic additivity in both the real and imaginary parts of the ordinary and hyperpolarizabilities. This effort is desirable not only from a theoretical point of view, but also because of the existence of a large body of complex refractive index data, which may be used to test the additivity principle with the complex valued ordinary dipole polarizability.

  1. 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.

  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. 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.

  4. Coupling ultracold atoms to mechanical oscillators

    CERN Document Server

    Hunger, David; Korppi, Maria; Jöckel, Andreas; Hänsch, Theodor W; Treutlein, Philipp

    2011-01-01

    In this article we discuss and compare different ways to engineer an interface between ultracold atoms and micro- and nanomechanical oscillators. We start by analyzing a direct mechanical coupling of a single atom or ion to a mechanical oscillator and show that the very different masses of the two systems place a limit on the achievable coupling constant in this scheme. We then discuss several promising strategies for enhancing the coupling: collective enhancement by using a large number of atoms in an optical lattice in free space, coupling schemes based on high-finesse optical cavities, and coupling to atomic internal states. Throughout the manuscript we discuss both theoretical proposals and first experimental implementations.

  5. Molecular model with quantum mechanical bonding information.

    Science.gov (United States)

    Bohórquez, Hugo J; Boyd, Russell J; Matta, Chérif F

    2011-11-17

    The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.

  6. 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...... for the other systems. This gave results in good agreement with the experimental data.The possibility of transferring interaction parameters is very interesting,especially as it can be applied to systems for which the additivity principle of the UNIFAC method fails.Simulations were carried out for 1......,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...

  7. High-order-harmonic generation in atomic and molecular systems

    Science.gov (United States)

    Suárez, Noslen; Chacón, Alexis; Pérez-Hernández, Jose A.; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.

    2017-03-01

    High-order-harmonic generation (HHG) results from the interaction of ultrashort laser pulses with matter. It configures an invaluable tool to produce attosecond pulses, moreover, to extract electron structural and dynamical information of the target, i.e., atoms, molecules, and solids. In this contribution, we introduce an analytical description of atomic and molecular HHG, that extends the well-established theoretical strong-field approximation (SFA). Our approach involves two innovative aspects: (i) First, the bound-continuum and rescattering matrix elements can be analytically computed for both atomic and multicenter molecular systems, using a nonlocal short range model, but separable, potential. When compared with the standard models, these analytical derivations make possible to directly examine how the HHG spectra depend on the driven media and laser-pulse features. Furthermore, we can turn on and off contributions having distinct physical origins or corresponding to different mechanisms. This allows us to quantify their importance in the various regions of the HHG spectra. (ii) Second, as reported recently [N. Suárez et al., Phys. Rev. A 94, 043423 (2016), 10.1103/PhysRevA.94.043423], the multicenter matrix elements in our theory are free from nonphysical gauge- and coordinate-system-dependent terms; this is accomplished by adapting the coordinate system to the center from which the corresponding time-dependent wave function originates. Our SFA results are contrasted, when possible, with the direct numerical integration of the time-dependent Schrödinger equation in reduced and full dimensionality. Very good agreement is found for single and multielectronic atomic systems, modeled under the single active electron approximation, and for simple diatomic molecular systems. Interference features, ubiquitously present in every strong-field phenomenon involving a multicenter target, are also captured by our model.

  8. Evolution of the atomic and molecular gas content of galaxies

    NARCIS (Netherlands)

    Popping, Gergö; Somerville, Rachel S.; Trager, Scott C.

    2014-01-01

    We study the evolution of atomic and molecular gas in galaxies in semi-analytic models of galaxy formation that include new modelling of the partitioning of cold gas in galactic discs into atomic, molecular, and ionized phases. We adopt two scenarios for the formation of molecules: one pressure base

  9. Molecular mechanisms of meditation.

    Science.gov (United States)

    Jindal, Vishal; Gupta, Sorab; Das, Ritwik

    2013-12-01

    Meditation is a complex process involving change in cognition, memory, and social and emotional control, and causes improvement in various cardiovascular, neurological, autoimmune, and renal pathologies. Meditation also become widely used in medical and psychological treatment therapies for stress-related physical and mental disorders. But still, biological mechanisms in terms of effect on brain and body are poorly understood. This paper explains the basic changes due to meditation in cerebral cortex, prefrontal area, cingulate gyrus, neurotransmitters, white matter, autonomic nervous system, limbic system, cytokines, endorphins, hormones, etc. The following is a review of the current literature regarding the various neurophysiological mechanisms, neuro-endocrine mechanisms, neurochemical substrates, etc. that underlies the complex processes of meditation.

  10. Discrete wave mechanics: The hydrogen atom.

    Science.gov (United States)

    Wall, F T

    1986-08-01

    The quantum mechanical problem of the hydrogen atom is treated by use of a finite difference equation in place of Schrödinger's differential equation. The exact solution leads to a wave vector energy expression that is readily converted to the Bohr-Rydberg formula. (The calculations here reported are limited to spherically symmetric states.) The wave vectors reduce to the familiar solutions of Schrödinger's equation as c --> infinity. The internal consistency and limiting behavior provide support for the view that the equations employed could well constitute an approach to a relativistic formulation of wave mechanics.

  11. Molecular mechanisms in gliomagenesis

    DEFF Research Database (Denmark)

    Hulleman, Esther; Helin, Kristian

    2005-01-01

    brain development, such as the differentiation of neural stem cells (NSCs) into astrocytes, might contribute to GBM formation. These pathways include growth factor-induced signal transduction routes and processes that control cell cycle progression, such as the p16-CDK4-RB and the ARF-MDM2-p53 pathways....... 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...

  12. 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.

  13. Molecular Mechanisms of Parturition

    Directory of Open Access Journals (Sweden)

    F. Ferré

    1997-01-01

    Full Text Available The initial signal for triggering human parturition might be fetal but of trophoblastic origin. Concomitantly, this placental signal would have as its target not only the uterus but also the fetus by activating its hypothalamo-pituitary-adrenocortical axis. The latter would represent a second fetal signal which, at the fetomaternal interface, would amplify and define in time the mechanisms responsible for the onset of labor, implying changes in the myometrial and cervical extracellular matrix associated with the accession of the contractile phenotype for myometrial cells. At each phase of these processes in the utero-feto-placental system, the nature of these signals remains to be identified. Is there a single substance, or rather, and more likely, a combination of several?

  14. 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.

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

    Science.gov (United States)

    1986-01-01

    The volume presents a program of research initiatives in atomic, molecular, and optical physics. The current state of atomic, molecular, and optical physics in the US is examined with respect to demographics, education patterns, applications, and the US economy. Recommendations are made for each field, with discussions of their histories and the relevance of the research to government agencies. The section on atomic physics includes atomic theory, structure, and dynamics; accelerator-based atomic physics; and large facilities. The section on molecular physics includes spectroscopy, scattering theory and experiment, and the dynamics of chemical reactions. The section on optical physics discusses lasers, laser spectroscopy, and quantum optics and coherence. A section elucidates interfaces between the three fields and astrophysics, condensed matter physics, surface science, plasma physics, atmospheric physics, and nuclear physics. Another section shows applications of the three fields in ultra-precise measurements, fusion, national security, materials, medicine, and other topics.

  16. R-matrix theory of atomic collisions. Application to atomic, molecular and optical processes

    Energy Technology Data Exchange (ETDEWEB)

    Burke, Philip G. [Queen' s Univ., Belfast (United Kingdom). School of Mathematics and Physics

    2011-07-01

    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 technological importance. Basic mathematical results and general and widely used R-matrix computer programs are summarized in the appendices. (orig.)

  17. 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.

  18. 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.

  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...

  20. STATINS AND MYOPATHY: MOLECULAR MECHANISMS

    Directory of Open Access Journals (Sweden)

    O. M. Drapkina

    2012-01-01

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

  1. 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.

  2. 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.

  3. 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.

  4. Trapping of molecular Oxygen together with Lithium atoms

    CERN Document Server

    Akerman, Nitzan; Segev, Yair; Bibelnik, Natan; Narevicius, Julia; Narevicius, Edvardas

    2016-01-01

    We demonstrate simultaneous deceleration and trapping of a cold atomic and molecular mixture. This is the first step towards studies of cold atom-molecule collisions at low temperatures as well as application of sympathetic cooling. Both atoms and molecules are cooled in a supersonic expansion and are loaded into a moving magnetic trap which brings them to rest via the Zeeman interaction from an initial velocity of 375 m/s. We use a beam seeded with molecular Oxygen, and entrain it with Lithium atoms by laser ablation prior to deceleration. The deceleration ends with loading of the mixture into a static quadrupole trap, which is generated by two permanent magnets. We estimate $10^9$ trapped O$_2$ molecules and $10^5$ Li atoms with background pressure limited lifetime on the order of 1 second. With further improvements to Lithium entrainment we expect that sympathetic cooling of molecules is within reach.

  5. 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...

  6. 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.

  7. Probing atomic and molecular dynamics from within

    Energy Technology Data Exchange (ETDEWEB)

    Berrah, N. E-mail: berrah@wmich.edu; Bilodeau, R.C.; Ackerman, G.; Bozek, J.D.; Turri, G.; Kukk, E.; Cheng, W.T.; Snell, G

    2004-08-01

    We have investigated with unprecedented levels of detail photodetachment of negative ions and photoionization of molecules using the brightness, spectral resolution, and tunability of the Advanced Light Source at Lawrence Berkeley National Laboratory. In particular, we report here on investigations carried out in K-shell photodetachment of atomic Li{sup -} and He{sup -}. We also report on angular distribution of core-level iodine 4d photoelectrons from the HI molecule. In both cases comparison with calculations is discussed.

  8. Intense Atomic and Molecular Beams via Neon Buffer Gas Cooling

    CERN Document Server

    Patterson, David; Doyle, John M

    2008-01-01

    We realize a continuous guided beam of cold deuterated ammonia with a flux of 3e11 ND3 molecules/s and a continuous free-space beam of cold potassium with a flux of 1e16 K atoms/s. A novel feature of the buffer gas source used to produce these beams is cold neon, which, due to intermediate Knudsen number beam dynamics, produces a forward velocity and low-energy tail that is comparable to much colder helium-based sources. We expect this source to be trivially generalizable to a very wide range of atomic and molecular species with significant vapor pressure below 1000 K. This source has properties that make it a good starting point for laser cooling of molecules or atoms, cold collision studies, trapping, or nonlinear optics in buffer-gas-cooled atomic or molecular gases.

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

    DEFF Research Database (Denmark)

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

    1998-01-01

    We have simulated the mechanical deformation of atomic-scale metallic contacts under tensile strain using molecular dynamics and effective medium theory potentials. The evolution of the structure of the contacts and the underlying deformation mechanisms are described along with the calculated...... electronic conductance. Various defects such as intersecting stacking faults, local disorder, and vacancies are created during the deformation. Disordered regions act as weak spots that reduce the strength of the contacts. The disorder tends to anneal out again during the subsequent atomic rearrangements......, 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...

  10. Atomic and molecular layer deposition for surface modification

    Science.gov (United States)

    Vähä-Nissi, Mika; Sievänen, Jenni; Salo, Erkki; Heikkilä, Pirjo; Kenttä, Eija; Johansson, Leena-Sisko; Koskinen, Jorma T.; Harlin, Ali

    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.

  11. 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. .

  12. Superspreading: mechanisms and molecular design.

    Science.gov (United States)

    Theodorakis, Panagiotis E; Müller, Erich A; Craster, Richard V; Matar, Omar K

    2015-03-03

    The intriguing ability of certain surfactant molecules to drive the superspreading of liquids to complete wetting on hydrophobic substrates is central to numerous applications that range from coating flow technology to enhanced oil recovery. Despite significant experimental efforts, the precise mechanisms underlying superspreading remain unknown to date. Here, we isolate these mechanisms by analyzing coarse-grained molecular dynamics simulations of surfactant molecules of varying molecular architecture and substrate affinity. We observe that for superspreading to occur, two key conditions must be simultaneously satisfied: the adsorption of surfactants from the liquid-vapor surface onto the three-phase contact line augmented by local bilayer formation. Crucially, this must be coordinated with the rapid replenishment of liquid-vapor and solid-liquid interfaces with surfactants from the interior of the droplet. This article also highlights and explores the differences between superspreading and conventional surfactants, paving the way for the design of molecular architectures tailored specifically for applications that rely on the control of wetting.

  13. Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides

    Science.gov (United States)

    Held, Marie; Nicolau, Dan V.

    2007-12-01

    The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA) and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity. Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues. The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an expected biomolecular activity from the immobilized biomolecules.

  14. 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...

  15. Atoms, molecules and photons An introduction to atomic-, molecular- and quantum-physics

    CERN Document Server

    Demtröder, Wolfgang

    2006-01-01

    This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed over the last two centuries both by many experimental discoveries and, from the theoretical side, by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of classical description. The interaction of electromagnetic radiation with atoms and molecules and its potential for spectroscopy is outlined in more detail and in particular lasers as modern spectroscopic tools are discussed more thoroughly. Many examples and problems with solutions are offered to encourage readers to actively engage in experimentation.

  16. Multiresolution molecular mechanics: Implementation and efficiency

    Science.gov (United States)

    Biyikli, Emre; To, Albert C.

    2017-01-01

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

  17. Anticancer molecular mechanisms of resveratrol

    Directory of Open Access Journals (Sweden)

    Elena Maria Varoni

    2016-04-01

    Full Text Available Resveratrol is a pleiotropic phytochemical belonging to the stilbene family. Despite 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; immune-surveillance and hormone signaling. Resveratrol also showed a promising role to counteract multi-drug 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.

  18. 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

  19. Single-atom quantum control of macroscopic mechanical oscillators

    Science.gov (United States)

    Bariani, F.; Otterbach, J.; Tan, Huatang; Meystre, P.

    2014-01-01

    We investigate a hybrid electromechanical system consisting of a pair of charged macroscopic mechanical oscillators coupled to a small ensemble of Rydberg atoms. The resonant dipole-dipole coupling between an internal atomic Rydberg transition and the mechanics allows cooling to its motional ground state with a single atom despite the considerable mass imbalance between the two subsystems. We show that the rich electronic spectrum of Rydberg atoms, combined with their high degree of optical control, paves the way towards implementing various quantum-control protocols for the mechanical oscillators.

  20. 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...

  1. 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...

  2. Molecular Mechanism of Somite Development

    Directory of Open Access Journals (Sweden)

    Gulfidan Coskun

    2013-06-01

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

  3. Molecular mechanisms of cryptococcal meningitis.

    Science.gov (United States)

    Liu, Tong-Bao; Perlin, David S; 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 cause meningitis after establishment of local infection are the dissemination of fungal cells to the bloodstream and invasion through the blood brain barrier to reach the CNS. In this review, we use cryptococcal CNS infection as an example to describe the current molecular understanding of fungal meningitis, including the establishment of the infection, dissemination, and brain invasion. Host and microbial factors that contribute to these infection steps are also discussed.

  4. Atomic and molecular physics in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Toburen, L.H.

    1990-09-01

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

  5. 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)

  6. Molecular Mechanisms of Bacterial Pathogenicity

    Science.gov (United States)

    Fuchs, Thilo Martin

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

  7. Graphene mechanics: II. Atomic stress distribution during indentation until rupture.

    Science.gov (United States)

    Costescu, Bogdan I; Gräter, Frauke

    2014-06-28

    Previous Atomic Force Microscopy (AFM) experiments found single layers of defect-free graphene to rupture at unexpectedly high loads in the micronewton range. Using molecular dynamics simulations, we modeled an AFM spherical tip pressing on a circular graphene sheet and studied the stress distribution during the indentation process until rupture. We found the graphene rupture force to have no dependency on the sheet size and a very weak dependency on the indenter velocity, allowing a direct comparison to experiment. The deformation showed a non-linear elastic behavior, with a two-dimensional elastic modulus in good agreement with previous experimental and computational studies. In line with theoretical predictions for linearly elastic sheets, rupture forces of non-linearly elastic graphene are proportional to the tip radius. However, as a deviation from the theory, the atomic stress concentrates under the indenter tip more strongly than predicted and causes a high probability of bond breaking only in this area. In turn, stress levels decrease rapidly towards the edge of the sheet, most of which thus only serves the role of mechanical support for the region under the indenter. As a consequence, the high ratio between graphene sheets and sphere radii, hitherto supposed to be necessary for reliable deformation and rupture studies, could be reduced to a factor of only 5-10 without affecting the outcome. Our study suggests time-resolved analysis of forces at the atomic level as a valuable tool to predict and interpret the nano-scale response of stressed materials beyond graphene.

  8. The Atomic to Molecular Transition in the Interstellar Medium

    Science.gov (United States)

    Goldsmith, Paul F.

    2012-01-01

    Study of H2 in UV and IR continues to surprise us with complexity of excitation state, OPR, and role in astrochemistry. Atomic H in molecular clouds is a very powerful tool suggesting that they are not "young" but that it takes millions of years to convert primarily atomic hydrogen clouds to 99.9% molecular form. Laboratory data suggests that H2 formation is efficient over broader range of temperatures than thought to be the case a few years ago, but range is still limited. Issues of complex grain morphology and surface structure make this a very difficult field in which to obtain definitively meaningful results. Ongoing and future observations of CI and CII will improve our understanding of the structure of clouds, their total mass, and how they have evolved and will continue to do so.

  9. 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'.

  10. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

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

  11. Rapid formation of molecular clouds from turbulent atomic gas

    Science.gov (United States)

    Glover, S. C. O.; Mac Low, M.-M.

    The characteristic lifetimes of molecular clouds remain uncertain and a topic of frequent debate, with arguments having recently been advanced both in support of short-lived clouds, with lifetimes of a few Myr or less (see e.g. Elmegreen 2000; Hartmann et al. 2001) and in support of much longer-lived clouds, with lifetimes of the order of 10 Myr or more (see e.g. Tassis & Mouschovias, 2004; Goldsmith & Li, 2005). An argument that has previously been advanced in favour of longer lived clouds is the apparent difficulty involved in converting sufficient atomic hydrogen to molecular hydrogen within the short timescale required by the rapid cloud formation scenario. However, previous estimates of the time required for this conversion to occur have not taken into account the effects of the supersonic turbulence which is inferred to be present in the atomic gas. In this contribution, we present results from a set of high resolution three-dimensional simulations of turbulence in gravitationally unstable atomic gas. These simulations were performed using a modified version of the ZEUS-MP hydrodynamical code (Norman 2000), and include a detailed treatment of the thermal balance of the gas and of the formation of molecular hydrogen. The effects of photodissociation of H2 by the Galactic UV field are also included, with a simple local approximation used to compute the effects of H2 self-shielding. The results of our simulations demonstrate that H2 formation occurs rapidly in turbulent atomic gas. Starting from purely atomic gas, large quantities of molecular gas can be produced on timescales of less than a Myr, given turbulent velocity dispersions and magnetic field strengths consistent with observations. Moreover, as our simulations underestimate the effectiveness of H2 self-shielding and dust absorption, we can be confident that the molecular fractions which we compute are strong lower limits on the true values. The formation of large quantities of molecular gas on the

  12. Molecular toxicity mechanism of nanosilver

    Directory of Open Access Journals (Sweden)

    Danielle McShan

    2014-03-01

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

  13. 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.

  14. Atoms, Molecules and Photons An Introduction to Atomic-, Molecular- and Quantum Physics

    CERN Document Server

    Demtröder, Wolfgang

    2010-01-01

    This introduction to Atomic and Molecular Physics explains how our present model of atoms and molecules has been developed over the last two centuries both by many experimental discoveries and, from the theoretical side, by the introduction of quantum physics to the adequate description of micro-particles. It illustrates the wave model of particles by many examples and shows the limits of classical description. The interaction of electromagnetic radiation with atoms and molecules and its potential for spectroscopy is outlined in more detail and in particular lasers as modern spectroscopic tools are discussed more thoroughly. Many examples and problems with solutions are offered to encourage readers to actively engage in applying and adapting the fundamental physics presented in this textbook to specific situations. Completely revised new edition with new sections covering all actual developments, like x-ray optics, ion-cyclotron-resonance spectrometer, attosecond lasers, ultraprecission frequency measurement ...

  15. Toggling bistable atoms via mechanical switching of bond angle.

    Science.gov (United States)

    Sweetman, Adam; Jarvis, Sam; Danza, Rosanna; Bamidele, Joseph; Gangopadhyay, Subhashis; Shaw, Gordon A; Kantorovich, Lev; Moriarty, Philip

    2011-04-01

    We reversibly switch the state of a bistable atom by direct mechanical manipulation of bond angle using a dynamic force microscope. Individual buckled dimers at the Si(100) surface are flipped via the formation of a single covalent bond, actuating the smallest conceivable in-plane toggle switch (two atoms) via chemical force alone. The response of a given dimer to a flip event depends critically on both the local and nonlocal environment of the target atom-an important consideration for future atomic scale fabrication strategies.

  16. 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.

  17. 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.

  18. Modified morphology of graphene sheets by Argon-atom bombardment: molecular dynamics simulations.

    Science.gov (United States)

    Wei, Xiao-Lin; Zhang, Kai-Wang; Wang, Ru-Zhi; Liu, Wen-Liang; Zhong, Jian-Xin

    2011-12-01

    By a molecular dynamics method, we simulated the process of Argon-atom bombardment on a graphene sheet with 2720 carbon atoms. The results show that, the damage of the bombardment on the graphene sheet depends not only on the incident energy but also on the particle flux density of Argon atoms. To compare and analyze the effect of the incident energy and the particle flux density in the Argon-atom bombardment, we defined the impact factor on graphene sheet by calculating the broken-hole area. The results indicate that, there is an exponential accumulated-damage for the impact of both the incident energy and the particle flux density and there is a critical incident energy ranging from 20-30 eV/atom in Argon-atom bombardment. Different configurations, such as sieve-like and circle-like graphene can be formed by controlling of different particle flux density as the incident energy is more than the critical value. Our results supply a feasible method on fabrication of porous graphene-based materials for gas-storages and molecular sieves, and it also helps to understand the damage mechanism of graphene-based electronic devices under high particle radiation.

  19. Molecular mechanisms of synaptic plasticity and memory.

    Science.gov (United States)

    Elgersma, Y; Silva, A J

    1999-04-01

    To unravel the molecular and cellular bases of learning and memory is one of the most ambitious goals of modern science. The progress of recent years has not only brought us closer to understanding the molecular mechanisms underlying stable, long-lasting changes in synaptic strength, but it has also provided further evidence that these mechanisms are required for memory formation.

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

    Science.gov (United States)

    Taylor, Kenneth T

    2002-06-15

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

  1. 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.

  2. Imaging Multi-Particle Atomic and Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-12

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

  3. 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 ...

  4. 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

  5. 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.

  6. 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.

  7. Molecular transport through capillaries made with atomic-scale precision

    Science.gov (United States)

    Radha, B.; Esfandiar, A.; Wang, F. C.; Rooney, A. P.; Gopinadhan, K.; Keerthi, A.; Mishchenko, A.; Janardanan, A.; Blake, P.; Fumagalli, L.; Lozada-Hidalgo, M.; Garaj, S.; Haigh, S. J.; Grigorieva, I. V.; Wu, H. A.; Geim, A. K.

    2016-10-01

    Nanometre-scale pores and capillaries have long been studied because of their importance in many natural phenomena and their use in numerous applications. A more recent development is the ability to fabricate artificial capillaries with nanometre dimensions, which has enabled new research on molecular transport and led to the emergence of nanofluidics. But surface roughness in particular makes it challenging to produce capillaries with precisely controlled dimensions at this spatial scale. Here we report the fabrication of narrow and smooth capillaries through van der Waals assembly, with atomically flat sheets at the top and bottom separated by spacers made of two-dimensional crystals with a precisely controlled number of layers. We use graphene and its multilayers as archetypal two-dimensional materials to demonstrate this technology, which produces structures that can be viewed as if individual atomic planes had been removed from a bulk crystal to leave behind flat voids of a height chosen with atomic-scale precision. Water transport through the channels, ranging in height from one to several dozen atomic planes, is characterized by unexpectedly fast flow (up to 1 metre per second) that we attribute to high capillary pressures (about 1,000 bar) and large slip lengths. For channels that accommodate only a few layers of water, the flow exhibits a marked enhancement that we associate with an increased structural order in nanoconfined water. Our work opens up an avenue to making capillaries and cavities with sizes tunable to ångström precision, and with permeation properties further controlled through a wide choice of atomically flat materials available for channel walls.

  8. Continuum Mechanics at the Atomic Scale.

    Science.gov (United States)

    1977-01-01

    stress is singular at t=o bu* also the stored elastic energy. For that reason we are forced to consider the Polution valid only in a hollow cylinder...Underwater Weapons Center U.S. Naval Academy Pasadena Annex Annapolis, Maryland 21402 3202 E. Foothill Blvd. Pasadena, California 91107 Naval Air Systems...Mechanics UCS. Naval Civil Engr. Lab. Naval Air Development Center Code L3r Johnsville Port Hueneme, California 93041 Warminster, Pennsylvania 1897A

  9. Atomic mechanisms of interdiffusion in metallic multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Zotov, N. [Centre of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175 Bonn (Germany)], E-mail: zotov@caesar.de; Ludwig, A. [Centre of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175 Bonn (Germany); Institute of Materials, Faculty of Mechanical Engineering, Ruhr-Universitaet Bochum, 44780 Bochum (Germany)

    2007-09-15

    Interdiffusion data (activation energies and pre-exponential factors) for different metal-metal multilayers (MLs) published in the literature and our own results on Fe/Pt MLs are reviewed. The analysis of the available data suggests that vacancy diffusion is the main interdiffusion mechanism in metallic MLs. An empirical relation between the activation energy for interdiffusion in metallic multilayers, the average activation energy of vacancy diffusion and the activation energy for in-plane grain-boundary diffusion is proposed.

  10. Molecular dynamics simulations of diffusion mechanisms in NiAl

    Energy Technology Data Exchange (ETDEWEB)

    Soule De Bas, B.; Farkas, D

    2003-03-14

    Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.

  11. Molecular mechanisms of NCAM function

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  12. Atomic, Molecular, and Optical Physics Workshop Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Jr., Lloyd [University of Southern California

    1997-09-21

    This document contains the final reports from the five panels that comprised a Workshop held to explore future directions, scientific impacts and technological connections of research in Atomic, Molecular and Optical Physics. This workshop was sponsored by the Department of Energy, Office of Basic Energy Sciences, Chemical Sciences Division and was held at the Westfields International Conference Center in Chantilly, Virginia on September 21-24, 1997. The workshop was chaired by Lloyd Armstrong, Jr., University of Southern California and the five panels focused on the following topics: Panel A: Interactions of Atoms and Molecules with Photons - Low Field Daniel Kleppner (Massachusetts Institute of Technology), chair Panel B: Interactions of Atoms and Molecules with Photons - High Field Phil Bucksbaum (University of Michigan), chair Panel C: Surface Interactions with Photons, Electrons, Ions, Atoms and Molecules J. Wayne Rabalais (University of Houston), chair Panel D: Theory of Structure and Dynamics Chris Greene (University of Colorado), chair Panel E: Nano- and Mesocopic Structures Paul Alivisatos (Lawrence Berkeley National Laboratory), chair The choice of focus areas reflects areas of significant interest to DOE/BES but is clearly not intended to span all fields encompassed by the designation of atomic, molecular and optical physics, nor even all areas that would be considered for review and funding under DOE’s AMOP program. In a similar vein, not all research that might be suggested under these topics in this report would be appropriate for consideration by DOE’s AMOP program. The workshop format included overview presentations from each of the panel chairs, followed by an intensive series of panel discussion sessions held over a two-day period. The panels were comprised of scientists from the U. S. and abroad, many of whom are not supported by DOE’s AMOP Program. This workshop was held in lieu of the customary “Contractors Meeting” held annually for

  13. 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.

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

    Science.gov (United States)

    Klocke, Michael; Wolf, Dietrich E

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Michael Klocke

    2016-05-01

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

  16. 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.

  17. 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...

  18. 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.

  19. 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...

  20. Near-atomic-resolution cryo-EM for molecular virology.

    Science.gov (United States)

    Hryc, Corey F; Chen, Dong-Hua; Chiu, Wah

    2011-08-01

    Electron cryo-microscopy (cryo-EM) is a technique in structural biology that is widely used to solve the three-dimensional structures of macromolecular assemblies, close to their biological and solution conditions. Recent improvements in cryo-EM and single-particle reconstruction methodologies have led to the determination of several virus structures at near-atomic resolution (3.3 - 4.6 Å). These cryo-EM structures not only resolve the Cα backbones and side-chain densities of viral capsid proteins, but also suggest functional roles that the protein domains and some key amino acid residues play. This paper reviews the recent advances in near-atomic-resolution cryo-EM for probing the mechanisms of virus assembly and morphogenesis.

  1. First-principles study on molecular dissociation under metallization pressure in aromatic monomolecular crystals with iodine atoms

    CERN Document Server

    Tateyama, Y

    2002-01-01

    We have examined the metallization mechanism and possibility of molecular dissociation in iodanil (IA) and hexa-iodobenzene (HIB) under pressure by using first-principles calculations. We found that the metallization in IA is caused by the band overlap in the molecular phase and dissociation does not follow the metallization. In HIB, on the other hand, the band overlap mechanism is found to be less probable, which implies that a structural transformation will occur before the metallization. Both mechanisms are completely different from that for I sub 2 diatomic molecular crystal, and suggest essential roles of C sub 6 rings and O atoms.

  2. 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...

  3. 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.

  4. Molecular mechanisms of antibiotic resistance.

    Science.gov (United States)

    Blair, Jessica M A; Webber, Mark A; Baylay, Alison J; Ogbolu, David O; Piddock, Laura J V

    2015-01-01

    Antibiotic-resistant bacteria that are difficult or impossible to treat are becoming increasingly common and are causing a global health crisis. Antibiotic resistance is encoded by several genes, many of which can transfer between bacteria. New resistance mechanisms are constantly being described, and new genes and vectors of transmission are identified on a regular basis. This article reviews recent advances in our understanding of the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to antibiotics, including the prevention of access to drug targets, changes in the structure and protection of antibiotic targets and the direct modification or inactivation of antibiotics.

  5. 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.

  6. VALD - an atomic and molecular database for astrophysics

    Energy Technology Data Exchange (ETDEWEB)

    Heiter, U; Barklem, P; Kochukhov, O; Piskunov, N [Department of Astronomy and Space Physics, Uppsala University (Sweden); Fossati, L; Obbrugger, M; Stuetz, Ch; Weiss, W W [Institute of Astronomy, University of Vienna (Austria); Kildiyarova, R [Institute of Spectroscopy, Russian Academy of Sciences, Moscow region, Troitsk (Russian Federation); Kupka, F [Max-Planck-Institute for Astrophysics, Garching (Germany); Plez, B [Universite Montpellier II, GRAAL, CNRS - UMR 5024 (France); Ryabchikova, T [Institute of Astronomy, Russian Academy of Sciences, Moscow (Russian Federation); Stempels, H C [School of Physics and Astronomy, University of St Andrews, Scotland (United Kingdom)], E-mail: ulrike@astro.uu.se

    2008-10-15

    The VALD database of atomic and molecular data aims to ensure a robust and consistent analysis of astrophysical spectra. We offer a convenient e-mail and web-based user interface to a vast collection of spectral line parameters for all chemical elements and in the future also for molecules. An international team is working on the following tasks: collecting line parameters from relevant theoretical and experimental publications, computing line parameters, evaluating the data quality by comparison of similar data from different sources and by comparison with astrophysical observations, and incorporating the data into VALD. A unique feature of VALD is its capability to provide the most comprehensive spectral line lists for specific astrophysical plasma conditions defined by the user.

  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. The Chemi-Ionization Processes in Slow Collisions of Rydberg Atoms with Ground State Atoms: Mechanism and Applications

    OpenAIRE

    Mihajlov, A. A.; Sreckovic, V. A.; Ignjatovic, Lj. M.; Klyucharev, A. N.

    2012-01-01

    In this article the history and the current state of research of the chemiionization processes in atom-Rydberg atom collisions is presented. The principal assumptions of the model of such processes based on the dipole resonance mechanism, as well as the problems of stochastic ionization in atom-Rydberg atom collisions, are exposed. The properties of the collision kinetics in atom beams of various types used in contemporary experimentations are briefly described. Results of the calculation of ...

  9. Molecular Mechanisms of Appetite Regulation

    Directory of Open Access Journals (Sweden)

    Ji Hee Yu

    2012-12-01

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

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

    Science.gov (United States)

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

    2016-09-01

    The Cologne Database for Molecular Spectroscopy, CDMS, was founded 1998 to provide in its catalog section line lists of mostly molecular species which are or may be observed in various astronomical sources (usually) by radio astronomical means. The line lists contain transition frequencies with qualified accuracies, intensities, quantum numbers, as well as further auxiliary information. They have been generated from critically evaluated experimental line lists, mostly from laboratory experiments, employing established Hamiltonian models. Separate 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, VAMDC, 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. A dedicated infrastructure was developed to provide a common data format in the various databases enabling queries to a large variety of databases on atomic and molecular data at once. For CDMS, the incorporation in VAMDC was combined with several modifications on the generation of CDMS catalog entries. Here we introduce related changes to the data structure and the data content in the CDMS. The new data scheme allows us to incorporate all previous data entries but in addition allows us also to include entries based on new theoretical descriptions. Moreover, the CDMS entries have been transferred into a mySQL database format. These developments within the VAMDC framework have in part been driven by the needs of the astronomical community to be able to deal efficiently with large data sets obtained with the Herschel Space Telescope or, more recently, with the Atacama Large

  11. 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.

  12. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  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. 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

  15. 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.

  16. General mechanism for helium blistering involving displaced atom transport

    Energy Technology Data Exchange (ETDEWEB)

    McDonell, W.R.

    1979-01-01

    A mechanism developed to account for formation of vertically elongated blisters in high displacement environments produced by /sup 252/Cf alpha particles and fission fragments has been extended to formation of done-shaped blisters in the low displacement environments produced by simple helium ion beams. In this mechanism, transport of displaced atoms to relieve compressive stresses in the helium-implanted layer allows interconnections of small, subsurface bubbles to form the blister cavity. The same transport may cause thickening of the blister caps at low implantation energies. The transition from dome-shaped to vertically elongated blistering occurs between the 300 and 3000 displacements per helium atom produced by simple helium ions and /sup 252/Cf radiations respectively.

  17. 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.

  18. Resonant Scattering of Muonic Hydrogen Atoms and Dynamics of Muonic Molecular Complex

    CERN Document Server

    Fujiwara, M C; Bailey, J M; Beer, G A; Beveridge, J L; Faifman, M P; Huber, T M; Kammel, P; Kim, S K; Knowles, P E; Kunselman, A R; Maier, M; Markushin, V E; Marshall, G M; Martoff, C J; Mason, G R; Mulhauser, F; Olin, A; Petitjean, C; Porcelli, T A; Wozniak, J; Zmeskal, J

    2001-01-01

    Resonant scattering of muonic hydrogen atoms via back decay of molecular complex, a key process in the understanding of epithermal muonic molecular formation, is analyzed. The limitations of the effective rate approximation are discussed and the importance of the explicit treatment of the back decay is stressed. An expression of the energy distribution for the back-decayed atoms is given.

  19. The evolution of the atomic and molecular interstellar medium in star-forming galaxies

    NARCIS (Netherlands)

    Popping, Gergö

    2014-01-01

    In this thesis I developed models to make predictions for the atomic and molecular gas content of galaxies. Main results of my thesis include that the atomic hydrogen content of galaxies remained relatively constant with over the last 10 Billion years, whereas the molecular hydrogen content decrease

  20. A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical-molecular-mechanical calculations.

    Science.gov (United States)

    Biswas, P K; Gogonea, V

    2005-10-22

    We describe a regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical (QM)-molecular-mechanical (MM) calculations. To remedy the nonphysical QM/MM Coulomb interaction at short distances arising from a point electrostatic potential (ESP) charge of the MM atom and also to accommodate the effect of polarized MM atom in the coupling Hamiltonian, we propose a partial-wave expansion of the ESP charge and describe the effect of a s-wave expansion, extended over the covalent radius r(c), of the MM atom. The resulting potential describes that, at short distances, large scale cancellation of Coulomb interaction arises intrinsically from the localized expansion of the MM point charge and the potential self-consistently reduces to 1r(c) at zero distance providing a renormalization to the Coulomb energy near interatomic separations. Employing this renormalized Hamiltonian, we developed an interface between the Car-Parrinello molecular-dynamics program and the classical molecular-dynamics simulation program Groningen machine for chemical simulations. With this hybrid code we performed QM/MM calculations on water dimer, imidazole carbon monoxide (CO) complex, and imidazole-heme-CO complex with CO interacting with another imidazole. The QM/MM results are in excellent agreement with experimental data for the geometry of these complexes and other computational data found in literature.

  1. Pathogenesis and Molecular Mechanisms of Zika Virus.

    Science.gov (United States)

    Nayak, Shriddha; Lei, Jun; Pekosz, Andrew; Klein, Sabra; Burd, Irina

    2016-09-01

    Zika virus (ZIKV) is one of the most important emerging viruses of 2016. A developing outbreak in the Americas has demonstrated an association between the virus and serious clinical manifestations, such as Guillain-Barré syndrome in adults and congenital malformations in infants born to infected mothers. Pathogenesis and mechanisms of neurologic or immune disease by ZIKV have not been clearly delineated. However, several pathways have been described to explain viral involvement in brain and immune system as well as other organ systems such as eye, skin, and male and female reproductive tracts. ZIKV activates toll-like receptor 3 and several pathways have been described to explain the mechanisms at a molecular level. The mechanism of microcephaly has been more difficult to demonstrate experimentally, likely due to the multifactorial and complex nature of the phenotype. This article provides an overview of existing literature on ZIKV pathogenicity and possible molecular mechanisms of disease as outlined to date.

  2. Modelling the molecular mechanisms of aging.

    Science.gov (United States)

    Mc Auley, Mark T; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M; Morgan, Amy E; Proctor, Carole J

    2017-02-28

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.

  3. Atomic-Scale Mechanism for Hydrogenation of o-Cresol on Pt Catalysis

    Science.gov (United States)

    Li, Yaping; Liu, Zhimin; Xue, Wenhua; Crossley, Steven; Jentoft, Friederike; Wang, Sanwu

    Biofuels derived from lignocellulosic biomass have received significant attention lately due to increasing environmental concerns. With first-principles density-functional theory and ab initio molecular dynamic simulations, we investigated the atomic-scale mechanism of o-cresol hydrogenation on the Pt(111) surface. The formation of 2-methyl-cyclohexanone (the intermediate product) was found to involve two steps. The first step is the dehydrogenation, that is, the H atom in the hydroxyl group moves to the Pt surface. The second step is the hydrogenation, that is, the H atoms on Pt react with the carbon atoms in the aromatic ring. The first step involves a smaller barrier, suggesting that dehydrogenation occurs first, followed by hydrogenation of the ring. In particular, tautomerization is found to occur via a two-step process over the catalyst. On the other hand, 2-methyl-cyclohexanol (the final product) is produced through two paths. One is direct hydrogenation of the aromatic ring. Another pathway includes partial hydrogenation of the ring, dehydrogenation of -OH group, finally hydrogenation of remaining C atoms and the O atom. Our theoretical results agree well with the experimental observations. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of NERSC, XSEDE, TACC.

  4. Molecular-dynamics study of detonation. II. The reaction mechanism

    Science.gov (United States)

    Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.

    1996-01-01

    In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.

  5. Thermal relaxation of molecular oxygen in collisions with nitrogen atoms

    Science.gov (United States)

    Andrienko, Daniil A.; Boyd, Iain D.

    2016-07-01

    Investigation of O2-N collisions is performed by means of the quasi-classical trajectory method on the two lowest ab initio potential energy surfaces at temperatures relevant to hypersonic flows. A complete set of bound-bound and bound-free transition rates is obtained for each precollisional rovibrational state. Special attention is paid to the vibrational and rotational relaxations of oxygen as a result of chemically non-reactive interaction with nitrogen atoms. The vibrational relaxation of oxygen partially occurs via the formation of an intermediate NO2 complex. The efficient energy randomization results in rapid vibrational relaxation at low temperatures, compared to other molecular systems with a purely repulsive potential. The vibrational relaxation time, computed by means of master equation studies, is nearly an order of magnitude lower than the relaxation time in N2-O collisions. The rotational nonequilibrium starts to play a significant effect at translational temperatures above 8000 K. The present work provides convenient relations for the vibrational and rotational relaxation times as well as for the quasi-steady dissociation rate coefficient and thus fills a gap in data due to a lack of experimental measurements for this system.

  6. Molecular mechanisms of drug-induced thrombocytopenia

    NARCIS (Netherlands)

    Burgess, Janette K.

    2001-01-01

    A wide range of drugs can induce thrombocytopenia. Molecular mechanisms for the formation of specific epitopes for all the drug-dependent antibodies appear to be very similar. A restricted set of glycoproteins on the platelet surface interacts with the drugs to form neoepitopes, to which the drug-de

  7. Quantum State Control of Trapped Atomic and Molecular Ions

    Science.gov (United States)

    Seck, Christopher M.

    Full quantum control of a molecule would have a significant impact in molecular coherent control (alignment and orientation) and ultracold and quantum chemistry, quantum computing and simulation as well as hybrid quantum devices, and precision spectroscopy of importance to fundamental physics research. Precision spectroscopy of even simple diatomic molecules offers the possibility of uncovering physics beyond the standard model, specifically time variation of the proton-to-electron mass ratio, which is currently constrained by astronomical molecular observations at the 10-16 1/yr level and laboratory atomic measurements at the 10-17 1/yr level. To achieve this level of measurement and to avoid the complications of diatomic structure on traditional spectroscopy methods, molecular quantum logic spectroscopy (mQLS) will be the spectroscopy technique of choice. We discuss development of in-house external-cavity diode laser (ECDL) systems and improvements to the Libbrecht-Hall circuit, which is a well-known, low-noise current driver for narrow-linewidth diode lasers. However, as the current approaches the maximum set limit, the noise in the laser current increases dramatically. This behavior is documented and simple circuit modifications to alleviate this issue are explored. We cool trapped AlH+ molecules to their ground rotational-vibrational quantum state using an electronically-exciting broadband laser to simultaneously drive cooling resonances from many different rotational levels. We demonstrate rotational cooling on the 140(20) ms timescale from room temperature to 3.8 K, with the ground state population increasing from 3% to 95.4%. Since QLS does not require the high gate fidelities usually associated with quantum computation and quantum simulation, it is possible to make simplifying choices in ion species and quantum protocols at the expense of some fidelity. We demonstrate sideband cooling and motional state detection protocols for 138Ba+ of sufficient fidelity

  8. Mechanical transduction mechanisms of RecA-like molecular motors.

    Science.gov (United States)

    Liao, Jung-Chi

    2011-12-01

    A majority of ATP-dependent molecular motors are RecA-like proteins, performing diverse functions in biology. These RecA-like molecular motors consist of a highly conserved core containing the ATP-binding site. Here I examined how ATP binding within this core is coupled to the conformational changes of different RecA-like molecular motors. Conserved hydrogen bond networks and conformational changes revealed two major mechanical transduction mechanisms: (1) intra-domain conformational changes and (2) inter-domain conformational changes. The intra-domain mechanism has a significant hydrogen bond rearrangement within the domain containing the P-loop, causing relative motion between two parts of the protein. The inter-domain mechanism exhibits little conformational change in the P-loop domain. Instead, the major conformational change is observed between the P-loop domain and an adjacent domain or subunit containing the arginine finger. These differences in the mechanical transduction mechanisms may link to the underlying energy surface governing a Brownian ratchet or a power stroke.

  9. 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.

  10. [Cellular and molecular mechanisms of memory].

    Science.gov (United States)

    Laroche, Serge

    2010-01-01

    A defining characteristic of the brain is its remarkable capacity to undergo activity-dependent functional and morphological remodelling via mechanisms of plasticity that form the basis of our capacity to encode and retain memories. Today, it is generally accepted that one key neurobiological mechanism underlying the formation of memories reside in activity-driven modifications of synaptic strength and structural remodelling of neural networks activated during learning. The discovery and detailed report of the phenomenon generally known as long-term potentiation, a long-lasting activity-dependent form of synaptic strengthening, opened a new chapter in the study of the neurobiological substrate of memory in the vertebrate brain, and this form of synaptic plasticity has now become the dominant model in the search for the cellular bases of learning and memory. To date, the key events in the cellular and molecular mechanisms underlying synaptic plasticity and memory formation are starting to be identified. They require the activation of specific receptors and of several molecular cascades to convert extracellular signals into persistent functional changes in neuronal connectivity. Accumulating evidence suggests that the rapid activation of neuronal gene programs is a key mechanism underlying the enduring modification of neural networks required for the laying down of memory. The recent developments in the search for the cellular and molecular mechanisms of memory storage are reviewed.

  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. Conduction of molecular electronic devices: qualitative insights through atom-atom polarizabilities.

    Science.gov (United States)

    Stuyver, T; Fias, S; De Proft, F; Fowler, P W; Geerlings, P

    2015-03-07

    The atom-atom polarizability and the transmission probability at the Fermi level, as obtained through the source-and-sink-potential method for every possible configuration of contacts simultaneously, are compared for polycyclic aromatic compounds. This comparison leads to the conjecture that a positive atom-atom polarizability is a necessary condition for transmission to take place in alternant hydrocarbons without non-bonding orbitals and that the relative transmission probability for different configurations of the contacts can be predicted by analyzing the corresponding atom-atom polarizability. A theoretical link between the two considered properties is derived, leading to a mathematical explanation for the observed trends for transmission based on the atom-atom polarizability.

  13. Teratogenic effects of thalidomide: molecular mechanisms.

    Science.gov (United States)

    Ito, Takumi; Ando, Hideki; Handa, Hiroshi

    2011-05-01

    Fifty years ago, prescription of the sedative thalidomide caused a worldwide epidemic of multiple birth defects. The drug is now used in the treatment of leprosy and multiple myeloma. However, its use is limited due to its potent teratogenic activity. The mechanism by which thalidomide causes limb malformations and other developmental defects is a long-standing question. Multiple hypotheses exist to explain the molecular mechanism of thalidomide action. Among them, theories involving oxidative stress and anti-angiogenesis have been widely supported. Nevertheless, until recently, the direct target of thalidomide remained elusive. We identified a thalidomide-binding protein, cereblon (CRBN), as a primary target for thalidomide teratogenicity. Our data suggest that thalidomide initiates its teratogenic effects by binding to CRBN and inhibiting its ubiquitin ligase activity. In this review, we summarize the biology of thalidomide, focusing on the molecular mechanisms of its teratogenic effects. In addition, we discuss the questions still to be addressed.

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

    Science.gov (United States)

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

    2016-09-13

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

  15. 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...

  16. Molecular Mechanisms of Neuroplasticity: An Expanding Universe.

    Science.gov (United States)

    Gulyaeva, N V

    2017-03-01

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

  17. Molecular mechanism of Endosulfan action in mammals

    Indian Academy of Sciences (India)

    ROBIN SEBASTIAN; SATHEES C RAGHAVAN

    2017-03-01

    Endosulfan is a broad-spectrum organochlorine pesticide, speculated to be detrimental to human health in areas ofactive exposure. However, the molecular insights to its mechanism of action remain poorly understood. In two recentstudies, our group investigated the physiological and molecular aspects of endosulfan action using in vitro, ex vivo andin vivo analyses. The results showed that apart from reducing fertility levels in male animals, Endosulfan inducedDNA damage that triggers compromised DNA damage response leading to undesirable processing of broken DNAends. In this review, pesticide use especially of Endosulfan in the Indian scenario is summarized and the importance ofour findings, especially the rationalized use of pesticides in the future, is emphasized.

  18. 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.

  19. Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

    CERN Document Server

    Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2011-01-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

  20. 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.

  1. Wave mechanics in quantum phase space: hydrogen atom

    Institute of Scientific and Technical Information of China (English)

    LU Jun

    2007-01-01

    The rigorous sohutions of the stationary Schr(o)dinger equation for hydrogen atom are solved with the wave-mechanics method within the framework of the quantum phase-space representation established by Torres-Vega and Frederick. The "Fourier-like"projection transformations of wave function from the phase space to position and momentum spaces are extended to three-dimensional systems. The eigenfunctions in general position and momentum spaces could be obtained through the transformations from eigenfunction in the phase space.

  2. Molecular mechanism for the umami taste synergism.

    Science.gov (United States)

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

    2008-12-30

    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 domain of T1R1, where L-glutamate binds close to the hinge region, and 5' ribonucleotides bind to an adjacent site close to the opening of the flytrap to further stabilize the closed conformation. This unique mechanism may apply to other class C G-protein-coupled receptors.

  3. Molecular mechanism of the sweet taste enhancers.

    Science.gov (United States)

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

    2010-03-01

    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 similar mechanism as the natural umami taste enhancer molecules. Whereas the sweeteners bind to the hinge region and induce the closure of the Venus flytrap domain of T1R2, the enhancers bind close to the opening and further stabilize the closed and active conformation of the receptor.

  4. Estrogenic endocrine disruptors: Molecular mechanisms of action.

    Science.gov (United States)

    Kiyama, Ryoiti; Wada-Kiyama, Yuko

    2015-10-01

    A comprehensive summary of more than 450 estrogenic chemicals including estrogenic endocrine disruptors is provided here to understand the complex and profound impact of estrogen action. First, estrogenic chemicals are categorized by structure as well as their applications, usage and effects. Second, estrogenic signaling is examined by the molecular mechanism based on the receptors, signaling pathways, crosstalk/bypassing and autocrine/paracrine/homeostatic networks involved in the signaling. Third, evaluation of estrogen action is discussed by focusing on the technologies and protocols of the assays for assessing estrogenicity. Understanding the molecular mechanisms of estrogen action is important to assess the action of endocrine disruptors and will be used for risk management based on pathway-based toxicity testing.

  5. 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.

  6. 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.

  7. Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

    Science.gov (United States)

    2015-08-01

    Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software by N Scott Weingarten and James P Larentzos Approved for...0687 ● AUG 2015 US Army Research Laboratory Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular...Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software 5a. CONTRACT NUMBER 5b

  8. Hydroxylation Reaction Mechanism for Nitrosodimethylamine by Oxygen Atom

    Institute of Scientific and Technical Information of China (English)

    LI Lan; LIN Xiao-yan; LI Zong-he

    2011-01-01

    The hydroxylation reaction mechanism of nitrosodimethylamine(NDMA)by oxygen atom was theoretically investigated at the B3LYP/6-31G** level.It has been found that the path of the oxydation of the C-H bond is easier than the path involving a Singlet/Triplet crossing.The study of the potential surface shows that both solvent effect at B3LYP/6-31G** level and different method at more credible MP2/6-311G** level in the gas phase have no effect on the hydroxylation reaction mechanism.The oxidation hydroxylation process of NDMA by O is exothermic reaction and easy to occur.

  9. 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

  10. 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.

  11. Molecular mechanisms for protein-encoded inheritance.

    Science.gov (United States)

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

    2009-09-01

    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.

  12. The H I Probability Distribution Function and the Atomic-to-molecular Transition in Molecular Clouds

    Science.gov (United States)

    Imara, Nia; Burkhart, Blakesley

    2016-10-01

    We characterize the column-density probability distribution functions (PDFs) of the atomic hydrogen gas, H i, associated with seven Galactic molecular clouds (MCs). We use 21 cm observations from the Leiden/Argentine/Bonn Galactic H i Survey to derive column-density maps and PDFs. We find that the peaks of the H i PDFs occur at column densities in the range ˜1-2 × 1021 {{cm}}-2 (equivalently, ˜0.5-1 mag). The PDFs are uniformly narrow, with a mean dispersion of {σ }{{H}{{I}}}≈ {10}20 {{cm}}-2 (˜0.1 mag). We also investigate the H i-to-H2 transition toward the cloud complexes and estimate H i surface densities ranging from 7 to 16 {M}⊙ {{pc}}-2 at the transition. We propose that the H i PDF is a fitting tool for identifying the H i-to-H2 transition column in Galactic MCs.

  13. The HI Probability Distribution Function and the Atomic-to-Molecular Transition in Molecular Clouds

    CERN Document Server

    Imara, Nia

    2016-01-01

    We characterize the column density probability distributions functions (PDFs) of the atomic hydrogen gas, HI, associated with seven Galactic molecular clouds (MCs). We use 21 cm observations from the Leiden/Argentine/Bonn Galactic HI Survey to derive column density maps and PDFs. We find that the peaks of the HI PDFs occur at column densities ranging from ~1-2$\\times 10^{21}$ cm$^2$ (equivalently, ~0.5-1 mag). The PDFs are uniformly narrow, with a mean dispersion of $\\sigma_{HI}\\approx 10^{20}$ cm$^2$ (~0.1 mag). We also investigate the HI-to-H$_2$ transition towards the cloud complexes and estimate HI surface densities ranging from 7-16 $M_\\odot$ pc$^{-2}$ at the transition. We propose that the HI PDF is a fitting tool for identifying the HI-to-H$_2$ transition column in Galactic MCs.

  14. 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.)

  15. 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.)

  16. Molecular mechanics conformational analysis of tylosin

    Science.gov (United States)

    Ivanov, Petko M.

    1998-01-01

    The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

  17. Studies of some problems related to atomic ordering, molecular motion and pair distribution function

    Science.gov (United States)

    Levashov, Valentin A.

    In this thesis the results of my work on three out of four projects on which I was working during my Ph.D. under supervision of Prof. M. F. Thorpe are summarized. The first project was devoted to the study of properties of a model that was developed to reproduce the ordering of ions in layered double hydroxides. In the model two types of positive ions occupy the sites of triangular lattice. The ordering of ions is assumed to occur due to the long-range Coulomb interaction. The charge neutrality is provided by the negative background charge, which is assumed to be the same at every site of the lattice. General properties of the model in 1d and 2d were studied and the phase diagrams were obtained. The obtained results predict multiple phase separations in this system of charges that can, in particularly, affect the stability of the layered double hydroxides. Some properties of the atomic pair distribution function (PDF) were studied during my work on the second project. Traditionally PDF was used to study atomic ordering at small distances, while it was assumed that at large distances PDF is featureless. Puzzled by the observation that PDF calculated for the crystalline Ni does not decay at large distances we studied the behavior, in particularly the origin of decay, of PDF at large distances. The obtained results potentially could be used to measure the amount of imperfections in crystalline materials and to test instrumental resolution in X-ray and neutron diffraction experiments. During my work on the third project we were developing a technique that would allow accurate calculation of PDF for the flexible molecules. Since quantum mechanical calculations are complicated and computationally demanding in calculations of PDF for molecules in liquid or gaseous phases, classical methods, like molecular dynamics are usually employed. Thus, quantum mechanical effects, like zero-point atomic motion, are usually ignored. However, it is necessary to take into account the

  18. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si3N4(0001) nanopixels

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 μm silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si3N4(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3 GPa and the stress is tensile, -1 GPa, in silicon below the interface.

  19. Determination of molecular, atomic, electronic cross-sections and effective atomic number of some boron compounds and TSW

    Energy Technology Data Exchange (ETDEWEB)

    Icelli, Orhan [Department of physics Education, Faculty of Education Erzincan University, 24030 Erzincan (Turkey)], E-mail: orhanicelli@gmail.com; Erzeneoglu, Salih [Department of physics, Faculty of Sciences, Atatuerk University, Erzurum (Turkey); Boncukcuoglu, Recep [Department of Environmental Engineering, Faculty of Engineering, Atatuerk University, Erzurum (Turkey)

    2008-07-15

    The transmission of gamma-rays of some boron compounds (H{sub 3}BO{sub 3}, Na{sub 2}B{sub 4}O{sub 7}) and the trommel sieve waste (TSW) have been measured by using an extremely narrow-collimated-beam transmission method in the energy range 15.74-40.93 keV. Molecular, atomic and electronic cross-sections and effective atomic numbers have been determinated on the basis of mixture rule and compared with the results obtained from theory.

  20. Modeling molecular mechanisms in the axon

    Science.gov (United States)

    de Rooij, R.; Miller, K. E.; Kuhl, E.

    2017-03-01

    Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena—both in isolation and in interaction—to explore emergent cellular-level features under physiological and pathological conditions.

  1. Molecular mechanisms of sex determination in reptiles.

    Science.gov (United States)

    Rhen, T; Schroeder, A

    2010-01-01

    Charles Darwin first provided a lucid explanation of how gender differences evolve nearly 140 years ago. Yet, a disconnect remains between his theory of sexual selection and the mechanisms that underlie the development of males and females. In particular, comparisons between representatives of different phyla (i.e., flies and mice) reveal distinct genetic mechanisms for sexual differentiation. Such differences are hard to comprehend unless we study organisms that bridge the phylogenetic gap. Analysis of variation within monophyletic groups (i.e., amniotes) is just as important if we hope to elucidate the evolution of mechanisms underlying sexual differentiation. Here we review the molecular, cellular, morphological, and physiological changes associated with sex determination in reptiles. Most research on the molecular biology of sex determination in reptiles describes expression patterns for orthologs of mammalian sex-determining genes. Many of these genes have evolutionarily conserved expression profiles (i.e., DMRT1 and SOX9 are expressed at a higher level in developing testes vs. developing ovaries in all species), which suggests functional conservation. However, expression profiling alone does not test gene function and will not identify novel sex-determining genes or gene interactions. For that reason, we provide a prospectus on various techniques that promise to reveal new sex-determining genes and regulatory interactions among these genes. We offer specific examples of novel candidate genes and a new signaling pathway in support of these techniques.

  2. 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 i...

  3. 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

    2016-01-01

    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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. [Molecular mechanisms regulating the activity of macrophages].

    Science.gov (United States)

    Onoprienko, L V

    2011-01-01

    This article reviews modern concepts of the most common types of macrophage activation: classical, alternative, and type II. Molecular mechanisms of induction and regulation of these three types of activation are discussed. Any population of macrophages was shown to change its properties depending on its microenvironment and concrete biological situation (the "functional plasticity of macrophages"). Many intermediate states of macrophages were described along with the most pronounced and well-known activation types (classical activation, alternative activation, and type II activation). These intermediate states are characterized by a variety of combinations of their biological properties, including elements of the three afore mentioned types of activation. Macrophage activity is regulated by a complex network of interrelated cascade mechanisms.

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

    Science.gov (United States)

    Shen, Lin; Wu, Jingheng; Yang, Weitao

    2016-10-11

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

  10. 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.

  11. 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.

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

    Science.gov (United States)

    Saintonge, Amelie; Catinella, Barbara; Cortese, Luca; Genzel, Reinhard; Giovanelli, Riccardo; Haynes, Martha P.; Janowiecki, Steven; Kramer, Carsten; Lutz, Katharina A.; Schiminovich, David; Tacconi, Linda J.; Wuyts, Stijn; Accurso, Gioacchino

    2016-10-01

    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 H I 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 MS galaxies, indicating that the flattening of the MS is due to the global decrease of the cold gas reservoirs of galaxies rather than to bottlenecks in the process of converting cold atomic gas to stars.

  14. 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.

  15. 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 test a wide spectrum of molecular replacement parameters, such as clusters of different conformations. The result is scored by the ability to identify heavy-atom positions, from anomalous difference Fourier maps, that allow meaningful phases to be determined. The strategy was successfully applied...... but correct molecular replacement solutions with maximum contrast to prime experimental phasing efforts....

  16. 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...... the identification of weak but correct molecular-replacement solutions with maximum contrast to prime experimental phasing efforts....

  17. Spectroscopic Studies of Atomic and Molecular Processes in the Edge Region of Magnetically Confined Fusion Plasmas

    Science.gov (United States)

    Hey, J. D.; Brezinsek, S.; Mertens, Ph.; Unterberg, B.

    2006-12-01

    Edge plasma studies are of vital importance for understanding plasma-wall interactions in magnetically confined fusion devices. These interactions determine the transport of neutrals into the plasma, and the properties of the plasma discharge. This presentation deals with optical spectroscopic studies of the plasma boundary, and their rôle in elucidating the prevailing physical conditions. Recorded spectra are of four types: emission spectra of ions and atoms, produced by electron impact excitation and by charge-exchange recombination, atomic spectra arising from electron impact-induced molecular dissociation and ionisation, visible spectra of molecular hydrogen and its isotopic combinations, and laser-induced fluorescence (LIF) spectra. The atomic spectra are strongly influenced by the confining magnetic field (Zeeman and Paschen-Back effects), which produces characteristic features useful for species identification, temperature determination by Doppler broadening, and studies of chemical and physical sputtering. Detailed analysis of the Zeeman components in both optical and LIF spectra shows that atomic hydrogen is produced in various velocity classes, some related to the relevant molecular Franck-Condon energies. The latter reflect the dominant electron collision processes responsible for production of atoms from molecules. This assignment has been verified by gas-puffing experiments through special test limiters. The higher-energy flanks of hydrogen line profiles probably also show the influence of charge-exchange reactions with molecular ions accelerated in the plasma sheath (`scrape-off layer') separating limiter surfaces from the edge plasma, in analogy to acceleration in the cathode-fall region of gas discharges. While electron collisions play a vital rôle in generating the spectra, ion collisions with excited atomic radiators act through re-distribution of population among the atomic fine-structure sublevels, and momentum transfer to the atomic nuclei

  18. Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation.

    Science.gov (United States)

    Polyak, Iakov; Benighaus, Tobias; Boulanger, Eliot; Thiel, Walter

    2013-08-14

    The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.

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

    Energy Technology Data Exchange (ETDEWEB)

    Pabst, Stefan Ulf

    2013-04-15

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

  20. 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 ...

  1. Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach.

    Science.gov (United States)

    Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro

    2012-03-28

    A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.

  2. Similarity recognition of molecular structures by optimal atomic matching and rotational superposition.

    Science.gov (United States)

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

    An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.

  3. 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.

  4. Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation

    Science.gov (United States)

    Liang, Shih-Wei; Wang, Chih-Hao; Fang, Te-Hua

    2016-09-01

    Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the grinding process are studied by the molecular dynamics simulation method.

  5. Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation.

    Science.gov (United States)

    Liang, Shih-Wei; Wang, Chih-Hao; Fang, Te-Hua

    2016-12-01

    Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the grinding process are studied by the molecular dynamics simulation method.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Molecular Mechanisms of Neonatal Brain Injury

    Directory of Open Access Journals (Sweden)

    Claire Thornton

    2012-01-01

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

  11. Phenotypic plasticity: molecular mechanisms and adaptive significance.

    Science.gov (United States)

    Kelly, Scott A; Panhuis, Tami M; Stoehr, Andrew M

    2012-04-01

    Phenotypic plasticity can be broadly defined as the ability of one genotype to produce more than one phenotype when exposed to different environments, as the modification of developmental events by the environment, or as the ability of an individual organism to alter its phenotype in response to changes in environmental conditions. Not surprisingly, the study of phenotypic plasticity is innately interdisciplinary and encompasses aspects of behavior, development, ecology, evolution, genetics, genomics, and multiple physiological systems at various levels of biological organization. From an ecological and evolutionary perspective, phenotypic plasticity may be a powerful means of adaptation and dramatic examples of phenotypic plasticity include predator avoidance, insect wing polymorphisms, the timing of metamorphosis in amphibians, osmoregulation in fishes, and alternative reproductive tactics in male vertebrates. From a human health perspective, documented examples of plasticity most commonly include the results of exercise, training, and/or dieting on human morphology and physiology. Regardless of the discipline, phenotypic plasticity has increasingly become the target of a plethora of investigations with the methodological approaches utilized ranging from the molecular to whole organsimal. In this article, we provide a brief historical outlook on phenotypic plasticity; examine its potential adaptive significance; emphasize recent molecular approaches that provide novel insight into underlying mechanisms, and highlight examples in fishes and insects. Finally, we highlight examples of phenotypic plasticity from a human health perspective and underscore the use of mouse models as a powerful tool in understanding the genetic architecture of phenotypic plasticity.

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

    Science.gov (United States)

    Sun, Qiming; Chan, Garnet Kin-Lic

    2014-09-09

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

  13. 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 ...

  14. 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.

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

    Science.gov (United States)

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

    2013-02-19

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

  16. 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…

  17. Comment on "Stimulated Raman adiabatic passage from an atomic to a molecular Bose-Einstein condensate"

    OpenAIRE

    2002-01-01

    Collective two-color photoassociation of a freely-interacting 87Rb Bose-Einstein condensate is theoretically examined, focusing on stimulated Raman adiabatic passage (STIRAP) from an atomic to a stable molecular condensate. In particular, Drummond et al. [Phys. Rev. A 65, 063619 (2002); cond-mat/0110578] have predicted that particle-particle interactions can limit the efficiency of collective atom-molecule STIRAP, and that optimizing the laser parameters can partially overcome this limitation...

  18. The formation of the W43 complex: constraining its atomic-to-molecular transition and searching for colliding clouds

    CERN Document Server

    Motte, F; Schneider, N; Heitsch, F; Glover, S; Carlhoff, P; Hill, T; Bontemps, S; Schilke, P; Louvet, F; Hennemann, M; Didelon, P; Beuther, H

    2014-01-01

    Numerical simulations have explored the possibility to form molecular clouds through either a quasi-static, self-gravitating mechanism or the collision of gas streams or lower-density clouds. They also quantitatively predict the distribution of matter at the transition from atomic to molecular gases. We aim to observationally test these models by studying the environment of W43, a molecular cloud complex near the tip of the Galactic long bar. Using Galaxy-wide HI and 12CO surveys we searched for gas flowing toward the W43 molecular cloud complex. We also estimated the HI and H2 mass surface densities to constrain the transition from atomic to molecular gas around and within W43. We found 3 cloud ensembles within the position-velocity diagrams of 12CO and HI gases. They are separated by 20km/s along the line of sight and extend into the 13CO velocity structure of W43. Since their velocity gradients are consistent with free-fall, they could be nearby clouds attracted by, and streaming toward, the W43 10^7Msun p...

  19. Diffuse Atomic and Molecular Gas near IC443

    CERN Document Server

    Hirschauer, A; Wallerstein, George; Means, T

    2009-01-01

    We present an analysis of results on absorption from Ca II, Ca I, K I, and the molecules CH+, CH, C2, and CN that probes gas interacting with the supernova remnant IC443. The eleven directions sample material across the visible nebula and beyond its eastern edge. Most of the neutral material, including the diatomic molecules, is associated with the ambient cloud detected via H I and CO emission. Analysis of excitation and chemistry yields gas densities that are typical of diffuse molecular gas. The low density gas probed by Ca II extends over a large range in velocities, from -120 to +80 km/s in the most extreme cases. This gas is distributed among several velocity components, unlike the situation for the shocked molecular clumps, whose emission occurs over much the same range but as very broad features. The extent of the high-velocity absorption suggests a shock velocity of 100 km/s for the expanding nebula.

  20. 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.

  1. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting.

    Science.gov (United States)

    Burger, Steven K; Schofield, Jeremy; Ayers, Paul W

    2013-12-05

    We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.

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

    Energy Technology Data Exchange (ETDEWEB)

    Du, Y., E-mail: yingge.du@pnnl.gov, E-mail: scott.chambers@pnnl.gov; Liyu, A. V. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Droubay, T. C.; Chambers, S. A., E-mail: yingge.du@pnnl.gov, E-mail: scott.chambers@pnnl.gov [Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Li, G. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

    2014-04-21

    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.

  3. Self-corrected Sensors Based On Atomic Absorption Spectroscopy For Atom Flux Measurements In Molecular Beam Epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Du, Yingge; Droubay, Timothy C.; Liyu, Andrey V.; Li, Guosheng; Chambers, Scott A.

    2014-04-24

    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 (CCD) detector in a double-beam configuration, we employ a non-resonant line or a resonant line with lower absorbance 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.

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Science.gov (United States)

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

    2015-06-01

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

  6. INVESTIGATION INTO THE MECHANISMS OF TISSUE ATOMIZATION BY HIGH INTENSITY FOCUSED ULTRASOUND

    OpenAIRE

    Simon, Julianna C.; Sapozhnikov, Oleg A.; Wang, Yak-Nam; Khokhlova, Vera A.; Crum, Lawrence A.; Bailey, Michael R.

    2015-01-01

    Ultrasonic atomization, or the emission of a fog of droplets, was recently proposed to explain tissue fractionation in boiling histotripsy. However, even though liquid atomization has been studied extensively, the mechanisms of tissue atomization remain unclear. In this paper, high-speed photography and overpressure were used to evaluate the role of bubbles in tissue atomization. As the static pressure increased, the degree of fractionation decreased, and the ex vivo tissue became thermally d...

  7. 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

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

    Science.gov (United States)

    Rong, Chunying; Lu, Tian; Liu, Shubin

    2014-01-14

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

  9. 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.

  10. 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

  11. 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

  12. Deciphering the Molecular Mechanisms of Breast Cancer

    Science.gov (United States)

    2005-03-01

    BRCA1 and BRCA2, by a Signalosome-like Subunit and its Role in DNA Repair. Molecular Cell 12; 1087-1099 (2003). Presentations/Abstracts...BRCA1 and BRCA2, by a Signalosome-like Subunit and its Role in DNA Repair. Molecular Cell 12; 1087-1099. APPENDICIES: CURRICULUM VITAE...Oncogenesis Program Member, Faculty Recruitment Committee Periodic Manuscript Reviews: Cell, Science, Molecular Cell , Molecular and Cellular

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

    Science.gov (United States)

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

    2017-02-14

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

  14. 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.

  15. Crossed-molecular-beams reactive scattering of oxygen atoms

    Energy Technology Data Exchange (ETDEWEB)

    Baseman, R.J.

    1982-11-01

    The reactions of O(/sup 3/P) with six prototypical unsaturated hydrocarbons, and the reaction of O(/sup 1/D) with HD, have been studied in high-resolution crossed-molecular-beams scattering experiments with mass-spectrometric detection. The observed laboratory-product angular and velocity distributions unambiguously identify parent-daughter ion pairs, distinguish different neutral sources of the same ion, and have been used to identify the primary products of the reactions. The derived center-of-mass product angular and translational energy distributions have been used to elucidate the detailed reaction dynamics. These results demonstrate that O(/sup 3/P)-unsaturated hydrocarbon chemistry is dominated by single bond cleavages, leading to radical products exclusively.

  16. INVESTIGATION INTO THE MECHANISMS OF TISSUE ATOMIZATION BY HIGH INTENSITY FOCUSED ULTRASOUND

    Science.gov (United States)

    Simon, Julianna C.; Sapozhnikov, Oleg A.; Wang, Yak-Nam; Khokhlova, Vera A.; Crum, Lawrence A.; Bailey, Michael R.

    2014-01-01

    Ultrasonic atomization, or the emission of a fog of droplets, was recently proposed to explain tissue fractionation in boiling histotripsy. However, even though liquid atomization has been studied extensively, the mechanisms of tissue atomization remain unclear. In this paper, high-speed photography and overpressure were used to evaluate the role of bubbles in tissue atomization. As the static pressure increased, the degree of fractionation decreased, and the ex vivo tissue became thermally denatured. The effect of surface wetness on atomization was also evaluated in vivo and in tissue-mimicking gels where surface wetness was found to enhance atomization by forming surface instabilities that augment cavitation. In addition, experimental results indicated that wetting collagenous tissues, such as the liver capsule, allowed atomization to breach such barriers. These results highlight the importance of bubbles and surface instabilities in atomization and could be used to enhance boiling histotripsy for transition to clinical use. PMID:25662182

  17. Investigation into the mechanisms of tissue atomization by high-intensity focused ultrasound.

    Science.gov (United States)

    Simon, Julianna C; Sapozhnikov, Oleg A; Wang, Yak-Nam; Khokhlova, Vera A; Crum, Lawrence A; Bailey, Michael R

    2015-05-01

    Ultrasonic atomization, or the emission of a fog of droplets, was recently proposed to explain tissue fractionation in boiling histotripsy. However, even though liquid atomization has been studied extensively, the mechanisms underlying tissue atomization remain unclear. In the work described here, high-speed photography and overpressure were used to evaluate the role of bubbles in tissue atomization. As static pressure increased, the degree of fractionation decreased, and the ex vivo tissue became thermally denatured. The effect of surface wetness on atomization was also evaluated in vivo and in tissue-mimicking gels, where surface wetness was found to enhance atomization by forming surface instabilities that augment cavitation. In addition, experimental results indicated that wetting collagenous tissues, such as the liver capsule, allowed atomization to breach such barriers. These results highlight the importance of bubbles and surface instabilities in atomization and could be used to enhance boiling histotripsy for transition to clinical use.

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

    Science.gov (United States)

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

    2016-03-01

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

  19. 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.

  20. Molecular Mechanism for LAMP1 Recognition by Lassa Virus

    Science.gov (United States)

    Cohen-Dvashi, Hadas; Cohen, Nadav; Israeli, Hadar

    2015-01-01

    ABSTRACT Lassa virus is a notorious human pathogen that infects many thousands of people each year in West Africa, causing severe viral hemorrhagic fevers and significant mortality. The surface glycoprotein of Lassa virus mediates receptor recognition through its GP1 subunit. Here we report the crystal structure of GP1 from Lassa virus, which is the first representative GP1 structure for Old World arenaviruses. We identify a unique triad of histidines that forms a binding site for LAMP1, a known lysosomal protein recently discovered to be a critical receptor for internalized Lassa virus at acidic pH. We demonstrate that mutation of this histidine triad, which is highly conserved among Old World arenaviruses, impairs LAMP1 recognition. Our biochemical and structural data further suggest that GP1 from Lassa virus may undergo irreversible conformational changes that could serve as an immunological decoy mechanism. Together with a variable region that we identify on the surface of GP1, those could be two distinct mechanisms that Lassa virus utilizes to avoid antibody-based immune response. IMPORTANCE Structural data at atomic resolution for viral proteins is key for understanding their function at the molecular level and can facilitate novel avenues for combating viral infections. Here we used X-ray protein crystallography to decipher the crystal structure of the receptor-binding domain (GP1) from Lassa virus. This is a pathogenic virus that causes significant illness and mortality in West Africa. This structure reveals the overall architecture of GP1 domains from the group of viruses known as the Old World arenaviruses. Using this structural information, we elucidated the mechanisms for pH switch and binding of Lassa virus to LAMP1, a recently identified host receptor that is critical for successful infection. Lastly, our structural analysis suggests two novel immune evasion mechanisms that Lassa virus may utilize to escape antibody-based immune response. PMID

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  2. Giant Atomic and Molecular Models and Other Lecture Demonstration Devices Designed for Concrete Operational Students.

    Science.gov (United States)

    Battino, Rubin

    1983-01-01

    Describes the design, construction, and use of oversize lecture-demonstration atomic/molecular models. These models appeal to both concrete and formal operational students. Also describes construction and use of an "spdf" sandwich board and an experiment using attribute blocks. (JN)

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

    Science.gov (United States)

    Engstrom, James R; Kummel, Andrew C

    2017-02-07

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

  4. Molecular and atomic gas in the Local Group galaxy M 33

    NARCIS (Netherlands)

    Gratier, P.; Braine, J.; Rodriguez-Fernandez, N. J.; Schuster, K. F.; Kramer, C.; Xilouris, E. M.; Tabatabaei, F. S.; Henkel, C.; Corbelli, E.; Israel, F.; van der Werf, P. P.; Calzetti, D.; Garcia-Burillo, S.; Sievers, A.; Combes, F.; Wiklind, T.; Brouillet, N.; Herpin, F.; Bontemps, S.; Aalto, S.; Koribalski, B.; van der Tak, F.; Wiedner, M. C.; Röllig, M.; Mookerjea, B.

    2010-01-01

    We present high-resolution large-scale observations of the molecular and atomic gas in the Local Group galaxy M 33. The observations were carried out using the HEterodyne Receiver Array (HERA) at the 30 m IRAM telescope in the CO(2-1) line, achieving a resolution of 12” × 2.6 km s-1, enabling indivi

  5. Molecular and atomic gas in the Local Group galaxy M 33

    NARCIS (Netherlands)

    Gratier, P.; Braine, J.; Rodriguez-Fernandez, N. J.; Schuster, K. F.; Kramer, C.; Xilouris, E. M.; Tabatabaei, F. S.; Henkel, C.; Corbelli, E.; Israel, F.; Calzetti, D.; Garcia-Burillo, S.; Sievers, A.; Combes, F.; Wiklind, T.; Brouillet, N.; Herpin, F.; Bontemps, S.; Aalto, S.; Koribalski, B.; van der Tak, F.; Wiedner, M. C.; Roellig, M.; Mookerjea, B.; van der Werf, Paul P.

    2010-01-01

    We present high-resolution large-scale observations of the molecular and atomic gas in the Local Group galaxy M 33. The observations were carried out using the HEterodyne Receiver Array (HERA) at the 30 m IRAM telescope in the CO(2-1) line, achieving a resolution of 12 '' x 2.6 km s(-1), enabling in

  6. Structural and chemical evolution of single-wall carbon nanotubes under atomic and molecular deuterium interaction

    NARCIS (Netherlands)

    Lisowski, W.; Keim, E.G.; Berg, van den A.H.J.; Smithers, M.A.

    2005-01-01

    The interaction of atomic (D) and molecular (D2) deuterium, as present in a (D + D2) gas mixture, with single-wall carbon nanotubes (SWNTs) has been studied by means of a combination of scanning electron microscopy, transmission electron microscopy and X-ray photoelectron spectroscopy. The SWNT samp

  7. Essay: Fifty years of atomic, molecular and optical physics in Physical Review Letters.

    Science.gov (United States)

    Haroche, Serge

    2008-10-17

    The fiftieth anniversary of Physical Review Letters is a good opportunity to review the extraordinary progress of atomic, molecular, and optical physics reported in this journal during the past half-century. As both a witness and an actor of this story, I recall personal experiences and reflect about the past, present, and possible future of my field of research.

  8. Molecular markers predicting radiotherapy response: report and recommendations from an International Atomic Energy Agency technical meeting.

    NARCIS (Netherlands)

    West, C.M.; McKay, M.J.; Holscher, T.; Baumann, M.; Stratford, I.J.; Bristow, R.G.; Iwakawa, M.; Imai, T.; Zingde, S.M.; Anscher, M.S.; Bourhis, J.; Begg, A.C.; Haustermans, K.; Bentzen, S.M.; Hendry, J.H.

    2005-01-01

    PURPOSE: There is increasing interest in radiogenomics and the characterization of molecular profiles that predict normal tissue and tumor radioresponse. A meeting in Amsterdam was organized by the International Atomic Energy Agency to discuss this topic on an international basis. METHODS AND MATERI

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

    Science.gov (United States)

    Engstrom, James R.; Kummel, Andrew C.

    2017-02-01

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

  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.

  11. Silica Synthesis by Sponges: Unanticipated Molecular Mechanism

    Science.gov (United States)

    Morse, D. E.; Weaver, J. C.

    2001-12-01

    substitutions of specific amino acid sidechains, in conjunction with computer-assisted molecular modeling and biomimetic synthesis, allowed us to probe the determinants of catalytic activity and confirm the identification of the amino acid sidechains required for hydrolysis of the silicon alkoxides. If, as suggested by the data of others, silicic acid is conjugated with organic moieties after its transport into the cell, the catalytic mechanism described here may be important in biosilicification by sponges. As is often the case, we have been better able to answer mechanistic questions about "how" silica can be formed biologically, than "why" the diversity of structures is elaborated. Studies of spicule formation during cellular regeneration in Tethya aurantia reveal that synthesis of the larger silica needles (megascleres) and smaller starburst-shaped microscleres may be independently regulated, presumably at the genetic level. The spatial segregation of these morphologically-distinct spicule types within the sponge further suggests an adaptive significance of the different skeletal elements.

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

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam

    2000-01-01

    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¯ 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam

    2000-01-10

    Mechanical behavior of the Si(111)/Si{sub 3}N{sub 4} (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.

  14. Molecular Mechanisms of Metastasis Suppression in Human Breast Cancer

    Science.gov (United States)

    2000-07-01

    and breast carcinoma metastasis, Wake Forest University Cancer Center, July 28 Molecular mechanisms controlling melanoma and breast carcinoma...Bowman Show, August 17 Molecular regulation of melanoma and breast carcinoma metastasis, Wake Forest University Cancer Center, July 28 Molecular...Institute, April 20, Pathology ofNeoplasia Cumberland Unit, American Cancer Society, April 19; Breast Cancer Research Ministerio de Sanidad y

  15. Atomization mechanisms and gas phase reactions in graphite furnace atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Frech, W.; Lindberg, A.O.; Lundberg, E.; Cedergren, A.

    1986-04-01

    The amounts of carbon monoxide as well as the total amounts of hydrocarbons generated in different types of graphite tubes were investigated under various experimental conditions. Depending on whether or not a matrix like 50 ..mu..g of sodium nitrate was added the amount of carbon monoxide formed during atomization at 1,700 K in a pyrocoated tube was in the range 60 to 600 nmoles when using a thermal pretreatment temperature of 1,200 K. The corresponding values for an uncoated tube were 250 to 1,300 nmoles. The effect of carbon monoxide on the atomization behaviour of silver, bismuth, chromium, copper and lead was investigated experimentally and the results were evaluated by means of thermodynamically based models. In accordance with theoretical predications, only lead, bismuth and chromium, which are assumed to be atomized by oxide decomposition, showed substantial shifts in their appearance temperatures in different gas mixtures, and changes in activation energies.

  16. 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

    2016-06-17

    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.

  17. 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

    2015-06-02

    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.

  18. Kinetic model of atomic and molecular emissions in laser-induced breakdown spectroscopy of organic compounds.

    Science.gov (United States)

    Ma, Qianli; Dagdigian, Paul J

    2011-07-01

    A kinetic model previously developed to predict the relative intensities of atomic emission lines in laser-induced breakdown spectroscopy has been extended to include processes related to CN and C(2) molecular emissions. Simulations with this model were performed to predict the relative excited-state populations. The results from the simulations are compared with experimentally determined excited-state populations from 1,064 nm laser irradiation of organic residues on aluminum foil. The model reasonably predicts the relative intensity of the molecular emissions. Significantly, the model reproduces the vastly different temporal profiles of the atomic and molecular emissions. The latter are found to extend to much longer times after the laser pulse, and this appears to be due to the increasing concentration of the molecules versus time. From the simulations, the important processes affecting the CN and C(2) concentrations are identified.

  19. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

    Science.gov (United States)

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2017-02-09

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

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

    Science.gov (United States)

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

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

  1. Molecular Dynamics Study of the Motion of Atomic Components of the DNA Molecule and its Environment.

    Science.gov (United States)

    Perez, Patricio

    It is of great interest for us to come to a better understanding of some biological processes through a study of the behavior of the atomic entities involved in them. One of the most important biological molecules in DNA. In the outer part of its helical structure, phosphate groups are known to be present. The natural environment of this molecule is liquid water. Some cations like Na('+) and Mg('2+) are often found in its surroundings. In this work we show results of applying a polarizable water model (the PE model) to the molecular dynamics simulation of hydrated sodium ion microclusters. We found that the PE model with just two adjustable parameters reproduces the experimental enthalpies of formation of the ion-water microclusters better than a number of other methods. We also found that for the case of six water molecules at O K, they do not form a regular octahedron around the sodium ion as predicted by other models. The predicted change in structure appears to be in agreement with experimental observations. We introduced later a phosphate group and performed a molecular dynamics simulation of its interaction with water and a sodium cation. We use polarizable models for both water and the phosphate group. According to our calculation, a potential fitted to quantum mechanical results produces a strong binding between the sodium and the phosphate group. This binding is such that hydration of the sodium is not clearly observed. Regardless of this we can conclude that the effect of assuming the phosphate group polarizable is not significant.

  2. Hydrogen in diffuse molecular clouds in the Milky Way. Atomic column densities and molecular fraction along prominent lines of sight

    Science.gov (United States)

    Winkel, B.; Wiesemeyer, H.; Menten, K. M.; Sato, M.; Brunthaler, A.; Wyrowski, F.; Neufeld, D.; Gerin, M.; Indriolo, N.

    2017-03-01

    Context. Recent submillimeter and far-infrared wavelength observations of absorption in the rotational ground-state lines of various simple molecules against distant Galactic continuum sources have opened the possibility of studying the chemistry of diffuse molecular clouds throughout the Milky Way. In order to calculate abundances, the column densities of molecular and atomic hydrogen, H i, must be known. Aims: We aim at determining the atomic hydrogen column densities for diffuse clouds located on the sight lines toward a sample of prominent high-mass star-forming regions that were intensely studied with the HIFI instrument onboard Herschel. Methods: Based on Jansky Very Large Array data, we employ the 21 cm H i absorption-line technique to construct profiles of the H i opacity versus radial velocity toward our target sources. These profiles are combined with lower resolution archival data of extended H i emission to calculate the H i column densities of the individual clouds along the sight lines. We employ Bayesian inference to estimate the uncertainties of the derived quantities. Results: Our study delivers reliable estimates of the atomic hydrogen column density for a large number of diffuse molecular clouds at various Galactocentric distances. Together with column densities of molecular hydrogen derived from its surrogates observed with HIFI, the measurements can be used to characterize the clouds and investigate the dependence of their chemistry on the molecular fraction, for example. The data sets are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/600/A2

  3. Stochastic growth theory of molecular beam epitaxy with atom correlation effects: A Monte-Carlo master equation method

    Science.gov (United States)

    Nakayama, Hiroshi; Furuichi, Akihisa; Kita, Takashi; Nishino, Taneo

    1997-04-01

    Structural phase transition of epitaxial growing layer is quite important to understand the atomic scale mechanism of molecular beam epitaxy (MBE). GaAs and related alloy semiconductors are typical systems which show variety of such structural transitions during MBE. Structural evolution of surface reconstruction phases and an order-disorder transition in III-V alloy semiconductors are typical cases where such phase transitions appear during epitaxial processes. In this work, a stochastic theory and the Monte-Carlo simulation have been presented to describe the structural evolution of epitaxial growth in binary system. This method, known here as the 'Monte-Carlo master equation (MCME) method', couples a master equation for epitaxial growth kinetics with an Ising Hamiltonian of growing surface. The Monte-Carlo (MC) simulation of binary growing surface with atom-correlation effects has successfully revealed the evolution of atomic structure and the formation of short-range ordering (SRO) during epitaxy. This demonstrates the usefulness of the MCME method in describing the atomic-structural dynamics as compared with a conventional theory of epitaxy based on a diffusion equation and standard nucleation theory.

  4. Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

    Science.gov (United States)

    Kukol, Andreas

    2009-03-10

    United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.

  5. 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

  6. Molecular modifiers reveal a mechanism of pathological crystal growth inhibition

    Science.gov (United States)

    Chung, Jihae; Granja, Ignacio; Taylor, Michael G.; Mpourmpakis, Giannis; Asplin, John R.; Rimer, Jeffrey D.

    2016-08-01

    Crystalline materials are crucial to the function of living organisms, in the shells of molluscs, the matrix of bone, the teeth of sea urchins, and the exoskeletons of coccoliths. However, pathological biomineralization can be an undesirable crystallization process associated with human diseases. The crystal growth of biogenic, natural and synthetic materials may be regulated by the action of modifiers, most commonly inhibitors, which range from small ions and molecules to large macromolecules. Inhibitors adsorb on crystal surfaces and impede the addition of solute, thereby reducing the rate of growth. Complex inhibitor-crystal interactions in biomineralization are often not well elucidated. Here we show that two molecular inhibitors of calcium oxalate monohydrate crystallization—citrate and hydroxycitrate—exhibit a mechanism that differs from classical theory in that inhibitor adsorption on crystal surfaces induces dissolution of the crystal under specific conditions rather than a reduced rate of crystal growth. This phenomenon occurs even in supersaturated solutions where inhibitor concentration is three orders of magnitude less than that of the solute. The results of bulk crystallization, in situ atomic force microscopy, and density functional theory studies are qualitatively consistent with a hypothesis that inhibitor-crystal interactions impart localized strain to the crystal lattice and that oxalate and calcium ions are released into solution to alleviate this strain. Calcium oxalate monohydrate is the principal component of human kidney stones and citrate is an often-used therapy, but hydroxycitrate is not. For hydroxycitrate to function as a kidney stone treatment, it must be excreted in urine. We report that hydroxycitrate ingested by non-stone-forming humans at an often-recommended dose leads to substantial urinary excretion. In vitro assays using human urine reveal that the molecular modifier hydroxycitrate is as effective an inhibitor of nucleation

  7. 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.

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

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2005-01-01

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

  9. A stepwise atomic, valence-molecular, and full-molecular optimisation of the Hartree-Fock/Kohn-Sham energy.

    Science.gov (United States)

    Jansík, Branislav; Høst, Stinne; Johansson, Mikael P; Olsen, Jeppe; Jørgensen, Poul; Helgaker, Trygve

    2009-07-21

    A hierarchical optimisation strategy has been introduced for minimising the Hartree-Fock/Kohn-Sham energy, consisting of three levels (3L): an atom-in-a-molecule optimisation, a valence-basis molecular optimisation, and a full-basis molecular optimisation. The density matrix formed at one level is used as a starting density matrix at the next level with no loss of information. To ensure a fast and reliable convergence to a minimum, the augmented Roothaan-Hall (ARH) algorithm is used in both the valence-basis and full-basis molecular optimisations. The performance of the ARH-3L method is compared with standard optimisation algorithms. Both for efficiency and reliability, we recommend to use the ARH-3L algorithm.

  10. The cognitive life of mechanical molecular models.

    Science.gov (United States)

    Charbonneau, Mathieu

    2013-12-01

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

  11. Nuclear magnetic shielding constants of liquid water: insights from hybrid quantum mechanics/molecular mechanics models.

    Science.gov (United States)

    Kongsted, Jacob; Nielsen, Christian B; Mikkelsen, Kurt V; Christiansen, Ove; Ruud, Kenneth

    2007-01-21

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the (17)O and (1)H isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4 ppm for the (17)O shielding and 1 ppm for the (1)H shielding.

  12. Nuclear magnetic shielding constants of liquid water: Insights from hybrid quantum mechanics/molecular mechanics models

    Science.gov (United States)

    Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-01-01

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the O17 and H1 isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4ppm for the O17 shielding and 1ppm for the H1 shielding.

  13. 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.

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

    Science.gov (United States)

    Hamada, Yojiro; Kanematsu, Yusuke; Tachikawa, Masanori

    2016-10-11

    The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

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

    Science.gov (United States)

    Teo, Boon K.; Li, Wai-Kee

    2011-01-01

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

  16. Electronic, mechanical and optical properties of atomically thin tow-dimensional crystals

    Directory of Open Access Journals (Sweden)

    A. Castellanos-Gómez

    2012-03-01

    Full Text Available This work is devoted to the study of electronic and mechanical properties of crystalline atomically thin two-dimensional sheets, such as graphene, MoS2, NbSe2 and mica by scanning probe microscopy.

  17. Trapping molecular ions formed via photo-associative ionization of ultracold atoms

    CERN Document Server

    Sullivan, Scott T; Kotochigova, Svetlana; Chen, Kuang; Schowalter, Steven J; Hudson, Eric R

    2011-01-01

    The formation of $^{40}$Ca$_2^+$ molecular ions is observed in a hybrid $^{40}$Ca magneto-optical and ion trap system. The molecular ion formation process is determined to be two-photon photo-associative ionization of ultracold $^{40}$Ca atoms. A lower bound for the two-body, two-photon rate constant is found to be $\\bar{\\beta} \\geq 2 \\pm 1 \\times 10^{-15}$ cm$^{3}$ Hz. $\\textit{Ab initio}$ molecular potential curves are calculated for the neutral Ca$_2$ and ionic Ca$_2^+$ molecules and used in a model that identifies the photo-associative ionization pathway. As this technique does not require a separate photo-association laser, it could find use as a simple, robust method for producing ultracold, state-selected molecular ions.

  18. Quantum Monte Carlo of atomic and molecular systems with heavy elements

    Science.gov (United States)

    Mitas, Lubos; Kulahlioglu, Adem; Melton, Cody; Bennett, Chandler

    2015-03-01

    We carry out quantum Monte Carlo calculations of atomic and molecular systems with several heavy atoms such as Mo, W and Bi. In particular, we compare the correlation energies vs their lighter counterparts in the same column of the periodic table in order to reveal trends with regard to the atomic number Z. One of the observations is that the correlation energy for the isoelectronic valence space/states is mildly decreasing with increasing Z. Similar observation applies also to the fixed-node errors, supporting thus our recent observation that the fixed-node error increases with electronic density for the same (or similar) complexity of the wave function and bonding. In addition, for Bi systems we study the impact of the spin-orbit on the electronic structure, in particular, on binding, correlation and excitation energies.

  19. Surface reactions of molecular and atomic oxygen with carbon phosphide films.

    Science.gov (United States)

    Gorham, Justin; Torres, Jessica; Wolfe, Glenn; d'Agostino, Alfred; Fairbrother, D Howard

    2005-11-01

    The surface reactions of atomic and molecular oxygen with carbon phosphide films have been studied using X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Carbon phosphide films were produced by ion implantation of trimethylphosphine into polyethylene. Atmospheric oxidation of carbon phosphide films was dominated by phosphorus oxidation and generated a carbon-containing phosphate surface film. This oxidized surface layer acted as an effective diffusion barrier, limiting the depth of phosphorus oxidation within the carbon phosphide film to phosphorus atoms as well as the degree of phosphorus oxidation. For more prolonged AO exposures, a highly oxidized phosphate surface layer formed that appeared to be inert toward further AO-mediated erosion. By utilizing phosphorus-containing hydrocarbon thin films, the phosphorus oxides produced during exposure to AO were found to desorb at temperatures >500 K under vacuum conditions. Results from this study suggest that carbon phosphide films can be used as AO-resistant surface coatings on polymers.

  20. Prediction of structural and mechanical properties of atom-decorated porous graphene via density functional calculations

    Science.gov (United States)

    Ansari, Reza; Ajori, Shahram; Malakpour, Sina

    2016-04-01

    The considerable demand for novel materials with specific properties has motivated the researchers to synthesize supramolecular nanostructures through different methods. Porous graphene is the first two-dimensional hydrocarbon synthesized quite recently. This investigation is aimed at studying the mechanical properties of atom-decorated (functionalized) porous graphene by employing density functional theory (DFT) calculation within both local density approximations (LDA) and generalized gradient approximations (GGA). The atoms are selected from period 3 of periodic table as well as Li and O atom from period 2. The results reveal that metallic atoms and noble gases are adsorbed physically on porous graphene and nonmetallic ones form chemical bonds with carbon atom in porous graphene structure. Also, it is shown that, in general, atom decoration reduces the values of mechanical properties such as Young's, bulk and shear moduli as well as Poisson's ratio, and this reduction is more considerable in the case of nonmetallic atoms (chemical adsorption), especially oxygen atoms, as compared to metallic atoms and noble gases (physical adsorption).

  1. 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.

  2. Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules

    Science.gov (United States)

    2015-01-01

    AFRL-RQ-ED-TR-2014-0025 Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules P.W. Langhoff J.D. Mills J.A...manufacture, use, or sell any patented invention that may relate to them. Qualified requestors may obtain copies of this report from the Defense...DATES COVERED (From - To) 15 Oct 2013 - 15 Oct 2014 4. TITLE AND SUBTITLE Quantum-Mechanical Definition of Atoms and Chemical Bonds in Molecules

  3. 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.

  4. Molecular mechanisms involved in convergent crop domestication.

    Science.gov (United States)

    Lenser, Teresa; Theißen, Günter

    2013-12-01

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

  5. 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.

  6. Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates

    OpenAIRE

    Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)

    2005-01-01

    We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.

  7. 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.

  8. Molecular Mechanisms of Sex Determination in Reptiles

    OpenAIRE

    Rhen, T; Schroeder, A

    2010-01-01

    Charles Darwin first provided a lucid explanation of how gender differences evolve nearly 140 years ago. Yet, a disconnect remains between his theory of sexual selection and the mechanisms that underlie the development of males and females. In particular, comparisons between representatives of different phyla (i.e., flies and mice) reveal distinct genetic mechanisms for sexual differentiation. Such differences are hard to comprehend unless we study organisms that bridge the phylogenetic gap. ...

  9. 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.

  10. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    Science.gov (United States)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  11. Symposium on molecular and cellular mechanisms of mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    1981-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jian Zhang

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

  13. Molecular and cellular mechanisms of pulmonary fibrosis

    Directory of Open Access Journals (Sweden)

    Todd Nevins W

    2012-07-01

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

  14. Molecular mechanisms of STIM/Orai communication

    Science.gov (United States)

    Derler, Isabella; Jardin, Isaac

    2016-01-01

    Ca2+ entry into the cell via store-operated Ca2+ release-activated Ca2+ (CRAC) channels triggers diverse signaling cascades that affect cellular processes like cell growth, gene regulation, secretion, and cell death. These store-operated Ca2+ channels open after depletion of intracellular Ca2+ stores, and their main features are fully reconstituted by the two molecular key players: the stromal interaction molecule (STIM) and Orai. STIM represents an endoplasmic reticulum-located Ca2+ sensor, while Orai forms a highly Ca2+-selective ion channel in the plasma membrane. Functional as well as mutagenesis studies together with structural insights about STIM and Orai proteins provide a molecular picture of the interplay of these two key players in the CRAC signaling cascade. This review focuses on the main experimental advances in the understanding of the STIM1-Orai choreography, thereby establishing a portrait of key mechanistic steps in the CRAC channel signaling cascade. The focus is on the activation of the STIM proteins, the subsequent coupling of STIM1 to Orai1, and the consequent structural rearrangements that gate the Orai channels into the open state to allow Ca2+ permeation into the cell. PMID:26825122

  15. 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.

  16. Evolution of Molecular and Atomic Gas Phases in the Milky Way

    CERN Document Server

    Koda, Jin; Heyer, Mark

    2016-01-01

    We analyze radial and azimuthal variations of the phase balance between the molecular and atomic ISM in the Milky Way. In particular, the azimuthal variations -- between spiral arm and interarm regions -- are analyzed without any explicit definition of spiral arm locations. We show that the molecular gas mass fraction, i.e., fmol=H2/ (HI+H2) in mass, varies predominantly in the radial direction: starting from ~100% at the center, remaining ~>50% (~>60%) to R~6kpc, and decreasing to ~10-20% (~50%) at R=8.5 kpc when averaged over the whole disk thickness (in the mid plane). Azimuthal, arm-interarm variations are secondary: only ~20%, in the globally molecule-dominated inner MW, but becoming larger, ~40-50%, in the atom-dominated outskirts. This suggests that in the inner MW, the gas stays highly molecular (fmol>50%) as it goes from an interarm region, into a spiral arm, and back into the next interarm region. Stellar feedback does not dissociate molecules much, and the coagulation and fragmentation of molecular...

  17. Male sex determination: insights into molecular mechanisms

    Institute of Scientific and Technical Information of China (English)

    Kathryn McClelland; Josephine Bowles; Peter Koopman

    2012-01-01

    Disorders of sex development often arise from anomalies in the molecular or cellular networks that guide the differentiation of the embryonic gonad into either a testis or an ovary,two functionally distinct organs.The activation of the Y-linked gene Sry(sexdetermining region Y) and its downstream target Sox9 (Sry box-containinggene 9) triggers testis differentiation by stimulating the differentiation of Sertoli cells,which then direct testis morphogenesis.Once engaged,a genetic pathway promotes the testis development while actively suppressing genes involved in ovarian development.This review focuses on the events of testis determination and the struggle to maintain male fate in the face of antagonistic pressure from the underlying female programme.

  18. Mechanism of Molecular Exchange in Copolymer Micelles

    Science.gov (United States)

    Choi, Soo-Hyung; Lodge, Timothy; Bates, Frank

    2010-03-01

    Compared to thermodynamic structure, much less has been known about the kinetics of block copolymer micelles which should underlay the attainment of thermodynamic equilibrium. In this presentation, molecular exchange between spherical micelles formed by isotopically labeled diblock copolymers was investigated using time-resolved small-angle neutron scattering. Two pairs of structurally matched poly(styrene-b-ethylene-alt-propylene) (PS-PEP) were synthesized and dispersed in isotopic mixture of squalane, highly selective to PEP block. Each pair includes polymers with fully deuterated (dPS-PEP) and a normal (hPS-PEP) PS blocks. Temperature dependence of the micelle exchange rate R(t) is consistent with melt dynamics for the core polymer. Furthermore, R(t) is significantly sensitive to the core block length N due to the thermodynamic penalty associated with ejecting a core block into the solvent. This hypersensitivity, combined with modest polydispersity in N, leads to an approximately logarithmic decay in R(t).

  19. Surface effects on the mechanical elongation of AuCu nanowires: De-alloying and the formation of mixed suspended atomic chains

    Energy Technology Data Exchange (ETDEWEB)

    Lagos, M. J. [Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, R. Sergio B. de Holanda 777, 13083-859 Campinas-SP (Brazil); Laboratório Nacional de Nanotecnologia-LNNANO, 13083-970 Campinas-SP (Brazil); Autreto, P. A. S.; Galvao, D. S., E-mail: galvao@ifi.unicamp.br; Ugarte, D. [Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, R. Sergio B. de Holanda 777, 13083-859 Campinas-SP (Brazil); Bettini, J. [Laboratório Nacional de Nanotecnologia-LNNANO, 13083-970 Campinas-SP (Brazil); Sato, F.; Dantas, S. O. [Departamento de Física, ICE, Universidade Federal de Juiz de Fora, 36036-330 Juiz de Fora-MG (Brazil)

    2015-03-07

    We report here an atomistic study of the mechanical deformation of Au{sub x}Cu{sub (1−x)} atomic-size wires (nanowires (NWs)) by means of high resolution transmission electron microscopy experiments. Molecular dynamics simulations were also carried out in order to obtain deeper insights on the dynamical properties of stretched NWs. The mechanical properties are significantly dependent on the chemical composition that evolves in time at the junction; some structures exhibit a remarkable de-alloying behavior. Also, our results represent the first experimental realization of mixed linear atomic chains (LACs) among transition and noble metals; in particular, surface energies induce chemical gradients on NW surfaces that can be exploited to control the relative LAC compositions (different number of gold and copper atoms). The implications of these results for nanocatalysis and spin transport of one-atom-thick metal wires are addressed.

  20. Negative differential resistance in a one-dimensional molecular wire with odd number of atoms

    Indian Academy of Sciences (India)

    S Lakshmi; Swapan K Pati

    2005-10-01

    We have investigated the effects of electron{phonon coupling on the current-voltage characteristics of a one-dimensional molecular wire with odd number of atoms. The wire has been modelled using the Su-Schreiffer-Heeger (SSH) Hamiltonian and the current{voltage characteristics have been obtained using the Landauer's formalism. In the presence of strong electron-lattice coupling, we find that there are regions of negative differential resistance (NDR) at some critical bias, due to the degeneracy in the energies of the frontier molecular orbitals. The presence of the applied bias and the electron{lattice coupling results in the delocalization of these low-lying molecular states leading to the NDR behaviour.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-21

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

  2. A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

    Science.gov (United States)

    Biswas, P K; Gogonea, Valentin

    2008-10-21

    We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the hybrid GROMACS-CPMD QM/MM program. Finally, we present a simpler prescription for adding isotropic polarizability to MM atoms in a QM/MM simulation. Employing this simpler scheme, we present QM/MM energy minimization results for the classic case of a water dimer and a hydrogen sulfide dimer. Also, we present single-point QM/MM results with and without the polarization to study the change in the ionization potential of tetrahydrobiopterin (BH(4)) in water and the change in the interaction energy of solvated BH(4) (described by MM) with the P(450) heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field.

  3. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    Science.gov (United States)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  4. Vancomycin Molecular Interactions: Antibiotic and Enantioselective Mechanisms

    Science.gov (United States)

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

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

  5. Molecular Mechanisms of Lymphocyte-Mediated Cytotoxicity

    Institute of Scientific and Technical Information of China (English)

    Zusen Fan; Qixiang Zhang

    2005-01-01

    Granule-mediated cytotoxicity is the major mechanism for lymphocytes to kill viruses, intracellular bacteria and tumors. The cytotoxic granules move to the immunological synapse by exocytosis after recognition of a killer cell.The contents of the granules are delivered into target cells with the help of perforin by endocytosis. A group of serine protease granzymes cleave their critical substrates to initiate DNA damage and cell death. The most abundant granzymes are granzyme A and B. They induce cell death through alternate and nonoverlapping pathways. The substrates and functions of the majority of the orphan granzymes have not yet been identified. It is possible that the diversity of granzymes provides fail-safe mechanisms for killing viruses and tumor cells.

  6. Towards a mechanical MPI scanner based on atomic magnetometry

    CERN Document Server

    Colombo, Simone; Tonyushkin, Alexey; Grujic, Zoran D; Dolgovskiy, Vladimir; Weis, Antoine

    2016-01-01

    We report on our progress in the development of an atomic magnetometer (AM) based low-frequency X-space MPI scanner, expected to be free from SAR and PNS constraints. We address major challenges in coil and sensor design due to specificAMproperties. Compared to our previous workwe have changed the AM's mode of operation towards its implementation for detecting weak SPIO response fields in the presence of nearby-located strong drive/selection fields. We demonstrate that a pump-probe AM scheme in a buffer gas filled alkali vapour cell can tolerate mT/m gradients while maintaining a sensitivity in the one-digit pT/Hz^(1/2) range over a bandwidth from DC to several kHz. We give a detailed description of the drive/selection coils' geometry and their hardware implementations that will provide both field-free-line (FFL) and field-free-point (FFP) modes of operation, compatible with a best performance AM operation. We estimate the achievable field of view and spatial resolution of the scanner as well as its sensitivi...

  7. Molecular Mechanisms of Mechanosensitivity in Focal Adhesions

    OpenAIRE

    2016-01-01

    Physical environment guides tissue regeneration and morphology in both health and disease. In the past three decades, several experiments illustrated that mechanical cues are captured and transduced to biochemical signals in the cellular level (mechanotransduction) mediated by cell adhesion. Cells adhere to their microenvironment through large protein assemblies known as focal adhesions that directly couple intra- and extra-cellular matrices and play a critical role in many vital cell functio...

  8. Toward an anisotropic atom-atom model for the crystalline phases of the molecular S8 compound

    OpenAIRE

    Pastorino, C.; Gamba, Z.

    2000-01-01

    We analize two anisotropic atom-atom models used to describe the crystalline alpha,beta and gamma phases of S8 crystals, the most stable compound of elemental sulfur in solid phases, at ambient pressure and T

  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.

  11. Photodetachment of a Homo-Nuclear Linear Tetra-Atomic Negative Molecular Ion

    Institute of Scientific and Technical Information of China (English)

    A. Rahman; Iftikhar Ahmad; A. Afaq; H. J. Zhao

    2012-01-01

    The photodetachment of a homo-nuclear linear tetra-atomic negative molecular ion is studied theoretically for an arbitrary laser polarization.An expression for the total cross section is obtained by using an extended version of the two center model,where each center acts as a source of coherent photodetached-electron waves.Strong oscillations on observation plane,placed at a large distance from the ion,are observed.The amplitude of these oscillations is maximum when the laser polarization is parallel to the molecular axis.Furthermore,the amplitude decreases as the angle between the laser polarization and molecular axis increases and consequently vanishes when they are perpendicular to each other.It is also found that if the distance between the adjacent centers is very small or very large,then the ampplitude of oscillations is negligibly small.%The photodetachment of a homo-nuclear linear tetra-atomic negative molecular ion is studied theoretically for an arbitrary laser polarization. An expression for the total cross section is obtained by using an extended version of the two center model, where each center acts as a source of coherent photodetached-electron waves. Strong oscillations on observation plane, placed at a large distance from the ion, are observed. The amplitude of these oscillations is maximum when the laser polarization is parallel to the molecular axis. Furthermore, the amplitude decreases as the angle between the laser polarization and molecular axis increases and consequently vanishes when they are perpendicular to each other. It is also found that if the distance between the adjacent centers is very small or very large, then the amplitude of oscillations is negligibly small.

  12. Density functional theory calculations of stability and diffusion mechanisms of impurity atoms in Ge crystals

    Energy Technology Data Exchange (ETDEWEB)

    Maeta, Takahiro [Graduate School of System Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); GlobalWafers Japan Co., Ltd., Higashikou, Seirou-machi, Kitakanbara-gun, Niigata 957-0197 (Japan); Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan)

    2014-08-21

    Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.

  13. MOL-D: A Collisional Database and Web Service within the Virtual Atomic and Molecular Data Center

    Indian Academy of Sciences (India)

    V. Vujčić; D. Jevremović; A. A. Mihajlov; Lj. M. Ignjatović; V. A. Srećković; M. S. Dimitrijević; M. Malović

    2015-12-01

    MOL-D database is a collection of cross-sections and rate coefficients for specific collisional processes and a web service within the Serbian Virtual Observatory (SerVO) and the Virtual Atomic and Molecular Data Center (VAMDC). This database contains photo-dissociation cross-sections for the individual ro-vibrational states of the diatomic molecular ions and rate coefficients for the atom-Rydberg atom chemiionization and inverse electron–ion–atom chemi-recombination processes. At the moment it contains data for photodissociation crosssections of hydrogen H+2 and helium H+2 molecular ions and the corresponding averaged thermal photodissociation cross-sections. The ro-vibrational energy states and the corresponding dipole matrix elements are provided as well. Hydrogen and helium molecular ion data are important for calculation of solar and stellar atmosphere models and for radiative transport, as well as for kinetics of other astrophysical and laboratory plasma (i.e. early Universe).

  14. Ultra-cold mechanical resonators coupled to atoms in an optical lattice

    CERN Document Server

    Geraci, Andrew A

    2009-01-01

    We propose an experiment utilizing an array of cooled micro-cantilevers coupled to a sample of ultra-cold atoms trapped near a micro-fabricated surface. The cantilevers allow individual lattice site addressing for atomic state control and readout, and potentially may be useful in optical lattice quantum computation schemes. Assuming resonators can be cooled to their vibrational ground state, the implementation of a two-qubit controlled-NOT gate with atomic internal states and the motional states of the resonator is described. We also consider a protocol for entangling two or more cantilevers on the atom chip with different resonance frequencies, using the trapped atoms as an intermediary. Although similar experiments could be carried out with magnetic microchip traps, the optical confinement scheme we consider may exhibit reduced near-field magnetic noise and decoherence. Prospects for using this novel system for tests of quantum mechanics at macroscopic scales or quantum information processing are discussed.

  15. Fast atom diffraction inside a molecular beam epitaxy chamber, a rich combination

    Science.gov (United States)

    Debiossac, M.; Atkinson, P.; Zugarramurdi, A.; Eddrief, M.; Finocchi, F.; Etgens, V. H.; Momeni, A.; Khemliche, H.; Borisov, A. G.; Roncin, P.

    2017-01-01

    Two aspects of the contribution of grazing incidence fast atom diffraction (GIFAD) to molecular beam epitaxy (MBE) are reviewed here: the ability of GIFAD to provide in-situ a precise description of the atomic-scale surface topology, and its ability to follow larger-scale changes in surface roughness during layer-by-layer growth. Recent experimental and theoretical results obtained for the He atom beam incident along the highly corrugated [ 1 1 bar 0 ] direction of the β2(2 × 4) reconstructed GaAs(001) surface are summarized. We also discuss the measurements and calculations for the beam incidence along the weakly corrugated [010] direction where a periodicity twice smaller than expected is observed. The combination of the experiment, quantum scattering matrix calculations, and semiclassical analysis allows structural characteristics of the surface to be revealed. For the in situ measurements of GIFAD during molecular beam epitaxy of GaAs on GaAs surface we analyze the change in elastic and inelastic contributions in the scattered beam, and the variation of the diffraction pattern in polar angle scattering. This analysis outlines the robustness, the simplicity and the richness of the GIFAD as a technique to monitor the layer-by-layer epitaxial growth.

  16. Molecular mechanisms of somatostatin receptor trafficking.

    Science.gov (United States)

    Csaba, Zsolt; Peineau, Stéphane; Dournaud, Pascal

    2012-02-01

    The neuropeptide somatostatin (SRIF) is an important modulator of neurotransmission in the central nervous system and acts as a potent inhibitor of hormone and exocrine secretion. In addition, SRIF regulates cell proliferation in normal and tumorous tissues. The six somatostatin receptor subtypes (sst1, sst2A, sst2B, sst3, sst4, and sst5), which belong to the G protein-coupled receptor (GPCR) family, share a common molecular topology: a hydrophobic core of seven transmembrane-spanning α-helices, three intracellular loops, three extracellular loops, an amino-terminus outside the cell, and a carboxyl-terminus inside the cell. For most of the GPCRs, intracytosolic sequences, and more particularly the C-terminus, are believed to interact with proteins that are mandatory for either exporting neosynthesized receptor, anchoring receptor at the plasma membrane, internalization, recycling, or degradation after ligand binding. Accordingly, most of the SRIF receptors can traffic not only in vitro within different cell types but also in vivo. A picture of the pathways and proteins involved in these processes is beginning to emerge.

  17. Molecular mechanisms of male germ cell differentiation.

    Science.gov (United States)

    Hecht, N B

    1998-07-01

    During spermatogenesis, diploid stem cells differentiate, undergo meiosis, and transform into haploid spermatozoa. As this precisely timed series of events proceeds, chromosomal ploidy is reduced and the nucleosomes of the chromatin are replaced by a transcriptionally quiescent protamine-containing nucleus. The premature termination of transcription during the haploid phase of spermatogenesis necessitates an especially prominent role for posttranscriptional regulation in the temporal and spatial expression of many testis-specific proteins and isozymes. In this review article, discussion will focus on novel mechanisms regulating gene expression in mammalian male germ cells from genome to protein.

  18. Is the microscopic stress computed from molecular simulations in mechanical equilibrium?

    Science.gov (United States)

    Torres-Sánchez, Alejandro; Vanegas, Juan M.; Arroyo, Marino

    The microscopic stress field connects atomistic simulations with the mechanics of materials at the nano-scale through statistical mechanics. However, its definition remains ambiguous. In a recent work we showed that this is not only a theoretical problem, but rather that it greatly affects local stress calculations from molecular simulations. We find that popular definitions of the local stress, which are continuously being employed to understand the mechanics of various systems at the nanoscale, violate the continuum statements of mechanical equilibrium. We exemplify these facts in local stress calculations of defective graphene, lipid bilayers, and fibrous proteins. Furthermore, we propose a new physical and sound definition of the microscopic stress that satisfies the continuum equations of balance, irrespective of the many-body nature of the inter-atomic potential. Thus, our proposal provides an unambiguous link between discrete-particle models and continuum mechanics at the nanoscale.

  19. Some reflections on the role of semi-classical atomic models in the teaching and learning of introductory quantum mechanics

    Science.gov (United States)

    O'Sullivan, Colm

    2016-03-01

    The role of "semi-classical" (Bohr-Sommerfeld) and "semi-quantum-mechanical" (atomic orbital) models in the context of the teaching of atomic theory is considered. It is suggested that an appropriate treatment of such models can serve as a useful adjunct to quantum mechanical study of atomic systems.

  20. X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations.

    Science.gov (United States)

    Jayatilaka, Dylan; Dittrich, Birger

    2008-05-01

    An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

  1. Membrane curvature in cell biology: An integration of molecular mechanisms.

    Science.gov (United States)

    Jarsch, Iris K; Daste, Frederic; Gallop, Jennifer L

    2016-08-15

    Curving biological membranes establishes the complex architecture of the cell and mediates membrane traffic to control flux through subcellular compartments. Common molecular mechanisms for bending membranes are evident in different cell biological contexts across eukaryotic phyla. These mechanisms can be intrinsic to the membrane bilayer (either the lipid or protein components) or can be brought about by extrinsic factors, including the cytoskeleton. Here, we review examples of membrane curvature generation in animals, fungi, and plants. We showcase the molecular mechanisms involved and how they collaborate and go on to highlight contexts of curvature that are exciting areas of future research. Lessons from how membranes are bent in yeast and mammals give hints as to the molecular mechanisms we expect to see used by plants and protists.

  2. All-atom Molecular-level Computational Simulations of Planar Longitudinal Shockwave Interactions with Polyurea, Soda-lime Glass and Polyurea/Glass Interfaces

    Science.gov (United States)

    2014-01-01

    All-atom molecular-level computational simulations of planar longitudinal shockwave interactions with polyurea, soda- lime glass and polyurea/glass...of this paper is to study the mechanical response of polyurea, soda- lime glass (glass, for short), polyurea/glass/polyurea and glass/polyurea/glass...methods, the interaction of shockwaves with material boundaries. Keywords Polyurea, Material interface, Shockwaves, Soda- lime glass Paper type Research

  3. 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

  4. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke

    2006-03-01

    have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO2 mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH)2. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO2 mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach has provided a deeper understanding of the key reaction mechanisms than either individual approach can alone. We used ab initio techniques to significantly advance our understanding of atomic-level processes at the solid

  5. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya

    2003-12-19

    DOE/NETL managed National Mineral Sequestration Working Group we have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO{sub 2} mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH){sub 2}. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO{sub 2} mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach will provide a deeper understanding of the key reaction mechanisms than either individual approach can alone. Ab initio techniques will

  6. Mechanical and Thermal Design and Qualification of an Atom Interferometer Sounding Rocket Payload

    Science.gov (United States)

    Grosse, J.; Seidel, S. T.; Krutzik, M.; Wendrich, T.; Stamminger, A.; Scharringhausen, M.; Quantus Consortium

    2015-09-01

    The MAIUS-1 experiment is a pathfinder quantum optics experiment about to fly on a VSB-30 sounding rocket in November 2015. The scientific objective of the mission is to demonstrate the feasibility of creating a Bose-Einstein Condensate and performing atom interferometry aboard a sounding rocket with Rubidium 87atoms. This paper will summarize the thermal and mechanical design of the payload and its (sub)systems. Moreover the qualification procedures and the results of the qualification test will be presented.

  7. Oxygen Atom Exchange Mechanism in Reaction of OH Radical with AsO

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Oxygen atom exchange reaction mechanism in the reaction of OH radicals with AsO was investigated by means of the density functional theory (DFT) with 6-311++G(3df,3pd) and 6-311++G(d,p) basis sets. The calculated results suggest that the reaction between OH and AsO should make the oxygen atoms exchange rapidly because the barrier to isomerization is significantly less than the HO-AsO bond dissociation energy.

  8. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites

    OpenAIRE

    Li, Z K; Fu, H. M.; Sha, P. F.; Zhu, Z. W.; A. M. Wang; Li, H.; Zhang, H. W.; Zhang, H. F.; Hu, Z. Q.

    2015-01-01

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on th...

  9. [Molecular mechanisms of skeletal muscle hypertrophy].

    Science.gov (United States)

    Astratenkova, I V; Rogozkin, V A

    2014-06-01

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

  10. Molecular and neuroendocrine mechanisms of cancer cachexia.

    Science.gov (United States)

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

    2015-09-01

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

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

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  12. Fabrication of atomically smooth SrRuO3 thin films by laser molecular beam epitaxy

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    High-quality SrRuO3 (SRO) thin films and SrTiO3/SRO bilayer were grown epitaxially on SrTiO3 (STO)(001) substrates by laser molecular beam epitaxy. The results of in situ observation of reflection high-energy electron diffraction and ex situ X-ray diffraction θ -2θ scan indicate that the SRO thin films have good crystallinity. The measurements of atomic force microscopy and scan tunneling microscopy reveal that the surface of the SRO thin film is atomically smooth. The resistivity of the SRO thin film is 300 μΩ·cm at room temperature. Furthermore, the transmission electron microscopy study shows that the interfaces of STO/SRO and SRO/STO are very clear and no interfacial reaction layer was observed. The experimental results show that the SRO thin film is an excellent electrode material for devices based on perovskite oxide materials.

  13. Study of Simulation Method of Time Evolution of Atomic and Molecular Systems by Quantum Electrodynamics

    CERN Document Server

    Ichikawa, Kazuhide; Tachibana, Akitomo

    2014-01-01

    We discuss a method to follow step-by-step time evolution of atomic and molecular systems based on QED (Quantum Electrodynamics). Our strategy includes expanding the electron field operator by localized wavepackets to define creation and annihilation operators and following the time evolution using the equations of motion of the field operator in the Heisenberg picture. We first derive a time evolution equation for the excitation operator, the product of two creation or annihilation operators, which is necessary for constructing operators of physical quantities such as the electronic charge density operator. We then describe our approximation methods to obtain time differential equations of the electronic density matrix, which is defined as the expectation value of the excitation operator. By solving the equations numerically, we show "electron-positron oscillations", the fluctuations originated from virtual electron-positron pair creations and annihilations, appear in the charge density of a hydrogen atom an...

  14. An open source digital servo for atomic, molecular, and optical physics experiments.

    Science.gov (United States)

    Leibrandt, D R; Heidecker, J

    2015-12-01

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of (27)Al(+) in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

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

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  16. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

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

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  17. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  18. Charge exchange collisions of slow C6 + with atomic and molecular H

    Science.gov (United States)

    Saha, Bidhan C.; Guevara, Nicolais L.; Sabin, John R.; Deumens, Erik; Öhrn, Yngve

    2016-04-01

    Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at projectile energies 0.1 motions. Both the total and partial cross sections are reported for the collision of C6+ ions with atomic and molecular hydrogen. A comparison with other theoretical and experimental results shows, in general good agreement except at very low energy, considered here. For H2, the one- and two-electron charge exchange cross sections are calculated and compared with other theoretical and experimental results. Small but non-negligible isotope effects are found at the lowest energy studied in the charge transfer of C6+ with H. In low energy region, it is observed that H2 has larger isotope effects than H atom due to the polarizability effect which is larger than the mass effect.

  19. Anharmonicity of internal atomic oscillation and effective antineutrino mass evaluation from gaseous molecular tritium \\beta -decay

    CERN Document Server

    Lokhov, Alexey V

    2016-01-01

    Data analysis of the next generation effective antineutrino mass measurement experiment KATRIN requires reliable knowledge of systematic corrections. In particular, the width of the daughter molecular ion excitation spectrum rovibrational band should be known with a better then 1% precision. Very precise ab initio quantum calculations exist, and we compare them with the well known tritium molecule parameters within the framework of a phenomenological model. The rovibrational band width with accuracy of a few percent is interpreted as a result of the zero-point atomic oscillation in the harmonic potential. The Morse interatomic potential is used to investigate the impact of anharmonic atomic oscillations. The calculated corrections cannot account for the difference between the ab initio quantum calculations and the phenomenological model.

  20. High-throughput all-atom molecular dynamics simulations using distributed computing.

    Science.gov (United States)

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

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

    Science.gov (United States)

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

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  2. Atomic-to-molecular gas phase transition triggered by the radio jet in Centaurus A

    CERN Document Server

    Salomé, Quentin; Combes, Françoise; Hamer, Stephen

    2016-01-01

    NGC 5128 (Centaurus A) is one of the best example to study AGN-feedback in the local Universe. At 13.5 kpc from the galaxy, optical filaments with recent star formation are lying along the radio-jet direction. We used the Atacama Pathfinder EXperiment (APEX) to map the CO(2-1) emission all along the filament structure. Molecular gas mass of 8.2x10^7 Msun was found over the 4.2 kpc-structure which represents about 3% of the total gas mass of the NGC 5128 cold gas content. Two dusty mostly molecular structure are identified, following the optical filaments. The region corresponds to the crossing of the radio jet with the Northern HI shell, coming from a past galaxy merger. One filament is located at the border of the HI shell, while the other is entirely molecular, and devoid of HI gas. The molecular mass is comparable to the HI mass in the shell, suggesting a scenario where the atomic gas was shocked and transformed in molecular clouds by the radio jet. Comparison with combined FIR Herschel and UV GALEX estima...

  3. Substrate binding and catalytic mechanism in phospholipase C from Bacillus cereus. a molecular mechanics and molecular dynamics study

    DEFF Research Database (Denmark)

    da Graça Thrige, D; Buur, J R; Jørgensen, Flemming Steen

    1997-01-01

    For the first time a consistent catalytic mechanism of phospholipase C from Bacillus cereus is reported based on molecular mechanics calculations. We have identified the position of the nucleophilic water molecule, which is directly involved in the hydrolysis of the natural substrate phosphatidyl...

  4. 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.

  5. 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...

  6. The Role of Super-Atom Molecular Orbitals in Doped Fullerenes in a Femtosecond Intense Laser Field.

    Science.gov (United States)

    Xiong, Hui; Mignolet, Benoit; Fang, Li; Osipov, Timur; Wolf, Thomas J A; Sistrunk, Emily; Gühr, Markus; Remacle, Francoise; Berrah, Nora

    2017-12-01

    The interaction of gas phase endohedral fullerene Ho3N@C80 with intense (0.1-5 × 10(14) W/cm(2)), short (30 fs), 800 nm laser pulses was investigated. The power law dependence of Ho3N@C80(q+), q = 1-2, was found to be different from that of C60. Time-dependent density functional theory computations revealed different light-induced ionization mechanisms. Unlike in C60, in doped fullerenes, the breaking of the cage spherical symmetry makes super atomic molecular orbital (SAMO) states optically active. Theoretical calculations suggest that the fast ionization of the SAMO states in Ho3N@C80 is responsible for the n = 3 power law for singly charged parent molecules at intensities lower than 1.2 × 10(14) W/cm(2).

  7. Molecular positional order in Langmuir-Blodgett films by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Bourdieu, L.; Ronsin, O.; Chatenay, D. (Inst. Curie, Paris (France))

    1993-02-05

    Langmuir-Blodgett films of barium arachidate have been studied on both macroscopic and microscopic scales by atomic force microscopy. As prepared, the films exhibit a disordered hexagonal structure; molecularly resolved images in direct space establish a connection between the extent of the positional order and the presence of defects such as dislocations. Upon heating, the films reorganize into a more condensed state with a centered rectangular crystallographic arrangement; in this new state the films exhibit long-range positional order and unusual structural features, such as a height modulation of the arachidic acid molecules. 22 refs., 4 figs.

  8. Molecular Positional Order in Langmuir-Blodgett Films by Atomic Force Microscopy

    Science.gov (United States)

    Bourdieu, L.; Ronsin, O.; Chatenay, D.

    1993-02-01

    Langmuir-Blodgett films of barium arachidate have been studied on both macroscopic and microscopic scales by atomic force microscopy. As prepared, the films exhibit a disordered hexagonal structure; molecularly resolved images in direct space establish a connection between the extent of the positional order and the presence of defects such as dislocations. Upon heating, the films reorganize into a more condensed state with a centered rectangular crystallographic arrangement; in this new state the films exhibit long-range positional order and unusual structural features, such as a height modulation of the arachidic acid molecules.

  9. ELASR – An electrostatic storage ring for atomic and molecular physics at KACST

    Directory of Open Access Journals (Sweden)

    Mohamed O.A. El Ghazaly

    2015-01-01

    Full Text Available A new ELectrostAtic Storage Ring (ELASR has been designed and built at the King Abdulaziz City for Science and Technology (KACST, in Riyadh, Saudi Arabia. It was developed to be the core of a new storage ring laboratory for atomic and molecular physics at KACST. ELASR follows the standard design of the pioneering storage ring ELISA and it thereby features a racetrack single-bend shaped ring. Complementary simulation code packages were used to work out the design under the requirements of the projected experiments. This paper reports a short description of the ELASR storage ring through an overview of its design and construction.

  10. Multistate APLIP and VibLIP: From molecular bond extension to atomic transport

    CERN Document Server

    Suominen, Kalle-Antti

    2013-01-01

    APLIP is a method for using a STIRAP-like three-state configuration with two laser pulses for continuous extension of a molecular bond, introduced in 1998. It is based on time-dependent light-induced potential surfaces (LIP). In VibLIP one extends the idea into a method for tailoring the vibrational state while changing the electronic state, introduced in 2000. Here I discuss the extension of both methods to situations that involve more than three electronic states, and note the possibility of using the method on adiabatic transport of atoms between microtraps or equivalent structures.

  11. Molecular ions in ultracold atomic gases: computed electronic interactions for \\MgHion with Rb

    CERN Document Server

    Tacconi, Mario

    2007-01-01

    The electronic structures of the manifold of potential energy surfaces generated in the lower energy range by the interaction of the MgH$^+$(X$^1\\Sigma^+$) cationic molecule with Rb($^2$S), neutral atom are obtained over a broad range of Jacobi coordinates from strongly correlated \\emph{ab initio} calculations which use a Multireference (MR) wavefunction within a Complete Active Space (CAS) approach. The relative features of the lowest five surfaces are analyzed in terms of possible collisional outcomes when employed to model the ultracold dynamics of ionic molecular partners.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  13. 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.

  14. 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.

  15. Molecular deformation mechanisms of the wood cell wall material.

    Science.gov (United States)

    Jin, Kai; Qin, Zhao; Buehler, Markus J

    2015-02-01

    Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. Although earlier work has shown that the cellular structure of wood is a key factor that renders it excellent mechanical properties at light weight, the mechanical properties of the wood cell wall material itself still needs to be understood comprehensively. The wood cell wall material features a fiber reinforced composite structure, where cellulose fibrils act as stiff fibers, and hemicellulose and lignin molecules act as soft matrix. The angle between the fiber direction and the loading direction has been found to be the key factor controlling the mechanical properties. However, how the interactions between theses constitutive molecules contribute to the overall properties is still unclear, although the shearing between fibers has been proposed as a primary deformation mechanism. Here we report a molecular model of the wood cell wall material with atomistic resolution, used to assess the mechanical behavior under shear loading in order to understand the deformation mechanisms at the molecular level. The model includes an explicit description of cellulose crystals, hemicellulose, as well as lignin molecules arranged in a layered nanocomposite. The results obtained using this model show that the wood cell wall material under shear loading deforms in an elastic and then plastic manner. The plastic regime can be divided into two parts according to the different deformation mechanisms: yielding of the matrix and sliding of matrix along the cellulose surface. Our molecular dynamics study provides insights of the mechanical behavior of wood cell wall material at the molecular level, and paves a way for the multi-scale understanding of the mechanical properties of wood.

  16. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  17. Aquaporin water channels: molecular mechanisms for human diseases.

    Science.gov (United States)

    Agre, Peter; Kozono, David

    2003-11-27

    Although water is the major component of all biological fluids, the molecular pathways for water transport across cell membranes eluded identification until the discovery of the aquaporin family of water channels. The atomic structure of mammalian AQP1 illustrates how this family of proteins is freely permeated by water but not protons (hydronium ions, H3O+). Definition of the subcellular sites of expression predicted their physiological functions and potential clinical disorders. Analysis of several human disease states has confirmed that aquaporins are involved in multiple different illnesses including abnormalities of kidney function, loss of vision, onset of brain edema, starvation, and arsenic toxicity.

  18. Quantum mechanics/molecular mechanics studies on the mechanism of action of cofactor pyridoxal 5'-phosphate in ornithine 4,5-aminomutase.

    Science.gov (United States)

    Pang, Jiayun; Scrutton, Nigel S; Sutcliffe, Michael J

    2014-09-01

    A computational study was performed on the experimentally elusive cyclisation step in the cofactor pyridoxal 5'-phosphate (PLP)-dependent D-ornithine 4,5-aminomutase (OAM)-catalysed reaction. Calculations using both model systems and a combined quantum mechanics/molecular mechanics approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor PLP and the active site of the enzyme. The captodative effect of PLP is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff-base nitrogen atom (N2). Furthermore, electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial "strain" energy on the orientation of the cyclic intermediate to control its trajectory. In addition the "strain" energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state. Our results provide new insights into several aspects of the radical mechanism in aminomutase catalysis and broaden our understanding of cofactor PLP-dependent reactions.

  19. A molecular dynamics simulation of hydrogen atoms collisions on an H-preadsorbed silica surface

    Science.gov (United States)

    Rutigliano, M.; Gamallo, P.; Sayós, R.; Orlandini, S.; Cacciatore, M.

    2014-08-01

    The interaction of hydrogen atoms and molecules with a silica surface is relevant for many research and technological areas. Here, the dynamics of hydrogen atoms colliding with an H-preadsorbed β-cristobalite (0 0 1) surface has been studied using a semiclassical collisional method in conjunction with a recently developed analytical potential energy surface based on density functional theory (DFT) calculations. The atomic recombination probability via an Eley-Rideal (E-R) mechanism, as well as the probabilities for other competitive surface processes, have been determined in a broad range of collision energies (0.04-3.0 eV) for off-normal (θv = 45°) and normal (θv = 0°) incidence and for two different surface temperatures (TS = 300 and 1000 K). H2,gas molecules form in roto-vibrational excited levels while the energy transferred to the solid surface is below 10% for all simulated conditions. Finally, the global atomic recombination coefficient (γE-R) and vibrational state resolved recombination coefficients (γ(v)) were calculated and compared with the available experimental values. The calculated collisional data are of interest in chemical kinetics studies and fluid dynamics simulations of silica surface processes in H-based low-temperature, low-pressure plasmas.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bernini, S. [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); Puosi, F. [Laboratoire de Physique de l’École Normale Supérieure de Lyon, UMR CNRS 5672, 46 allée d’Italie, 69007 Lyon (France); Leporini, D., E-mail: dino.leporini@df.unipi.it [Dipartimento di Fisica “Enrico Fermi,” Università di Pisa, Largo B. Pontecorvo 3, I-56127 Pisa (Italy); IPCF-CNR, UOS Pisa, Pisa (Italy)

    2015-03-28

    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 a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  1. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    Science.gov (United States)

    Jarvis, Samuel Paul

    2015-01-01

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. PMID:26307976

  2. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

    Science.gov (United States)

    Jarvis, Samuel Paul

    2015-08-21

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

  3. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  4. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Samuel Paul Jarvis

    2015-08-01

    Full Text Available A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

  5. Deformation behavior of metallic glasses with shear band like atomic structure: a molecular dynamics study.

    Science.gov (United States)

    Zhong, C; Zhang, H; Cao, Q P; Wang, X D; Zhang, D X; Ramamurty, U; Jiang, J Z

    2016-08-02

    Molecular dynamics simulations were employed to investigate the plastic deformation within the shear bands in three different metallic glasses (MGs). To mimic shear bands, MG specimens were first deformed until flow localization occurs, and then the volume of the material within the localized regions was extracted and replicated. Homogeneous deformation that is independent of the size of the specimen was observed in specimens with shear band like structure, even at a temperature that is far below the glass transition temperature. Structural relaxation and rapid cooling were employed to examine the effect of free volume content on the deformation behavior. This was followed by detailed atomic structure analyses, employing the concepts of Voronoi polyhedra and "liquid-like" regions that contain high fraction of sub-atomic size open volumes. Results suggest that the total fraction of atoms in liquid-like regions is a key parameter that controls the plastic deformation in MGs. These are discussed in the context of reported experimental results and possible strategies for synthesizing monolithic amorphous materials that can accommodate large tensile plasticity are suggested.

  6. Test of Variational Methods for Studying Molecular and Solid State Properties by Application to Sodium Atom

    Science.gov (United States)

    Das, T. P.; Pink, R. H.; Dubey, Archana; Scheicher, R. H.; Chow, Lee

    2011-03-01

    As part of our continuing test of accuracy of the variational methods, Variational Hartree-Fock Many Body Perturbation Theory (VHFMBPT) and Variational Density Functional Theory (VDFT) for study of energy and wave-function dependent properties in molecular and solid state systems we are studying the magnetic hyperfine interactions in the ground state of sodium atom for comparison by these methods with the available results from experiment 1 and the linked cluster many-body many body perturbation theory (LCMBPT) for atoms 2 , which has provided very accurate results for the one-electron and many-electron contributions and total hyperfine constants in atomic systems. Comparison will also be made with the corresponding results obtained already from the (VHFMBPT) and (VDFT) methods in lithium 3 to draw general conclusions about the nature of possible improvements needed for the variational methods. 1. M. Arditi and R. T. Carver, Phys. Rev. 109, 1012 (1958); 2. T. Lee, N.C. Dutta, and T.P. Das, Hyperfine Structure of Sodium, Phys. Rev. A 1, 995 (1970); 3. Third Joint HFI-NQI International Conference on Hyperfine Interactions, CERN, Geneva, September 2010.

  7. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Science.gov (United States)

    Sun, Xiao-Yu; Qi, Yi-Zhou; Ouyang, Wengen; Feng, Xi-Qiao; Li, Qunyang

    2016-08-01

    Although atomic stick-slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competition of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves normally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effectively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  8. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yu Sun; Yi-Zhou Qi; Wengen Ouyang; Xi-Qiao Feng; Qunyang Li

    2016-01-01

    Although atomic stick–slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competi-tion of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves nor-mally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effec-tively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  9. Simulation of the Cosmic Evolution of Atomic and Molecular Hydrogen in Galaxies

    CERN Document Server

    Obreschkow, D; De Lucia, G; Khochfar, S; Rawlings, S

    2009-01-01

    We present a simulation of the cosmic evolution of the atomic and molecular phases of the cold hydrogen gas in about 3e7 galaxies, obtained by post-processing the virtual galaxy catalog produced by (De Lucia et al. 2007) on the Millennium Simulation of cosmic structure (Springel et al. 2005). Our method uses a set of physical prescriptions to assign neutral atomic hydrogen (HI) and molecular hydrogen (H2) to galaxies, based on their total cold gas masses and a few additional galaxy properties. These prescriptions are specially designed for large cosmological simulations, where, given current computational limitations, individual galaxies can only be represented by simplistic model-objects with a few global properties. Our recipes allow us to (i) split total cold gas masses between HI, H2, and Helium, (ii) assign realistic sizes to both the HI- and H2-disks, and (iii) evaluate the corresponding velocity profiles and shapes of the characteristic radio emission lines. The results presented in this paper include ...

  10. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study

    Science.gov (United States)

    Sliozberg, Yelena R.; Chantawansri, Tanya L.

    2016-05-01

    To elucidate the mechanism of ion transport through a transmembrane pore, all-atom molecular dynamics simulations were employed. A model membrane where a pore connects the intra- and extra-cellular compartment was considered. Pores with radii of 1.5 nm or less exhibited resealing over the course of 135 ns simulations, and ionic disturbance is minimal. Ion transport through a larger pore (2 nm radius) leads to a substantial change in the intra- and extra-cellular ionic concentrations. The influx of Na+ and Cl- ions down their concentration gradients is greater than the efflux of K+ leading to an osmotic influx of water.

  11. Palladium-atom catalyzed formic acid decomposition and the switch of reaction mechanism with temperature.

    Science.gov (United States)

    He, Nan; Li, Zhen Hua

    2016-04-21

    Formic acid decomposition (FAD) reaction has been an innovative way for hydrogen energy. Noble metal catalysts, especially palladium-containing nanoparticles, supported or unsupported, perform well in this reaction. Herein, we considered the simplest model, wherein one Pd atom is used as the FAD catalyst. With high-level theoretical calculations of CCSD(T)/CBS quality, we investigated all possible FAD pathways. The results show that FAD catalyzed by one Pd atom follows a different mechanism compared with that catalyzed by surfaces or larger clusters. At the initial stage of the reaction, FAD follows a dehydration route and is quickly poisoned by CO due to the formation of very stable PdCO. PdCO then becomes the actual catalyst for FAD at temperatures approximately below 1050 K. Beyond 1050 K, there is a switch of catalyst from PdCO to Pd atom. The results also show that dehydration is always favoured over dehydrogenation on either the Pd-atom or PdCO catalyst. On the Pd-atom catalyst, neither dehydrogenation nor dehydration follows the formate mechanism. In contrast, on the PdCO catalyst, dehydrogenation follows the formate mechanism, whereas dehydration does not. We also systematically investigated the performance of 24 density functional theory methods. We found that the performance of the double hybrid mPW2PLYP functional is the best, followed by the B3LYP, B3PW91, N12SX, M11, and B2PLYP functionals.

  12. Molecular mechanisms controlling the cell cycle in embryonic stem cells.

    Science.gov (United States)

    Abdelalim, Essam M

    2013-12-01

    Embryonic stem (ES) cells are originated from the inner cell mass of a blastocyst stage embryo. They can proliferate indefinitely, maintain an undifferentiated state (self-renewal), and differentiate into any cell type (pluripotency). ES cells have an unusual cell cycle structure, consists mainly of S phase cells, a short G1 phase and absence of G1/S checkpoint. Cell division and cell cycle progression are controlled by mechanisms ensuring the accurate transmission of genetic information from generation to generation. Therefore, control of cell cycle is a complicated process, involving several signaling pathways. Although great progress has been made on the molecular mechanisms involved in the regulation of ES cell cycle, many regulatory mechanisms remain unknown. This review summarizes the current knowledge about the molecular mechanisms regulating the cell cycle of ES cells and describes the relationship existing between cell cycle progression and the self-renewal.

  13. Computational exploration of single-protein mechanics by steered molecular dynamics

    Science.gov (United States)

    Sotomayor, Marcos

    2015-12-01

    Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their "single-molecule responses" to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.

  14. Computational exploration of single-protein mechanics by steered molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Sotomayor, Marcos [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio (United States)

    2015-12-31

    Hair cell mechanotransduction happens in tens of microseconds, involves forces of a few picoNewtons, and is mediated by nanometer-scale molecular conformational changes. As proteins involved in this process become identified and their high resolution structures become available, multiple tools are being used to explore their “single-molecule responses” to force. Optical tweezers and atomic force microscopy offer exquisite force and extension resolution, but cannot reach the high loading rates expected for high frequency auditory stimuli. Molecular dynamics (MD) simulations can reach these fast time scales, and also provide a unique view of the molecular events underlying protein mechanics, but its predictions must be experimentally verified. Thus a combination of simulations and experiments might be appropriate to study the molecular mechanics of hearing. Here I review the basics of MD simulations and the different methods used to apply force and study protein mechanics in silico. Simulations of tip link proteins are used to illustrate the advantages and limitations of this method.

  15. ADATOM, VACANCY AND SPUTTERING YIELDS OF ENERGETIC Pt ATOMS IMPACTING ON Pt(100) BY MOLECULAR DYNAMICS SIMULATION

    Institute of Scientific and Technical Information of China (English)

    YE ZI-YAN; ZHANG QING-YU

    2001-01-01

    We have studied the influence of incident atoms with low energy on the Pt(100) surface by molecular dynamics simulation. The interaction potential obtained by the embedded atom method (EAM) was used in the simulation. The incident energy changes from 0.leV to 200eV, and the target temperature ranges from 100 to 500 K. The target scales are 6×6×4 and 8×8×4 fcc cells for lower and higher incident energies, respectively. The adatom, sputtering, vacancy and backscattering yields are calculated. It was found that there is a sputtering threshold for the incident energy. When the incident energy is higher than the sputtering threshold, the sputtering yield increases with the increase of incident energy, and the sputtering shows a symmetrical pattern. We found that the adatom and vacancy yields increase as the incident energy increases. The vacancy yields are much higher than those obtained by Monte Carlo simulation. The dependence of the adatom and sputtering yields on the incident energy and the relative atomistic mechanisms are discussed.

  16. Combination of metformin with chemotherapeutic drugs via different molecular mechanisms.

    Science.gov (United States)

    Peng, Mei; Darko, Kwame Oteng; Tao, Ting; Huang, Yanjun; Su, Qiongli; He, Caimei; Yin, Tao; Liu, Zhaoqian; Yang, Xiaoping

    2017-03-01

    Metformin, a widely prescribed drug for treating type II diabetes, is one of the most extensively recognized metabolic modulators which has shown an important anti-cancer property. However, fairly amount of clinical trials on its single administration have not demonstrated a convincing efficiency yet. Thus, recent studies tend to combine metformin with clinical commonly used chemotherapeutic drugs to decrease their toxicity and attenuate their tumor resistance. These strategies have displayed promising clinical benefits. Interestingly, metformin experiences a diversity of molecular mechanisms when it combines different chemotherapeutic drugs. For example, AMPK/mTOR signaling pathway activation plays a major role when it combines with hormone modulating drugs. In contrast, suppression of HIF-1, p-gp and MRP1 protein expression is its main mechanism when metformin combines with anti-metabolites. Furthermore, when combining of metformin with antibiotics, inhibition of oxidative stress and inflammatory signaling pathway becomes a novel pharmaceutical mechanism for its cardio-protective effect. Induction of apoptotic mitochondria and nucleus could be the major player for the synergistic effect of its combination with cisplatin. In contrast, down-regulation of lipoprotein or cholesterol synthesis might be the undefined molecular base when metformin combines with taxane. Thus, deep exploration of molecular mechanisms of metformin with these different drugs is critical to understand its synergistic effect and help for personalized administration. In this mini-review, detailed molecular mechanisms of these combinations are discussed and summarized. This work will promote better understanding of molecular mechanisms of metformin and provide precise targets to identify specific patient groups to achieve satisfactory treatment efficacy.

  17. Atomic interaction mechanism for designing the interface of W/Zr-based bulk metallic glass composites

    Science.gov (United States)

    Li, Z. K.; Fu, H. M.; Sha, P. F.; Zhu, Z. W.; Wang, A. M.; Li, H.; Zhang, H. W.; Zhang, H. F.; Hu, Z. Q.

    2015-03-01

    The interaction between active element Zr and W damages the W fibers and the interface and decreases the mechanical properties, especially the tensile strength of the W fibers reinforced Zr-based bulk metallic glass composites (BMGCs). From the viewpoint of atomic interaction, the W-Zr interaction can be restrained by adding minor elements that have stronger interaction with W into the alloy. The calculation about atomic interaction energy indicates that Ta and Nb preferred to segregate on the W substrate surface. Sessile drop experiment proves the prediction and corresponding in-situ coating appears at the interface. Besides, the atomic interaction mechanism was proven to be effective in many other systems by the sessile drop technique. Considering the interfacial morphology, Nb was added into the alloy to fabricate W/Zr-based BMGCs. As expected, the Nb addition effectively suppressed the W-Zr reaction and damage to W fibers. Both the compressive and tensile properties are improved obviously.

  18. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions.

    Science.gov (United States)

    Liu, Haiyan; Lu, Zhenyu; Cisneros, G Andres; Yang, Weitao

    2004-07-08

    The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

  19. Resveratrol and calcium signaling: molecular mechanisms and clinical relevance.

    Science.gov (United States)

    McCalley, Audrey E; Kaja, Simon; Payne, Andrew J; Koulen, Peter

    2014-06-05

    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. Wilson's disease: a comprehensive review of the molecular mechanisms.

    Science.gov (United States)

    Wu, Fei; Wang, Jing; Pu, Chunwen; Qiao, Liang; Jiang, Chunmeng

    2015-01-01

    Wilson's disease (WD), also known as hepatolenticular degeneration, is an autosomal recessive inherited disorder resulting from abnormal copper metabolism. Reduced copper excretion causes an excessive deposition of the copper in many organs such as the liver, central nervous system (CNS), cornea, kidney, joints, and cardiac muscle where the physiological functions of the affected organs are impaired. The underlying molecular mechanisms for WD have been extensively studied. It is now believed that a defect in P-type adenosine triphosphatase (ATP7B), the gene encoding the copper transporting P-type ATPase, is responsible for hepatic copper accumulation. Deposited copper in the liver produces toxic effects via modulating several molecular pathways. WD can be a lethal disease if left untreated. A better understanding of the molecular mechanisms causing the aberrant copper deposition and organ damage is the key to developing effective management approaches.

  1. Molecular mechanisms in muscular dystrophy : a gene expression profiling study.

    NARCIS (Netherlands)

    Turk, Rolf

    2006-01-01

    The muscular dystrophies are a group of neuromuscular disorders characterized by progres¬sive muscle weakness and wasting. Although the underlying genetic defects of a large number of muscular dystrophies are now know, the molecular mechanisms resulting in the devastating effects of the disease are

  2. Molecular mechanisms of novel regulators in cytokine signal transduction

    NARCIS (Netherlands)

    Xiaofei, Zhang

    2013-01-01

    By identifying and studying novel regulators, the studies described in this thesis give substantive insights into the molecular mechanisms and different levels of control of TGF-β/BMP, IL-1β and Wnt signaling pathways. Crucially, our work for the first time demonstrated the monoubiquitination of an

  3. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si{sub 3}N{sub 4}(0001) nanopixels

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, M.E.; Omeltchenko, A.; Nakano, A.; Kalia, R.K.; Vashishta, P. [Concurrent Computing Laboratory for Materials Simulations, Department of Physics Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana70803-4001 (United States); Ebbsjoe, I. [Studsvik Neutron Research Laboratory, University of Uppsala, S-611 82Nykoeping (Sweden); Madhukar, A. [Department of Materials Science and Engineering, University of Southern California, Los Angeles, California90089-0241 (United States); Messina, P. [Center for Advanced Computing Research, California Institute of Technology, Pasadena, California91125 (United States)

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 {mu}m silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si{sub 3}N{sub 4}(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3GPa and the stress is tensile, {minus}1GPa, in silicon below the interface. {copyright} {ital 1998 American Institute of Physics.}

  4. Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.

    Science.gov (United States)

    Bykhovski, Alexei; Woolard, Dwight

    2013-07-01

    Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.

  5. Destructive quantum interference in electron transport: A reconciliation of the molecular orbital and the atomic orbital perspective

    Science.gov (United States)

    Zhao, Xin; Geskin, Victor; Stadler, Robert

    2017-03-01

    Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.

  6. Understanding the mechanism of H atom absorption in the Pd(1 1 0) surface

    Energy Technology Data Exchange (ETDEWEB)

    Padama, Allan Abraham B. [Institute of Mathematical Sciences and Physics, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031 (Philippines); Kasai, Hideaki, E-mail: kasai@dyn.ap.eg.osaka-u.ac.jp [Department of Applied Physics, Osaka University, Suita, Osaka 565-0871 (Japan); Center for Atomic and Molecular Technologies, Osaka University, Suita, Osaka 565-0871 (Japan); Center for Continuing Professional Development, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871 (Japan)

    2015-10-05

    Highlights: • This study elucidates the absorption of H in Pd(1 1 0) (1 × 2) missing-row surface. • Electronic structure depicts the stronger adsorption on ridge than on trough site. • The geometry of missing-row Pd(1 1 0) allows Pd atoms to accommodate H and H{sub 2}. • Assisted absorption is facilitated by the repulsion between H atoms. - Abstract: The underlying mechanism of H atom absorption in the Pd(1 1 0) (1 × 2) missing-row reconstructed surface is investigated by performing density functional theory based calculations. The stronger binding energy of H on ridge than on trough site of the missing-row surface is due to the more pronounced creation of derived bonding state as had been depicted from the electronic structure of the system. Hydrogen absorption takes place with the involvement of other incoming H atoms through an assisted absorption process that is facilitated by the repulsion between the incoming H and the absorbing H. The geometry of the missing-row surface enables the Pd atoms to accommodate the H atoms efficiently leading to H absorption as well as H{sub 2} dissociation.

  7. Molecular dynamics simulations of highly cross-linked polymer networks: prediction of thermal and mechanical properties

    Science.gov (United States)

    Shenogina, Natalia; Tsige, Mesfin; Mukhopadhyay, Sharmila; Patnaik, Soumya

    2012-02-01

    We use all-atom molecular dynamics (MD) simulations to predict the mechanical and thermal properties of thermosetting polymers. Atomistic simulation is a promising tool which can provide detailed structure-property relationships of densely cross-linked polymer networks. In this work we study the thermo-mechanical properties of thermosetting polymers based on amine curing agents and epoxy resins and have focused on the DGEBA/DETDA epoxy system. At first we describe the modeling approach to construction of realistic all-atom models of densely cross-linked polymer matrices. Subsequently, a series of atomistic simulations was carried out to examine the simulation cell size effect as well as the role of cross-linking density and chain length of the resin strands on thermo-mechanical properties at different temperatures. Two different methods were used to deform the polymer networks. Both static and dynamic approaches to calculating the mechanical properties were considered and the thermo-mechanical properties obtained from our simulations were found in reasonable agreement with experimental values.

  8. Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

    Science.gov (United States)

    Slone, Scott Michael; Li, Chen-Yu; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-05-01

    The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design.

  9. Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

    Science.gov (United States)

    Bayse, Craig A; Merz, Kenneth M

    2014-08-05

    Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

  10. Mechanical properties of stanene under uniaxial and biaxial loading: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Mojumder, Satyajit [Department of Mechanical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000 (Bangladesh); Amin, Abdullah Al [Department of Mechanical and Aerospace Engineering, Case western Reverse University, Cleveland, Ohio 44106 (United States); Islam, Md Mahbubul, E-mail: mmi122@psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2015-09-28

    Stanene, a graphene like two dimensional honeycomb structure of tin has attractive features in electronics application. In this study, we performed molecular dynamics simulations using modified embedded atom method potential to investigate mechanical properties of stanene. We studied the effect of temperature and strain rate on mechanical properties of α-stanene for both uniaxial and biaxial loading conditions. Our study suggests that with the increasing temperature, both the fracture strength and strain of the stanene decrease. Uniaxial loading in zigzag direction shows higher fracture strength and strain compared to the armchair direction, while no noticeable variation in the mechanical properties is observed for biaxial loading. We also found at a higher loading rate, material exhibits higher fracture strength and strain. These results will aid further investigation of stanene as a potential nano-electronics substitute.

  11. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Science.gov (United States)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  12. Molecular mechanisms underlying the fetal programming of adult disease.

    Science.gov (United States)

    Vo, Thin; Hardy, Daniel B

    2012-08-01

    Adverse events in utero can be critical in determining quality of life and overall health. It is estimated that up to 50 % of metabolic syndrome diseases can be linked to an adverse fetal environment. However, the mechanisms linking impaired fetal development to these adult diseases remain elusive. This review uncovers some of the molecular mechanisms underlying how normal physiology may be impaired in fetal and postnatal life due to maternal insults in pregnancy. By understanding the mechanisms, which include epigenetic, transcriptional, endoplasmic reticulum (ER) stress, and reactive oxygen species (ROS), we also highlight how intervention in fetal and neonatal life may be able to prevent these diseases long-term.

  13. Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes.

    Science.gov (United States)

    Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

    2014-01-07

    AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N(1) -methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)-oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ- and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.

  14. Spatially resolved atomic and molecular emission from the very low-mass star IRS54

    CERN Document Server

    Lopez, R Garcia; Weigelt, G; Nisini, B; Antoniucci, S

    2013-01-01

    Molecular outflows from very low-mass stars (VLMSs) and brown dwarfs (BDs) have been studied very little, and only a few objects have been directly imaged. Using VLT SINFONI K-band observations, we spatially resolved, for the first time, the H2 emission around IRS54, a ~0.1-0.2 Msun Class I source. The molecular emission shows a complex structure delineating a large outflow cavity and an asymmetric molecular jet. In addition, new [FeII] VLT ISAAC observations at 1.644um allowed us to discover the atomic jet counterpart which extends down to the central source. The outflow structure is similar to those found in low-mass Class I young stellar objects (YSOs) and Classical TTauri stars (CTTSs). However, its Lacc/Lbol ratio is very high (~80%), and the derived mass accretion rate is about one order of magnitude higher than in objects with similar mass, pointing to the young nature of the investigated source.

  15. Atomic carbon as a tracer of molecular gas in high-redshift galaxies: perspectives for ALMA

    CERN Document Server

    Tomassetti, Matteo; Romano-Diaz, Emilio; Ludlow, Aaron D; Papadopoulos, Padelis P

    2014-01-01

    We use a high-resolution simulation that tracks the non-equilibrium abundance of molecular hydrogen, H2, within a massive high-redshift galaxy to produce mock ALMA maps of the fine-structure lines of atomic carbon CI 1-0 and CI 2-1. Inspired by recent observational and theoretical work, we assume that CI is thoroughly mixed in giant molecular clouds and demonstrate that its emission is an excellent proxy for H2. The entire H2 mass of a galaxy at redshift z<4 can be detected using a compact interferometric configuration with a large synthesized beam (that does not resolve the target galaxy) in less than 1 hour of integration time. Low-resolution imaging of the CI lines (in which the target galaxy is resolved into 3-4 beams) will detect nearly 50-60 per cent of the molecular hydrogen in less than 12 hours. In this case, the data cube also provides valuable information regarding the dynamical state of the galaxy. We conclude that ALMA observations of the CI 1-0 and 2-1 emission will widely extend the interval...

  16. Molecular mechanics methods for individual carbon nanotubes and nanotube assemblies

    Science.gov (United States)

    Eberhardt, Oliver; Wallmersperger, Thomas

    2015-04-01

    Since many years, carbon nanotubes (CNTs) have been considered for a wide range of applications due to their outstanding mechanical properties. CNTs are tubular structures, showing a graphene like hexagonal lattice. Our interest in the calculation of the mechanical properties is motivated by several applications which demand the knowledge of the material behavior. One application in which the knowledge of the material behavior is vital is the CNT based fiber. Due to the excellent stiffness and strength of the individual CNTs, these fibers are expected to be a promising successor for state of the art carbon fibers. However, the mechanical properties of the fibers fall back behind the properties of individual CNTs. It is assumed that this gap in the properties is a result of the van-der-Waals interactions of the individual CNTs within the fiber. In order to understand the mechanical behavior of the fibers we apply a molecular mechanics approach. The mechanical properties of the individual CNTs are investigated by using a modified structural molecular mechanics approach. This is done by calculating the properties of a truss-beam element framework representing the CNT with the help of a chemical force field. Furthermore, we also investigate the interactions of CNTs arranged in basic CNT assemblies, mimicking the ones in a simple CNT fiber. We consider the van-der-Waals interactions in the structure and calculate the potential surface of the CNT assemblies.

  17. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    Science.gov (United States)

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments.

  18. Exploring the binding of 4-thiothymidine with human serum albumin by spectroscopy, atomic force microscopy, and molecular modeling methods.

    Science.gov (United States)

    Zhang, Juling; Gu, Huaimin; Zhang, Xiaohui

    2014-01-30

    The interaction of 4-thiothymidine (S(4)TdR) with human serum albumin (HSA) was studied by equilibrium dialysis under normal physiological conditions. In this work, the mechanism of the interaction between S(4)TdR and human serum albumin (HSA) was exploited by fluorescence, UV, CD circular, and SERS spectroscopic. Fluorescence and UV spectroscopy suggest that HSA intensities are significantly decreased when adding S(4)TdR to HAS, and the quenching mechanism of the fluorescence is static. Also, the ΔG, ΔH, and ΔS values across temperature indicated that hydrophobic interaction was the predominant binding force. The CD circular results show that there is little change in the secondary structure of HSA except the environment of amino acid changes when adding S(4)TdR to HSA. The surface-enhanced Raman scattering (SERS) shows that the interaction between S(4)TdR and HSA can be achieved through different binding sites which are probably located in the II A and III A hydrophobic pockets of HSA which correspond to Sudlow's I and II binding sites. In addition, the molecular modeling displays that S(4)TdR-HSA complex is stabilized by hydrophobic forces, which result from amino acid residues. The atomic force microscopy results revealed that the single HSA molecular dimensions were larger after interaction of 4-thiothymidine. This work would be useful to understand the state of the transportation, distribution, and metabolism of the anticancer drugs in the human body, and it could provide a useful biochemistry parameter for the development of new anti-cancer drugs and research of pharmacology mechanisms.

  19. Kibble-Zurek mechanism in the self-organization of a cold atomic cloud

    CERN Document Server

    Labeyrie, Guillaume

    2016-01-01

    When applying two counter-propagating laser beams to a cold cloud of Rubidium atoms, we observe the spontaneous formation of intensity patterns associated with a spatial structuration of the atomic spins. We study the average number of defects in these patterns as a function of the sweep time employed to cross the transition threshold. We observe a power-law decrease of the number of defects with increasing sweep time, typical of the Kibble-Zurek mechanism. The measured exponent is consistent with the prediction for a supercritical bifurcation.

  20. Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

    Science.gov (United States)

    Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

    2017-03-14

    Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design.

  1. Microscopic and macroscopic polarization within a combined quantum mechanics and molecular mechanics model

    NARCIS (Netherlands)

    Jensen, L; Swart, M; van Duijnen, PT

    2005-01-01

    A polarizable quantum mechanics and molecular mechanics model has been extended to account for the difference between the macroscopic electric field and the actual electric field felt by the solute molecule. This enables the calculation of effective microscopic properties which can be related to mac

  2. Dissecting molecular mechanisms in the living brain of dementia patients.

    Science.gov (United States)

    Barrio, Jorge R; Satyamurthy, Nagichettiar; Huang, Sung-Cheng; Petric, Andrej; Small, Gary W; Kepe, Vladimir

    2009-07-21

    Understanding the molecular mechanisms associated with the development of dementia is essential for designing successful interventions. Dementia, like cancer and cardiovascular disease, requires early detection to potentially arrest or prevent further disease progression. By the time a neurologist begins to manage clinical symptoms, the disease has often damaged the brain significantly. Because successful treatment is the logical goal, detecting the disease when brain damage is still limited is of the essence. The role of chemistry in this discovery process is critical. With the advent of molecular imaging, the understanding of molecular mechanisms in human neurodegenerative diseases has exploded. Traditionally, knowledge of enzyme and neurotransmitter function in humans has been extrapolated from animal studies, but now we can acquire data directly from both healthy and diseased human subjects. In this Account, we describe the use of molecular imaging probes to elucidate the biochemical and cellular bases of dementia (e.g., Alzheimer's disease) and the application of these discoveries to the design of successful therapeutic interventions. Molecular imaging permits observation and evaluation of the basic molecular mechanisms of disease progression in the living brains of patients. 2-Deoxy-2-[(18)F]fluoro-d-glucose is used to assess the effect of Alzheimer's disease progression on neuronal circuits projecting from and to the temporal lobe (one of the earliest metabolic signs of the disease). Recently, we have developed imaging probes for detection of amyloid neuropathology (both tau and beta-amyloid peptide deposits) and neuronal losses. These probes allow us to visualize the development of pathology in the living brain of dementia patients and its consequences, such as losses of critical neurons associated with memory deficits and other neuropsychiatric impairments. Because inflammatory processes are tightly connected to the brain degenerative processes

  3. Molecular mechanisms involved in mammalian primary sex determination.

    Science.gov (United States)

    She, Zhen-Yu; Yang, Wan-Xi

    2014-08-01

    Sex determination refers to the developmental decision that directs the bipotential genital ridge to develop as a testis or an ovary. Genetic studies on mice and humans have led to crucial advances in understanding the molecular fundamentals of sex determination and the mutually antagonistic signaling pathway. In this review, we summarize the current molecular mechanisms of sex determination by focusing on the known critical sex determining genes and their related signaling pathways in mammalian vertebrates from mice to humans. We also discuss the underlying delicate balance between testis and ovary sex determination pathways, concentrating on the antagonisms between major sex determining genes.

  4. Molecular and atomic gas in the Local Group galaxy M 33

    Science.gov (United States)

    Gratier, P.; Braine, J.; Rodriguez-Fernandez, N. J.; Schuster, K. F.; Kramer, C.; Xilouris, E. M.; Tabatabaei, F. S.; Henkel, C.; Corbelli, E.; Israel, F.; van der Werf, P. P.; Calzetti, D.; Garcia-Burillo, S.; Sievers, A.; Combes, F.; Wiklind, T.; Brouillet, N.; Herpin, F.; Bontemps, S.; Aalto, S.; Koribalski, B.; van der Tak, F.; Wiedner, M. C.; Röllig, M.; Mookerjea, B.

    2010-11-01

    We present high-resolution large-scale observations of the molecular and atomic gas in the Local Group galaxy M 33. The observations were carried out using the HEterodyne Receiver Array (HERA) at the 30 m IRAM telescope in the CO(2-1) line, achieving a resolution of 12” × 2.6 km s-1, enabling individual giant molecular clouds (GMCs) to be resolved. The observed region is 650 square arcminutes mainly along the major axis and out to a radius of 8.5 kpc, and covers entirely the 2' × 40' radial strip observed with the HIFI and PACS Spectrometers as part of the HERM33ES Herschel key program. The achieved sensitivity in main-beam temperature is 20-50 mK at 2.6 km s-1 velocity resolution. The CO(2-1) luminosity of the observed region is 1.7±0.1 × 107 K km s-1 pc2 and is estimated to be 2.8±0.3 × 107 K km s-1 pc2 for the entire galaxy, corresponding to H2 masses of 1.9 × 108 Msun and 3.3 × 108 Msun respectively (including He), calculated with N(H2)/ICO(1-0) twice the Galactic value due to the half-solar metallicity of M 33. The H i 21 cm VLA archive observations were reduced, and the mosaic was imaged and cleaned using the multi-scale task in the CASA software package, yielding a series of datacubes with resolutions ranging from 5” to 25”. The H i mass within a radius of 8.5 kpc is estimated to be 1.4 × 109 Msun. The azimuthally averaged CO surface brightness decreases exponentially with a scale length of 1.9±0.1 kpc whereas the atomic gas surface density is constant at ΣH I = 6±2 Msun pc-2 deprojected to face-on. For an N(H2)/ICO(1-0) conversion factor twice that of the Milky Way, the central kiloparsec H2 surface density is ΣH2 = 8.5±0.2 Msun pc-2. The star formation rate per unit molecular gas (SF efficiency, the rate of transformation of molecular gas into stars), as traced by the ratio of CO to Hα and FIR brightness, is constant with radius. The SFE, with a N(H2)/ICO(1-0) factor twice galactic, appears 2-4 times greater than for large spiral

  5. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  6. 2012 ATOMIC AND MOLECULAR INTERACTIONS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, JULY 15-20, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Zwier, Timothy

    2012-07-20

    At the 2012 Atomic and Molecular Interactions Gordon Conference, there will be talks in several broadly defined and partially overlapping areas:  Intramolecular and single-collision reaction dynamics;  Photophysics and photochemistry of excited states;  Clusters, aerosols and solvation;  Interactions at interfaces;  Conformations and folding of large molecules;  Interactions under extreme conditions of temperature and pressure. The theme of the Gordon Research Seminar on Atomic & Molecular Interactions, in keeping with the tradition of the Atomic and Molecular Interactions Gordon Research Conference, is far-reaching and involves fundamental research in the gas and condensed phases along with application of these ideas to practical chemical fields. The oral presentations, which will contain a combination of both experiment and theory, will focus on four broad categories:  Ultrafast Phenomena;  Excited States, Photoelectrons, and Photoions;  Chemical Reaction Dynamics;  Biomolecules and Clusters.

  7. Quantum Mechanical/Molecular Mechanical Studies on Spectral Tuning Mechanisms of Visual Pigments and Other Photoactive Proteins†

    Science.gov (United States)

    Altun, Ahmet; Yokoyama, Shozo; Morokuma, Keiji

    2008-01-01

    The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants. PMID:18331400

  8. Quantum Mechanical/Molecular Mechanical Studies on Spectral Tuning Mechanisms of Visual Pigments and Other Photoactive Proteins†

    OpenAIRE

    Altun, Ahmet; Yokoyama, Shozo; Morokuma, Keiji

    2008-01-01

    The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.

  9. Photodissociation of Trapped Rb2+: Implications for Simultaneous Trapping of Atoms and Molecular Ions

    Science.gov (United States)

    Jyothi, S.; Ray, Tridib; Dutta, Sourav; Allouche, A. R.; Vexiau, Romain; Dulieu, Olivier; Rangwala, S. A.

    2016-11-01

    The direct photodissociation of trapped 85Rb2+ (rubidium) molecular ions by the cooling light for the 85Rb magneto-optical trap (MOT) is studied, both experimentally and theoretically. Vibrationally excited Rb2+ ions are created by photoionization of Rb2 molecules formed photoassociatively in the Rb MOT and are trapped in a modified spherical Paul trap. The decay rate of the trapped Rb2+ ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is observed. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  10. Photodissociation of trapped Rb$^+_2$ : Implications for hybrid molecular ion-atom trapping

    CERN Document Server

    Jyothi, S; Dutta, Sourav; Allouche, A R; Vexiau, Romain; Dulieu, Olivier; Rangwala, S A

    2016-01-01

    We observe direct photodissociation of trapped $^{85}$Rb$_2^+$ molecular ions in the presence of cooling light for the $^{85}$Rb magneto optical trap (MOT). Vibrationally excited Rb$_{2}^{+}$ ions are created by photoionization of Rb$_{2}$ molecules formed photoassociatively in the rubidium (Rb) MOT and are trapped in a modified spherical Paul trap co-centric with the MOT. The decay rate of the trapped Rb$_{2}^{+}$ ion signal in the presence of the MOT cooling light is measured and agreement with our calculated rates for molecular ion photodissociation is established. The photodissociation mechanism due to the MOT light is expected to be active and therefore universal for all homonuclear diatomic alkali metal molecular ions.

  11. Genetic classification and molecular mechanisms of primary dystonia

    Institute of Scientific and Technical Information of China (English)

    Xueping Chen; Huifang Shang; Zuming Luo

    2008-01-01

    BACKGROUND: Primary dystonia is a heterogeneous disease, with a complex genetic basis. In previous studies, primary dystonia was classified according to age of onset, involved regions, and other clinical characteristics. With the development of molecular genetics, new virulence genes and sites have been discovered. Therefore, there is a gradual understanding of the various forms of dystonia, based on new viewpoints. There are 15 subtypes of dystonia, based on the molecular level, i.e., DYT1 to DYT15. OBJECTIVE: To analyze the genetic development of dystonia in detail, and to further investigate molecular mechanisms of dystonia. RETRIEVAL STRATEGY: A computer-based online search was conducted in PubMed for English language publications containing the keywords "dystonia and genetic" from January 1980 to March 2007. There were 105 articles in total. Inclusion criteria: ① the contents of the articles should closely address genetic classification and molecular mechanisms of primary dystonia; ② the articles published in recent years or in high-impact journals took preference. Exclusion criteria: duplicated articles. LITERATURE EVALUATION: The selected articles were on genetic classification and molecular genetics mechanism of primary dystonia. Of those, 27 were basic or clinical studies. DATA SYNTHESIS: ① Dystonia is a heterogeneous disease, with a complex genetic basis. According to the classification of the Human Genome Organization, there are 15 dystonia subtypes, based on genetics, i.e., DYT1-DYT15,including primary dystonia, dystonia plus syndrome, degeneration plus dystonia, and paroxysmal dyskinesia plus dystonia. ② To date, the chromosomes of 13 subtypes have been localized; however, DYT2 and DYT4 remain unclear. Six subtypes have been located within virulence genes. Specifically, torsinA gene expression results in the DYT1 genotype; autosomal dominant GTP cyclohydrolase I gene expression and recessive tyrosine hydroxylase expression result in the DYT5

  12. Atomic force microscopy for the investigation of molecular and cellular behavior.

    Science.gov (United States)

    Ozkan, Alper D; Topal, Ahmet E; Dana, Aykutlu; Guler, Mustafa O; Tekinay, Ayse B

    2016-10-01

    The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.

  13. Atomic layer deposition by reaction of molecular oxygen with tetrakisdimethylamido-metal precursors

    Energy Technology Data Exchange (ETDEWEB)

    Provine, J, E-mail: jprovine@stanford.edu; Schindler, Peter; Torgersen, Jan; Kim, Hyo Jin [Department of Mechanical Engineering, Stanford University, Stanford, California 94305 (United States); Karnthaler, Hans-Peter [Physics of Nanostructured Materials, University of Vienna, 1090 Vienna (Austria); Prinz, Fritz B. [Department of Mechanical Engineering, Stanford University, Stanford, California 94305 and Department of Materials Science and Engineering, Stanford University, Stanford, California 94305 (United States)

    2016-01-15

    Tetrakisdimethylamido (TDMA) based precursors are commonly used to deposit metal oxides such as TiO{sub 2}, ZrO{sub 2}, and HfO{sub 2} by means of chemical vapor deposition and atomic layer deposition (ALD). Both thermal and plasma enhanced ALD (PEALD) have been demonstrated with TDMA-metal precursors. While the reactions of TDMA-type precursors with water and oxygen plasma have been studied in the past, their reactivity with pure O{sub 2} has been overlooked. This paper reports on experimental evaluation of the reaction of molecular oxygen (O{sub 2}) and several metal organic precursors based on TDMA ligands. The effect of O{sub 2} exposure duration and substrate temperature on deposition and film morphology is evaluated and compared to thermal reactions with H{sub 2}O and PEALD with O{sub 2} plasma.

  14. Synthesis of atomically thin hexagonal boron nitride films on nickel foils by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Nakhaie, S.; Wofford, J. M.; Schumann, T.; Jahn, U.; Ramsteiner, M.; Hanke, M.; Lopes, J. M. J., E-mail: lopes@pdi-berlin.de; Riechert, H. [Paul-Drude-Institut für Festkörperelektronik, Hausvogteiplatz 5-7, 10117 Berlin (Germany)

    2015-05-25

    Hexagonal boron nitride (h-BN) is a layered two-dimensional material with properties that make it promising as a dielectric in various applications. We report the growth of h-BN films on Ni foils from elemental B and N using molecular beam epitaxy. The presence of crystalline h-BN over the entire substrate is confirmed by Raman spectroscopy. Atomic force microscopy is used to examine the morphology and continuity of the synthesized films. A scanning electron microscopy study of films obtained using shorter depositions offers insight into the nucleation and growth behavior of h-BN on the Ni substrate. The morphology of h-BN was found to evolve from dendritic, star-shaped islands to larger, smooth triangular ones with increasing growth temperature.

  15. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1

    Science.gov (United States)

    Zhu, Kongkai; Lu, Junyan; Liang, Zhongjie; Kong, Xiangqian; Ye, Fei; Jin, Lu; Geng, Heji; Chen, Yong; Zheng, Mingyue; Jiang, Hualiang; Li, Jun-Qian; Luo, Cheng

    2013-03-01

    New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.

  16. A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.

    Science.gov (United States)

    Zhu, Kongkai; Lu, Junyan; Liang, Zhongjie; Kong, Xiangqian; Ye, Fei; Jin, Lu; Geng, Heji; Chen, Yong; Zheng, Mingyue; Jiang, Hualiang; Li, Jun-Qian; Luo, Cheng

    2013-03-01

    New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C-N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.

  17. Construction of Different Kinds of Atomic and Molecular Orbitals Using Complete Orthonormal Sets of -ETO in Single Exponent Approximation

    Institute of Scientific and Technical Information of China (English)

    Guseinov I. Israfil; Erturk Murat

    2008-01-01

    Using complete orthonormal sets of Ψα -exponential type orbitals in single exponent approximation the new approach has been suggested for construction of different kinds of functions which can be useful in the theory of linear combination of atomic orbitals. These functions can be chosen properly according to the nature of the problems under consideration. This is rather important because the choice of the basis set may be play a crucial role in applications to atomic and molecular problems. As an example of application, different atomic orbitals for the ground states of the neutral and the first ten cationic members of the isoelectronic series of He atom are constructed by the solution of Hartree-Fock Roothaan equations using Ψ1, Ψ0 and Ψ-1 basis sets. The calculated results are close to the numerical Hartree-Fock values. The total energy, expansion coefficients, orbital exponents and virial ratio for each atom are presented.

  18. Mechanically functional amyloid fibrils in the adhesive of a marine invertebrate as revealed by Raman spectroscopy and atomic force microscopy.

    Science.gov (United States)

    S Mostaert, Anika; Crockett, Rowena; Kearn, Graham; Cherny, Izhack; Gazit, Ehud; C Serpell, Louise; P Jarvis, Suzanne

    2009-01-01

    Amyloid fibrils are primarily known in a pathogenic context for their association with a wide range of debilitating human diseases. Here we show a marine invertebrate (Entobdella soleae) utilizes functional amyloid fibrils comparable to those of a unicellular prokaryote (Escherichia coli). Thioflavin-T binding and Raman spectroscopy provided evidence for the presence of amyloid in the adhesive of Entobdella soleae. We elucidated that for these two very different organisms, amyloid fibrils provide adhesive and cohesive strength to their natural adhesives. Comparing the nanoscale mechanical responses of these fibrils with those of pathogenic amyloid by atomic force microscopy revealed that the molecular level origin of the cohesive strength was associated with the generic intermolecular β-sheet structure of amyloid fibrils. Functional adhesive residues were found only in the case of the functional amyloid. Atomic force microscopy provided a useful means to characterize the internal structural forces within individual amyloid fibrils and how these relate to the mechanical performance of both functional and pathogenic amyloid. The mechanistic link of amyloid-based cohesive and adhesive strength could be widespread amongst natural adhesives, irrespective of environment, providing a new strategy for biomimicry and a new source of materials for understanding the formation and stability of amyloid fibrils more generally.

  19. Molecular dynamics studies of the inhibitory mechanism of copper(Ⅱ) on aggregation of amyloid β-peptide

    Institute of Scientific and Technical Information of China (English)

    Yong Jiao; Pin Yang

    2007-01-01

    The inhibitory mechanism of copper(Ⅱ) on the aggregation of amyloid β-peptide (Aβ) was investigated by molecular dynamics simulations. The binding mode of copper(Ⅱ) with Aβ is characterized by the imidazole nitrogen atom, Nπ, of the histidine residue H13,acting as the anchoring site, and the backbone's deprotoned amide nitrogen atoms as the main binding sites. Drove by the coordination bonds and their induced hydrogen bond net, the conformations of Aβ converted from β-sheet non-β-sheet conformations, which destabilized the aggregation of Aβ into fibrils.

  20. Quantum molecular dynamics study of expanded beryllium: evolution from warm dense matter to atomic fluid.

    Science.gov (United States)

    Li, Dafang; Liu, Haitao; Zeng, Siliang; Wang, Cong; Wu, Zeqing; Zhang, Ping; Yan, Jun

    2014-07-31

    By performing quantum molecular dynamics (QMD) simulations, we investigate the equation of states, electrical and optical properties of the expanded beryllium at densities two to one-hundred lower than the normal solid density, and temperatures ranging from 5000 to 30000 K. With decreasing the density of Be, the optical response evolves from the one characteristic of a simple metal to the one of an atomic fluid. By fitting the optical conductivity spectra with the Drude-Smith model, it is found that the conducting electrons become localized at lower densities. In addition, the negative derivative of the electrical resistivity on temperature at density about eight lower than the normal solid density demonstrates that the metal to nonmetal transition takes place in the expanded Be. To interpret this transition, the electronic density of states is analyzed systematically. Furthermore, a direct comparison of the Rosseland opacity obtained by using QMD and the standard opacity code demonstrates that QMD provides a powerful tool to validate plasma models used in atomic physics approaches in the warm dense matter regime.

  1. Site-dependent atomic and molecular affinities of hydrocarbons, amines and thiols on diamond nanoparticles

    Science.gov (United States)

    Lai, Lin; Barnard, Amanda S.

    2016-04-01

    Like many of the useful nanomaterials being produced on the industrial scale, the surface of diamond nanoparticles includes a complicated mixture of various atomic and molecular adsorbates, attaching to the facets following synthesis. Some of these adsorbates may be functional, and adsorption is encouraged to promote applications in biotechnology and nanomedicine, but others are purely adventurous and must be removed prior to use. In order to devise more effective treatments it is advantageous to know the relative strength of the interactions of the adsorbates with the surface, and ideally how abundant they are likely to be under different conditions. In this paper we use a series of explicit electronic structure simulations to map the distribution of small hydrocarbons, amines and thiols on a 2.9 nm diamond nanoparticle, with atomic level resolution, in 3-D. We find a clear relationship between surface reconstructions, facet orientation, and the distribution of the different adsorbates; with a greater concentration expected on the (100) and (110) facets, particularly when the supersaturation in the reservoir is high. Adsorption on the (111) facets is highly unlikely, suggesting that controlled graphitization may be a useful stage in the cleaning and treatment of nanodiamonds, prior to the deliberate coating with functional adsorbates needed for drug delivery applications.

  2. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

    Science.gov (United States)

    Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2017-03-05

    We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

  3. Atomic and Molecular Photoelectron and Auger Electron SpectroscopyStudies Using Synchrotron Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Southworth, Stephen H.

    1982-01-01

    Electron spectroscopy, combined with synchrotron radiation, was used to measure the angular distributions of photoelectrons and Auger electrons from atoms and molecules as functions of photon energy. The branching ratios and partial cross sections were a 130 measured in certain cases. By comparison with theoretical calculations, the experimental results are interpreted in terms of the characteristic electronic structure and ionization dynamics of the atomic or molecular sample. The time structure of the synchrotron radiation source was used to record time-of-flight (TOF) spectra o f the ejected electrons. The ''a double-angle-TOF'' method for the measurement of photoelectron angular distributions is discussed. This technique offers the advantages of increased electron collect ion efficiency and the elimination of certain systematic errors. Several results were obtained for Xe using photon energies in the range hv {approx_equal} 60-190 eV, where excitation and ionization of the inner-subshell 4d electrons dominates. The 4d asymmetry parameter {beta} exhibits strong oscillations with energy, in agreement with several theoretical calculations. As predicted, the 5p asymmetry parameter was observed to deviate strongly from that calculated using the independent-electron model, due to intershell correlation with the 4d electrons.

  4. Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces.

    Science.gov (United States)

    Kim, Hyun-Joon; Kim, Dae-Eun

    2012-07-01

    Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than that of a smooth surface under specific contact conditions. The effect of applied load on the friction coefficient was dependent on the size of the corrugation. Furthermore, stiffness of the nano-structure was identified to be an important variable in dictating the frictional behavior.

  5. Intense electron beams from GaAs photocathodes as a tool for molecular and atomic physics

    Energy Technology Data Exchange (ETDEWEB)

    Krantz, Claude

    2009-10-28

    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 usable cathode lifetimes of 24 h or more. The benefits of the cold electron beam with respect to its application to electron cooling and electron-ion recombination experiments are discussed. Benchmark experiments demonstrate the superior cooling force and energy resolution of the photoelectron beam compared to its thermionic counterparts. The long period of operation allowed to study the long-time behaviour of the GaAs samples during multiple usage cycles at the Electron Target and repeated in-vacuum surface cleaning by atomic hydrogen exposure. An electron emission spectroscopy setup has been implemented at the photocathode preparation chamber of the Electron Target. Among others, this new facility opened the way to a novel application of GaAs (Cs) photocathodes as robust, ultraviolet-driven electron emitters. Based on this principle, a prototype of an electron gun, designed for implementation at the HITRAP setup at GSI, has been built and taken into operation successfully. (orig.)

  6. Modeling of adhesion in tablet compression - I. atomic force microscopy and molecular simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J. J.; Li, T.; Bateman, S. D.; Erck, R.; Morris, K. R.; Energy Technology; Purdue Univ.; Novartis Pharmaceutical Corp.

    2003-04-01

    Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of profen compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ {center_dot} m-2, respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius2 is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems

  7. Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models.

    Science.gov (United States)

    Chen, Jianhan

    2010-09-14

    The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to molecular volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the "exact" Poisson-Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bonding and charge-charge interactions demonstrates that GBSW/MS2 correctly captures the first desolvation peaks, a key signature of true MS. Physical parameters including atomic input radii and peptide backbone torsion were subsequently optimized on the basis of solvation free energies of model compounds, potentials of mean force of their interactions, and conformational equilibria of a set of helical and β-hairpin model peptides. The resulting GBSW/MS2 protein force field reasonably recapitulates the structures and stabilities of these model peptides. Several remaining limitations and possible future developments are also discussed.

  8. Quantum-mechanical calculations of cross sections for electron collisions with atoms and molecules

    CERN Document Server

    Bartschat, Klaus; Zatsarinny, Oleg

    2016-01-01

    An overview of quantum-mechanical methods to generate cross-section data for electron collisions with atoms and molecules is presented. Particular emphasis is placed on the time-independent close-coupling approach, since it is particularly suitable for low-energy collisions and also allows for systematic improvements as well as uncertainty estimates. The basic ideas are illustrated with examples for electron collisions with argon atoms and methane. For many atomic systems, such as e-Ar collisions, highly reliable cross sections can now be computed with quantified uncertainties. On the other hand, while electron collision calculations with molecules do provide key input data for plasma models, the methods and computer codes presently used require further development to make these inputs robust.

  9. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

    Directory of Open Access Journals (Sweden)

    Ilko Bald

    2014-09-01

    Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

  10. Atomistic insight into the catalytic mechanism of glycosyltransferases by combined quantum mechanics/molecular mechanics (QM/MM) methods.

    Science.gov (United States)

    Tvaroška, Igor

    2015-02-11

    Glycosyltransferases catalyze the formation of glycosidic bonds by assisting the transfer of a sugar residue from donors to specific acceptor molecules. Although structural and kinetic data have provided insight into mechanistic strategies employed by these enzymes, molecular modeling studies are essential for the understanding of glycosyltransferase catalyzed reactions at the atomistic level. For such modeling, combined quantum mechanics/molecular mechanics (QM/MM) methods have emerged as crucial. These methods allow the modeling of enzymatic reactions by using quantum mechanical methods for the calculation of the electronic structure of the active site models and treating the remaining enzyme environment by faster molecular mechanics methods. Herein, the application of QM/MM methods to glycosyltransferase catalyzed reactions is reviewed, and the insight from modeling of glycosyl transfer into the mechanisms and transition states structures of both inverting and retaining glycosyltransferases are discussed.

  11. Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wei Ye

    Full Text Available MicroRNAs are endogenous 23-25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0 mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2 are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.

  12. Molecular Mechanisms Behind the Chemopreventive Effects of Anthocyanidins

    Directory of Open Access Journals (Sweden)

    De-Xing Hou

    2004-01-01

    Full Text Available Anthocyanins are polyphenolic ring-based flavonoids, and are widespread in fruits and vegetables of red-blue color. Epidemiological investigations and animal experiments have indicated that anthocyanins may contribute to cancer chemoprevention. The studies on the mechanism have been done recently at molecular level. This review summarizes current molecular bases for anthocyanidins on several key steps involved in cancer chemoprevention: (i inhibition of anthocyanidins in cell transformation through targeting mitogen-activated protein kinase (MAPK pathway and activator protein 1 (AP-1 factor; (ii suppression of anthocyanidins in inflammation and carcinogenesis through targeting nuclear factor kappa B (NF-κB pathway and cyclooxygenase 2 (COX-2 gene; (iii apoptotic induction of cancer cells by anthocyanidins through reactive oxygen species (ROS / c-Jun NH2-terminal kinase (JNK-mediated caspase activation. These data provide a first molecular view of anthocyanidins contributing to cancer chemoprevention.

  13. Design of mechanical components for vibration reduction in an atomic force microscope.

    Science.gov (United States)

    Kim, Chulsoo; Jung, Jongkyu; Youm, Woosub; Park, Kyihwan

    2011-03-01

    Vibration is a key factor to be considered when designing the mechanical components of a high precision and high speed atomic force microscope (AFM). It is required to design the mechanical components so that they have resonant frequencies higher than the external and internal vibration frequencies. In this work, the mechanical vibration in a conventional AFM system is analyzed by considering its mechanical components, and a vibration reduction is then achieved by reconfiguring the mechanical components. To analyze the mechanical vibration, a schematic of the lumped model of the AFM system is derived and the vibrational influences of the AFM components are experimentally examined. Based on this vibration analysis, a reconfigured AFM system is proposed and its effects are compared to a conventional system through a series of simulations and experiments.

  14. Molecular mechanisms of insulin resistance in chronic hepatitis C

    Institute of Scientific and Technical Information of China (English)

    Mark W Douglas; Jacob George

    2009-01-01

    It is now widely recognized that chronic hepatitis C (CHC) is associated with insulin resistance (IR) and type 2 diabetes, so can be considered a metabolic disease. IR is most strongly associated with hepatitis C virus (HCV) genotype 1, in contrast to hepatic steatosis, which is associated with genotype 3 infection. Apart from the well-described complications of diabetes, IR in CHC predicts faster progression to fibrosis and cirrhosis that may culminate in liver failure and hepatocellular carcinoma. More recently, it has been recognized that IR in CHC predicts a poor response to antiviral therapy. The molecular mechanisms for the association between IR and HCV infection are not well defined. This review will elaborate on the clinical associations between CHC and IR and summarize current knowledge regarding the molecular mechanisms that potentially mediate HCV-associated IR.

  15. Engineering molecular mechanics: an efficient static high temperature molecular simulation technique.

    Science.gov (United States)

    Subramaniyan, Arun K; Sun, C T

    2008-07-16

    Inspired by the need for an efficient molecular simulation technique, we have developed engineering molecular mechanics (EMM) as an alternative molecular simulation technique to model high temperature (T>0 K) phenomena. EMM simulations are significantly more computationally efficient than conventional techniques such as molecular dynamics simulations. The advantage of EMM is achieved by converting the dynamic atomistic system at high temperature (T>0 K) into an equivalent static system. Fundamentals of the EMM methodology are derived using thermal expansion to modify the interatomic potential. Temperature dependent interatomic potentials are developed to account for the temperature effect. The efficiency of EMM simulations is demonstrated by simulating the temperature dependence of elastic constants of copper and nickel and the thermal stress developed in a confined copper system.

  16. Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

    Science.gov (United States)

    Zhou, Mengying; Li, Yini; Hu, Qi; Bai, Xiao-Chen; Huang, Weiyun; Yan, Chuangye; Scheres, Sjors H W; Shi, Yigong

    2015-11-15

    The apoptotic protease-activating factor 1 (Apaf-1) controls the onset of many known forms of intrinsic apoptosis in mammals. Apaf-1 exists in normal cells as an autoinhibited monomer. Upon binding to cytochrome c and dATP, Apaf-1 oligomerizes into a heptameric complex known as the apoptosome, which recruits and activates cell-killing caspases. Here we present an atomic structure of an intact mammalian apoptosome at 3.8 Å resolution, determined by single-particle, cryo-electron microscopy (cryo-EM). Structural analysis, together with structure-guided biochemical characterization, uncovered how cytochrome c releases the autoinhibition of Apaf-1 through specific interactions with the WD40 repeats. Structural comparison with autoinhibited Apaf-1 revealed how dATP binding triggers a set of conformational changes that results in the formation of the apoptosome. Together, these results constitute the molecular mechanism of cytochrome c- and dATP-mediated activation of Apaf-1.

  17. Molecular mechanisms of TRAIL-induced apoptosis of cancer cells

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL) is a recently identified member of the tumor necrosis factor (TNF) family[1]. Numerous studies indicate that TRAIL can induce apoptosis of cancer cells but not of normal cells, pointing to the possibility of de-veloping TRAIL into a cancer drug[2-4]. This review will summary the molecular mechanisms of TRAIL-induced apoptosis and discuss the questions to be resolved in this field.

  18. Molecular Transport Mechanisms for Associating and Solvating Penetrant in Polymers

    Science.gov (United States)

    2007-11-02

    PIB ) at different vapor activities in order to understand complex diffusion mechanisms and probe molecular structures above the glass tranisition. The...the individual diffusion coefficients can be separated and that they are equal to each other for the acetic acid/ PIB system. The values of the...BOH) mixtures in polyisobutylene ( PIB ) was studied at varying mixture compositions. Diffusion coefficients and hydrogen bonding interactions were

  19. Molecular mechanisms in muscular dystrophy: a gene expression profiling study.

    OpenAIRE

    2006-01-01

    The muscular dystrophies are a group of neuromuscular disorders characterized by progres¬sive muscle weakness and wasting. Although the underlying genetic defects of a large number of muscular dystrophies are now know, the molecular mechanisms resulting in the devastating effects of the disease are not yet clear. Furthermore, the muscular dystrophies differ in clinical presentation and severity. The processes responsible for this di¬vergence are largely unknown as well. In this thesis, gene e...

  20. Molecular mechanisms and treatment options for muscle wasting eiseases

    OpenAIRE

    Rüegg, Markus A; Glass, David J.

    2010-01-01

    Loss of muscle mass can be the consequence of pathological changes, as observed in muscular dystrophies; or it can be secondary to cachexia-inducing diseases that cause muscle atrophy, such as cancer, heart disease, or chronic obstructive pulmonary disease; or it can be a consequence of aging or simple disuse. Although muscular dystrophies are rare, muscle loss affects millions of people worldwide.Wediscuss the molecular mechanisms involved in muscular dystrophy and in muscle atrophy and pres...

  1. Molecular Composites: Processing, Post-Treatment and Mechanics

    Science.gov (United States)

    1987-07-01

    Mechanical Analyzer was used. 3.2 Articulated Matricies Several isotropic solutions (2.5, 3.0, and 3.2 wt%) were made from PBT36 and ABPBI in MSA at a fixed...built to address this problem. 22 3.3 Thermoplastic Matricies Thermoplastic matrix molecular composites could potentially be melt processed. This would...provide obvious advantages over PBT which is, of course, limited to solution processing. Several candidates were considered for matricies . The only re

  2. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  3. Molecular mechanism of signaling by tumor necrosis factor

    Institute of Scientific and Technical Information of China (English)

    ZHA; Jikun(查纪坤); SHU; Hongbing(舒红兵)

    2002-01-01

    Tumor necrosis factor (TNF) is an important cytokine with multiple biological effects,including cell growth,differentiation,apoptosis,immune regulation and induction of inflammation. The effects of TNF are mediated by two receptors,TNF-R1 and TNF-R2. The major signal transduction pathways triggered by TNF include those that lead to apoptosis,activation of transcription factor NF-??B and protein kinase JNK. This review will discuss the molecular mechanisms of these signaling pathways.

  4. Molecular simulation of the reversible mechanical unfolding of proteins.

    Science.gov (United States)

    Rathore, Nitin; Yan, Qiliang; de Pablo, Juan J

    2004-03-22

    In this work we have combined a Wang-Landau sampling scheme [F. Wang and D. Landau, Phys. Rev. Lett. 86, 2050 (2001)] with an expanded ensemble formalism to yield a simple and powerful method for computing potentials of mean force. The new method is implemented to investigate the mechanical deformation of proteins. Comparisons are made with analytical results for simple model systems such as harmonic springs and Rouse chains. The method is then illustrated on a model 15-residue alanine molecule in an implicit solvent. Results for mechanical unfolding of this oligopeptide are compared to those of steered molecular dynamics calculations.

  5. Molecular mechanism of abnormal aggregation of α-synuclein

    Institute of Scientific and Technical Information of China (English)

    HU HongYua; LIN XiaoJing

    2007-01-01

    The abnormal aggregation of α-synuclein (α-Syn) is thought to be closely associated with Parkinson's disease, but the pathogenesis is still unclear. In this review, we survey the latest development in the molecular mechanism of abnormal α-Syn aggregation, especially in the aspects of the core sequences, aggregation inhibitors, structural transformation and filament morphologies. By exploring the mechanism of α-Syn aggregation, we will have a better understanding of the disease pathogenesis, and develop strategies for preventing and treating this severe disease.

  6. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    Science.gov (United States)

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  7. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes

    Science.gov (United States)

    Eskhan, Asma Omar

    Atomic force microscopy has been used to quantify the adherence and mechanical properties of an array of L. monocytogenes strains and their surface biopolymers. First, eight L. monocytogenes strains that represented the two major lineages of the species were compared for their adherence and mechanics at cellular and molecular levels. Our results indicated that strains of lineage' II were characterized by higher adhesion and Young's moduli, longer and more rigid surface biopolymers and lower specific and nonspecific forces when compared to lineage' I strains. Additionally, adherence and mechanical properties of eight L. monocytogenes epidemic and environmental strains were probed. Our results pointed to that environmental and epidemic strains representative of a given lineage were similar in their adherence and mechanical properties when investigated at a cellular level. However, when the molecular properties of the strains were considered, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. Second, the role of environmental pH conditions of growth on the adhesion and mechanics of a pathogenic L. monocytogenes EGDe was investigated. Our results pointed to a transition in the adhesion energies for cells cultured at pH 7. In addition, when the types of molecular forces that govern the adhesion were quantified using Poisson statistical approach and using a new proposed method, specific hydrogen-bond energies dominated the bacterial adhesion process. Such a finding is instrumental to researchers designing methods to control bacterial adhesion. Similarly, bacterial cells underwent a transition in their mechanical properties. We have shown that cells cultured at pH 7 were the most rigid compared to those cultured in lower or higher pH conditions of growth. Due to transitions observed in adherence and mechanics when cells were cultured at pH 7, we hypothesized that

  8. A recoil ion momentum spectrometer for molecular and atomic fragmentation studies

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Arnab; Tribedi, Lokesh C.; Misra, Deepankar, E-mail: dmisra@tifr.res.in [Department of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005 (India)

    2015-04-15

    We report the development and performance studies of a newly built recoil ion momentum spectrometer for the study of atomic and molecular fragmentation dynamics in gas phase upon the impact of charged particles and photons. The present design is a two-stage Wiley-McLaren type spectrometer which satisfies both time and velocity focusing conditions and is capable of measuring singly charged ionic fragments up-to 13 eV in all directions. An electrostatic lens has been introduced in order to achieve velocity imaging. Effects of the lens on time-of-flight as well as on the position have been investigated in detail, both, by simulation and in experiment. We have used 120 keV proton beam on molecular nitrogen gas target. Complete momentum distributions and kinetic energy release distributions have been derived from the measured position and time-of-flight spectra. Along with this, the kinetic energy release spectra of fragmentation of doubly ionized nitrogen molecule upon various projectile impacts are presented.

  9. Molecular and Atomic Gas in the Local Group Galaxy M33

    CERN Document Server

    Gratier, P; Rodriguez-Fernandez, N J; Schuster, K F; Kramer, C; Xilouris, E M; Tabatabaei, F S; Henkel, C; Corbelli, E; Israel, F; van der Werf, P P; Calzetti, D; Garcia-Burillo, S; Sievers, A; Combes, F; Wiklind, T; Brouillet, N; Herpin, F; Bontemps, S; Aalto, S; Koribalski, B; van der Tak, F; Wiedner, M C; Roellig, M; Mookerjea, B

    2010-01-01

    We present high resolution large scale observations of the molecular and atomic gas in the Local Group Galaxy M33. The observations were carried out using the HERA multibeam receiver at the 30m IRAM telescope in the CO(2-1) line achieving a resolution of 12" x 2.6km/s, enabling individual Giant Molecular Clouds (GMCs) to be resolved. The observed region is 650 square arcminutes mainly along the major axis and out to a radius of 8.5 kpc, and covers entirely the 2' x40' radial strip observed with the HIFI and PACS Spectrometers as part of the HERM33ES Herschel key program. The achieved sensitivity in main beam temperature is 20-50mK at 2.6km/s velocity resolution. The CO(2-1) luminosity of the observed region is 1.7+/-0.1x10^7 Kkm/s pc^2 and is estimated to be 2.8+/-0.3x10^7 Kkm/s pc^2 for the entire galaxy, corresponding to H_2 masses of 1.9x10^8 M_sun and 3.3x10^8 M_sun respectively (including He), calculated with a NH2/ICO twice the Galactic value due to the half-solar metallicity of M33. HI 21 cm VLA archiv...

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-28

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

  12. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  13. Electron Impact Ionization and Fragmentation Dynamics of Small Atomic and Molecular Clusters

    Science.gov (United States)

    Dorn, Alexander

    2016-09-01

    New ionization and fragmentation reactions emerge if target atoms or molecules are embedded in an environment as it is the case in small clusters or in the condensed phase. These can be intermolecular energy and charge transfer processes or a completely modified fragmentation behavior of the molecular ions. Here we study low energy electron impact induced ionization with a multi-electron and ion imaging spectrometer (reaction microscope) and a supersonic gas jet target which can produce small clusters of various target species. Interatomic reactions are studied for the model system of weakly bound Ar2 dimers. Here, the coincident detection of three electrons and two ions gives detailed insight in interatomic Coulombic decay and radiative charge transfer processes. Such processes were also found in bio-relevant systems like water clusters. We studied pure and water-mixed clusters of tetrahydrofuran (C4H8O, THF) which is the simplest analog of deoxyribose in the DNA backbone. One observation is that ionization of the outermost valence orbital for the monomer leads to stable THF ions. In contrast if THF is bound to another THF or a water molecule the molecular ring breaks. In addition we identify intermolecular Coulombic decay induced by energy transfer from a water molecule ionized in the inner valence shell to the neighboring THF molecule.

  14. Molecular and Atomic Gas in the Large Magellanic Cloud - I. Conditions for CO Detection

    CERN Document Server

    Wong, T; Fukui, Y; Kawamura, A; Mizuno, N; Ott, J; Müller, E; Pineda, J L; Welty, D E; Kim, S; Mizuno, Y; Murai, M; Onishi, T

    2009-01-01

    We analyze the conditions for detection of CO(1-0) emission in the Large Magellanic Cloud (LMC), using the recently completed second NANTEN CO survey. In particular, we investigate correlations between CO integrated intensity and HI integrated intensity, peak brightness temperature, and line width at a resolution of 2.6' (~40 pc). We find that significant HI column density and peak brightness temperature are necessary but not sufficient conditions for CO detection, with many regions of strong HI emission not associated with molecular clouds. The large scatter in CO intensities for a given HI intensity persists even when averaging on scales of >200 pc, indicating that the scatter is not solely due to local conversion of HI into H_2 near GMCs. We focus on two possibilities to account for this scatter: either there exist spatial variations in the I(CO) to N(H_2) conversion factor, or a significant fraction of the atomic gas is not involved in molecular cloud formation. A weak tendency for CO emission to be suppr...

  15. The Fueling Diagram: Linking Galaxy Molecular-to-Atomic Gas Ratios to Interactions and Accretion

    CERN Document Server

    Stark, David V; Wei, Lisa H; Baker, Andrew J; Leroy, Adam K; Eckert, Kathleen D; Vogel, Stuart N

    2013-01-01

    To assess how external factors such as local interactions and fresh gas accretion influence the global ISM of galaxies, we analyze the relationship between recent enhancements of central star formation and total molecular-to-atomic (H2/HI) gas ratios, using a broad sample of field galaxies spanning early-to-late type morphologies, stellar masses of 10^(7.2-11.2) Msun, and diverse stages of evolution. We find that galaxies occupy several loci in a "fueling diagram" that plots H2/HI vs. mass-corrected blue-centeredness, a metric tracing the degree to which galaxies have bluer centers than the average galaxy at their stellar mass. Spiral galaxies show a positive correlation between H2/HI and mass-corrected blue-centeredness. When combined with previous results linking mass-corrected blue-centeredness to external perturbations, this correlation suggests a link between local galaxy interactions and molecular gas inflow/replenishment. Intriguingly, E/S0 galaxies show a more complex picture: some follow the same cor...

  16. Outflowing atomic and molecular gas at z ~ 0.67 towards 1504 + 377

    Science.gov (United States)

    Kanekar, Nissim; Chengalur, Jayaram N.

    2008-02-01

    We report the detection of OH 1667-MHz and wide HI 21-cm absorption at z ~ 0.67 towards the red quasar 1504 + 377, with the Green Bank Telescope and the Giant Metrewave Radio Telescope. The HI 21-cm absorption extends over a velocity range of ~600kms-1 blueward of the quasar redshift (z = 0.674), with the new OH 1667-MHz absorption component at ~-430kms-1, nearly coincident with earlier detections of millimetre-wave absorption at z ~ 0.6715. The atomic and molecular absorption appear to arise from a fast gas outflow from the quasar, with a mass outflow rate and a molecular hydrogen fraction . The radio structure of 1504 + 377 is consistent with the outflow arising as a result of a jet-cloud interaction, followed by rapid cooling of the cloud material. The observed ratio of HCO+ and OH column densities is ~20 times higher than typical values in Galactic and high-z absorbers. This could arise because of small-scale structure in the outflowing gas on sub-parsec scales, which would also explain the observed variability in the HI 21-cm line.

  17. Outflowing atomic and molecular gas at $z \\sim 0.67$ towards 1504+377

    CERN Document Server

    Kanekar, Nissim

    2007-01-01

    We report the detection of OH 1667 MHz and wide HI 21cm absorption at $z \\sim 0.67$ towards the red quasar 1504+377, with the Green Bank Telescope and the Giant Metrewave Radio Telescope. The HI 21cm absorption extends over a velocity range of $\\sim 600$ km/s blueward of the quasar redshift ($z=0.674$), with the new OH 1667 MHz absorption component at $\\sim -430$ \\kms, nearly coincident with earlier detections of mm-wave absorption at $z \\sim 0.6715$. The atomic and molecular absorption appear to arise from a fast gas outflow from the quasar, with a mass outflow rate ${\\dot M} \\sim 12 M_\\odot$ yr$^{-1}$ and a molecular hydrogen fraction $f_{\\rm H_2} \\equiv (N_{\\rm H_2}/N_{\\rm HI}) \\sim 0.2$. The radio structure of 1504+377 is consistent with the outflow arising due to a jet-cloud interaction, followed by rapid cooling of the cloud material. The observed ratio of HCO$^+$ to OH column densities is $\\sim 20$ times higher than typical values in Galactic and high-$z$ absorbers. This could arise due to small-scale ...

  18. Molecular Mechanism of Isocupressic Acid Supresses MA-10 Cell Steroidogenesis

    Directory of Open Access Journals (Sweden)

    Kuan-Hao Tsui

    2012-01-01

    Full Text Available Consumption of ponderosa pine needles causes late-term abortions in cattle and is a serious poisonous plant problem in foothill and mountain rangelands. Isocupressic acid (IA is the component of pine needles responsible for the abortifacient effect, its abortifacient effect may be due to inhibition of steroidogenesis. To investigate the more detail molecular mechanism, we used MA-10 cell, which is wild used to investigate molecular mechanism of steroidogenesis, to characterize the molecular mechanisms underlying the actions of IA in more detail. In this report, we focus on the function of IA on important steroidogenic genes, including steroidogenic acute regulatory protein (StAR, cytochrome P450 cholesterol side-chain cleavage (P450scc, and 3β-hydroxysteroid dehydrogenase (3β-HSD. We found that IA does not affect enzyme activities of these genes but inhibits transcription of P450scc and translation of StAR and P450scc through attenuating cAMP-PKA signaling. Thus, steroid productions of cells were suppressed.

  19. Genomic and molecular mechanisms for efficient biodegradation of aromatic dye.

    Science.gov (United States)

    Sun, Su; Xie, Shangxian; Chen, Hu; Cheng, Yanbing; Shi, Yan; Qin, Xing; Dai, Susie Y; Zhang, Xiaoyu; Yuan, Joshua S

    2016-01-25

    Understanding the molecular mechanisms for aromatic compound degradation is crucial for the development of effective bioremediation strategies. We report the discovery of a novel phenomenon for improved degradation of Direct Red 5B azo dye by Irpex lacteus CD2 with lignin as a co-substrate. Transcriptomics analysis was performed to elucidate the molecular mechanisms of aromatic degradation in white rot fungus by comparing dye, lignin, and dye/lignin combined treatments. A full spectrum of lignin degradation peroxidases, oxidases, radical producing enzymes, and other relevant components were up-regulated under DR5B and lignin treatments. Lignin induced genes complemented the DR5B induced genes to provide essential enzymes and redox conditions for aromatic compound degradation. The transcriptomics analysis was further verified by manganese peroxidase (MnP) protein over-expression, as revealed by proteomics, dye decolorization assay by purified MnP and increased hydroxyl radical levels, as indicated by an iron reducing activity assay. Overall, the molecular and genomic mechanisms indicated that effective aromatic polymer degradation requires synergistic enzymes and radical-mediated oxidative reactions to form an effective network of chemical processes. This study will help to guide the development of effective bioremediation and biomass degradation strategies.

  20. Molecular structure and elastic properties of thermotropic liquid crystals: Integrated molecular dynamics—Statistical mechanical theory vs molecular field approach

    Science.gov (United States)

    Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.

    2013-03-01

    The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.

  1. Topography and Mechanical Property Mapping of International Simple Glass Surfaces with Atomic Force Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Pierce, Eric M [ORNL

    2014-01-01

    Quantitative Nanomechanical Peak Force (PF-QNM) TappingModeTM atomic force microscopy measurements are presented for the first time on polished glass surfaces. The PF-QNM technique allows for topography and mechanical property information to be measured simultaneously at each pixel. Results for the international simple glass which represents a simplified version of SON68 glass suggests an average Young s modulus of 78.8 15.1 GPa is within the experimental error of the modulus measured for SON68 glass (83.6 2 GPa) with conventional approaches. Application of the PF-QNM technique will be extended to in situ glass corrosion experiments with the goal of gaining atomic-scale insights into altered layer development by exploiting the mechanical property differences that exist between silica gel (e.g., altered layer) and pristine glass surface.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Molecular-dynamics simulations are used to investigate lateral friction in contact-mode atomic force microscopy of tetracosane (n-C24H50) films. We find larger friction coefficients on the surface of monolayer and bilayer films in which the long axis of the molecules is parallel to the interface ...

  3. Phase transition and mechanical properties of tungsten nanomaterials from molecular dynamic simulation

    Science.gov (United States)

    Chen, L.; Fan, J. L.; Gong, H. R.

    2017-03-01

    Molecular dynamic simulation is used to systematically find out the effects of the size and shape of nanoparticles on phase transition and mechanical properties of W nanomaterials. It is revealed that the body-centered cubic (BCC) to face-centered cubic (FCC) phase transition could only happen in cubic nanoparticles of W, instead of the shapes of sphere, octahedron, and rhombic dodecahedron, and that the critical number to trigger the phase transition is 5374 atoms. Simulation also shows that the FCC nanocrystalline W should be prevented due to its much lower tensile strength than its BCC counterpart and that the octahedral and rhombic dodecahedral nanoparticles of W, rather than the cubic nanoparticles, should be preferred in terms of phase transition and mechanical properties. The derived results are discussed extensively through comparing with available observations in the literature to provide a deep understanding of W nanomaterials.

  4. Selenosugar determination in porcine liver using multidimensional HPLC with atomic and molecular mass spectrometry.

    Science.gov (United States)

    Lu, Ying; Pergantis, Spiros A

    2009-01-01

    A methodology based on liquid chromatography coupled online with atomic and molecular mass spectrometry was developed for identifying trace amounts of the selenosugar methyl 2-acetamido-2-deoxy-1-seleno-β-D-galactopyranoside (SeGalNAc) in porcine liver, obtained from an animal that had not received selenium supplementation. Sample preparation was especially critical for the identification of SeGalNAc by molecular mass spectrometry. This involved liver extraction using a Tris buffer, followed by sequential centrifugations. The resulting cytosolic fraction was pre-concentrated and the low molecular weight selenium (LMWSe) fraction obtained from a size exclusion column was collected, concentrated, and subsequently analyzed using a tandem dual-column HPLC-ICP-MS system which consisted of strong cation exchange (SCX) and reversed phase (RP) columns coupled in tandem. Hepatocytosolic SeGalNAc was tentatively identified by retention time matching and spiking. Its identity was further confirmed by using the same type of chromatography on-line with atmospheric pressure chemical ionization tandem mass spectrometry operated in the selected reaction monitoring (SRM) mode. Four SRM transitions, characteristic of SeGalNAc, were monitored and their intensity ratios determined in order to confirm SeGalNAc identification. Instrument limits of detection for SeGalNAc by SCX-RP HPLC-ICP-MS and SCX-RP HPLC-APCI-MS/MS were 3.4 and 2.9 μg Se L(-1), respectively. Selenium mass balance analysis revealed that trace amounts of SeGalNAc, 2.16±0.94 μg Se kg(-1) liver (wet weight) were present in the liver cytosol, corresponding to 0.4% of the total Se content in the porcine liver.

  5. Hydrogen-Like Atom Description in the Framework of Quantum Mechanics with Consequently Probabilistic Interpretation

    CERN Document Server

    Zhidkov, E P

    2000-01-01

    In the paper a research of spectrum of the energy operator of the hydrogen-like atom in quantum mechanics with non-negative quantum function of distribution (QFD) is carried out. As a principle spectral property of the Hamiltonian its essential spectrum has been established. We have not got the theoretical response on questions of the evaluation of numbers and quantities of eigenvalues, which do not belong the essential spectrum. A method of numerical searching to answer these questions has been proposed.

  6. Coupling of a nano mechanical oscillator and an atomic three-level medium

    CERN Document Server

    Sanz-Mora, A; Wüster, S; Rost, J -M

    2015-01-01

    We theoretically investigate the coupling of an ultracold three-level atomic gas and a nano-mechanical mirror via classical electromagnetic radiation. The radiation pressure on the mirror is modulated by absorption of a probe light field, caused by the atoms which are electromagnetically rendered nearly transparent, allowing the gas to affect the mirror. In turn, the mirror can affect the gas as its vibrations generate opto-mechanical sidebands in the control field. We show that the sidebands cause modulations of the probe intensity at the mirror frequency, which can be enhanced near atomic resonances. Through the radiation pressure from the probe beam onto the mirror, this results in resonant driving of the mirror. Controllable by the two photon detuning, the phase relation of the driving to the mirror motion decides upon amplification or damping of mirror vibrations. This permits direct phase locking of laser amplitude modulations to the motion of a nano-mechanical element opening a perspective for cavity-f...

  7. The superspreading mechanism unveiled via molecular dynamics simulations

    Science.gov (United States)

    Theodorakis, Panagiotis; Muller, Erich; Craster, Richard; Matar, Omar

    2014-11-01

    Superspreading, by which aqueous droplets laden with specific surfactants wet hydrophobic substrates, is an unusual and dramatic phenomenon. This is attributed to various factors, e.g., a particular surfactant geometry, Marangoni flow, unique solid-fluid interactions, however, direct evidence for a plausible mechanism for superspreading has not yet been provided. Here, we use molecular dynamics simulations of a coarse-grained model with force fields obtained from the SAFT- γ equation of state to capture the superspreading mechanism of water drops with surfactants on model surfaces. Our simulations highlight and monitor the main features of the molecular behavior that lead to the superspreading mechanism, and reproduce and explain the experimentally-observed characteristic maxima of the spreading rate of the droplet vs. surfactant concentration and wettability. We also present a comparison between superspreading and non-superspreading surfactants underlining the main morphological and energetic characteristics of superspreaders. We believe that this is the first time a plausible superspreading mechanism based on a microscopic description is proposed; this will enable the design of surfactants with enhanced spreading ability specifically tailored for applications. EPSRC Grant Number EP/J010502/1.

  8. MOL-D: A Collisional Database and Web Service within the Virtual Atomic and Molecular Data Center

    Science.gov (United States)

    Vujčič, V.; Jevremović, D.; Mihajlov, A. A.; Ignjatović, Lj. M.; Srećković, V. A.; Dimitrijević, M. S.; Malović, M.

    2015-12-01

    MOL-D database is a collection of cross-sections and rate coefficients for specific collisional processes and a web service within the Serbian Virtual Observatory (SerVO) and the Virtual Atomic and Molecular Data Center (VAMDC). This database contains photo-dissociation cross-sections for the individual ro-vibrational states of the diatomic molecular ions and rate coefficients for the atom-Rydberg atom chemi-ionization and inverse electron-ion-atom chemi-recombination processes. At the moment it contains data for photodissociation cross-sections of hydrogen H2+ and helium He2+ molecular ions and the corresponding averaged thermal photodissociation cross-sections. The ro-vibrational energy states and the corresponding dipole matrix elements are provided as well. Hydrogen and helium molecular ion data are important for calculation of solar and stellar atmosphere models and for radiative transport, as well as for kinetics of other astrophysical and laboratory plasma (i.e. early Universe).

  9. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    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 simulation...

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

    DEFF Research Database (Denmark)

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

    2006-01-01

    The atomic-scale structure of naturally occurring screw dislocations intersecting a Au(111) surface has been investigated both experimentally by scanning tunneling microscopy (STM) and theoretically using molecular dynamics (MD) simulations. The step profiles of 166 dislocations were measured usi...

  11. Symmetry-resolved spectroscopy by detection of a metastable hydrogen atom for investigating the doubly excited states of molecular hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Odagiri, Takeshi; Kumagai, Yoshiaki; Tanabe, Takehiko; Nakano, Motoyoshi; Kouchi, Noriyuki [Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551 (Japan); Suzuki, Isao H, E-mail: joe@chem.titech.ac.j [Photon Factory, IMSS, KEK, Tsukuba, Ibaraki 305-0801 (Japan)

    2009-11-01

    Symmetry-resolved spectroscopy for investigating the doubly excited states of molecular hydrogen has been newly developed, where a metastable hydrogen atom dissociating in a direction parallel and perpendicular to the electric vector of the linearly polarized incident light is detected.

  12. MOL-D: A Collisional Database and Web Service within the Virtual Atomic and Molecular Data Center

    CERN Document Server

    Vujčić, V; Mihajlov, A A; Ignjatović, Lj M; Srećković, V A; Dimitrijević, M S; Malović, M

    2016-01-01

    MOL-D database is a collection of cross-sections and rate coefficients for specific collisional processes and a web service within the Serbian Virtual Observatory (SerVO) and the Virtual Atomic and Molecular Data Center (VAMDC). This database contains photo-dissociation cross-sections for the individual ro-vibrational states of the diatomic molecular ions and rate coefficients for the atom-Rydberg atom chemi-ionization and inverse electron-ion-atom chemi-recombination processes. At the moment it contains data for photodissociation cross-sections of hydrogen H2+ and helium He2+ molecular ions and the corresponding averaged thermal photodissociation cross-sections. The ro-vibrational energy states and the corresponding dipole matrix elements are provided as well. Hydrogen and helium molecular ion data are important for calculation of solar and stellar atmosphere models and for radiative transport, as well as for kinetics of other astrophysical and laboratory plasma (i.e. early Universe).

  13. Analytic solutions and their dynamics of atomic-molecular Bose-Einstein condensates with time- and space-modulated nonlinearities

    Science.gov (United States)

    Wu, Huilan; Yao, Yuqin

    2017-01-01

    The time- and space-modulated nonlinearity is the important character of the Bose-Einstein condensates (BECs). Many works have been done on atomic BECs with spatially modulated nonlinearity, but there is little work on atomic-molecular BECs. In this paper, we construct one family of explicitly exact solutions of the atomic-molecular BECs with time- and space-modulated nonlinearities and trapping potential by similarity transformations. We discuss the dynamics of matter waves including breathing solitons, quasi-breathing solitons, resonant solitons and moving solitons. We analyze the linear stability of the solutions by adding various initial stochastic noise. We also provide the experimental parameters to produce these phenomena in future experiments.

  14. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  15. Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation.

    Science.gov (United States)

    Shigematsu, Taiki; Koshiyama, Kenichiro; Wada, Shigeo

    2015-10-16

    Rupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation.

  16. Investigation of the torsional barrier of EDOT using molecular mechanics and DFT methods.

    Science.gov (United States)

    Durães, Jussara A; da Silva Filho, Demétrio A; Ceschin, Artemis M; Sales, Maria J A; Martins, João B L

    2014-08-01

    When heterocyclic monomers are polymerized by electrochemical or chemical methods, they form fully conjugated polymers which have a wide range of applications due to their outstanding electronic properties. Among this class of compounds, thiophene derivatives are widely used due to their chemical stability and synthesis flexibility. With the goal to investigate the torsion barrier of polymer chains, a few units of 3,4-ethylenedioxythiophene (EDOT) were chosen and submitted to molecular mechanics (MM), density functional theory (DFT) and coupled cluster CCSD(T) calculations. This study helps to understand the performance and transferability of force fields used in molecular mechanics and molecular dynamics simulations often used to describe structure-property relationships of those systems. Determination of inter-ring torsion angle was performed in a comparative study using both force field, DFT and CCSD(T) methods. A good agreement was noticed between MM and QC results and highlights the importance of the description of the interactions involving the oxygen atoms present in the structure of EDOT. These observations are related to the α,α-coupling that occurs between the monomer units and yields a linear polymer. DFT HOMO and LUMO orbitals were also presented. Finally, UV-vis spectra of EDOT units were obtained using several levels of theory by means of time-dependent DFT calculations (TD-DFT).

  17. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mathiazhagan, S., E-mail: smathi.research@gmail.com; Anup, S., E-mail: anupiist@gmail.com

    2016-08-19

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  18. T cell mediated pathogenesis in EAE: Molecular mechanisms

    Directory of Open Access Journals (Sweden)

    Florian C Kurschus

    2015-06-01

    Full Text Available T cells are major initiators and mediators of disease in multiple sclerosis (MS and in its animal model experimental autoimmune encephalomyelitis (EAE. EAE is an antigen-driven autoimmune model in which immunization against myelin autoantigens elicits strong T cell responses which initiate its pathology with CNS myelin destruction. T cells cause pathogenic events by several mechanisms; some work in a direct fashion in the CNS, such as direct cytokine-induced damage, granzyme-mediated killing, or glutamate-induced neurotoxicity, whereas most are indirect mechanisms, such as activation of other cell types like macrophages, B cells, or neutrophils. This review aims to describe and discuss the molecular effector mechanism by which T cells harm the CNS during EAE.

  19. Physiological, Molecular and Genetic Mechanisms of Long-Term Habituation

    Energy Technology Data Exchange (ETDEWEB)

    Calin-Jageman, Robert J

    2009-09-12

    Work funded on this grant has explored the mechanisms of long-term habituation, a ubiquitous form of learning that plays a key role in basic cognitive functioning. Specifically, behavioral, physiological, and molecular mechanisms of habituation have been explored using a simple model system, the tail-elicited siphon-withdrawal reflex (T-SWR) in the marine mollusk Aplysia californica. Substantial progress has been made on the first and third aims, providing some fundamental insights into the mechanisms by which memories are stored. We have characterized the physiological correlates of short- and long-term habituation. We found that short-term habituation is accompanied by a robust sensory adaptation, whereas long-term habituation is accompanied by alterations in sensory and interneuron synaptic efficacy. Thus, our data indicates memories can be shifted between different sites in a neural network as they are consolidated from short to long term. At the molecular level, we have accomplished microarray analysis comparing gene expression in both habituated and control ganglia. We have identified a network of putatively regulated transcripts that seems particularly targeted towards synaptic changes (e.g. SNAP25, calmodulin) . We are now beginning additional work to confirm regulation of these transcripts and build a more detailed understanding of the cascade of molecular events leading to the permanent storage of long-term memories. On the third aim, we have fostered a nascent neuroscience program via a variety of successful initiatives. We have funded over 11 undergraduate neuroscience scholars, several of whom have been recognized at national and regional levels for their research. We have also conducted a pioneering summer research program for community college students which is helping enhance access of underrepresented groups to life science careers. Despite minimal progress on the second aim, this project has provided a) novel insight into the network mechanisms by

  20. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    Science.gov (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  1. Studies on the molecular mechanisms of seed germination.

    Science.gov (United States)

    Han, Chao; Yang, Pingfang

    2015-05-01

    Seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. Successful germination is not only crucial for seedling establishment but also important for crop yield. After being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. Owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and more proteomic and genetic studies concerning cereal seed germination were performed on rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed structure and domestication background with Arabidopsis. In this review, both the common features and the distinct mechanisms of seed germination are compared among different plant species including Arabidopsis, rice, and maize. These features include morphological changes, cell and its related structure recovery, metabolic activation, hormone behavior, and transcription and translation activation. This review will provide more comprehensive insights into the molecular mechanisms of seed germination.

  2. Deciphering Molecular Mechanism Underlying Hypolipidemic Activity of Echinocystic Acid

    Directory of Open Access Journals (Sweden)

    Li Han

    2014-01-01

    Full Text Available Our previous study showed that a triterpene mixture, consisting of echinocystic acid (EA and oleanolic acid (OA at a ratio of 4 : 1, dose-dependently ameliorated the hyperlipidemia and atherosclerosis in rabbits fed with high fat/high cholesterol diets. This study was aimed at exploring the mechanisms underlying antihyperlipidemic effect of EA. Molecular docking simulation of EA was performed using Molegro Virtual Docker (version: 4.3.0 to investigate the potential targets related to lipid metabolism. Based on the molecular docking information, isotope labeling method or spectrophotometry was applied to examine the effect of EA on the activity of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA reductase, acyl-CoA:cholesterol acyltransferase (ACAT, and diacylglycerol acyltransferase (DGAT in rat liver microsomes. Our results revealed a strong affinity of EA towards ACAT and DGAT in molecular docking analysis, while low binding affinity existed between EA and HMG-CoA reductase as well as between EA and cholesteryl ester transfer protein. Consistent with the results of molecular docking, in vitro enzyme activity assays showed that EA inhibited ACAT and DGAT, with IC50 values of 103 and 139 μM, respectively, and exhibited no significant effect on HMG-CoA reductase activity. The present findings suggest that EA may exert hypolipidemic effect by inhibiting the activity of ACAT and DGAT.

  3. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  4. Introduction to the physics of matter basic atomic, molecular, and solid-state physics

    CERN Document Server

    Manini, Nicola

    2014-01-01

    This book offers an up-to-date, compact presentation of basic topics in the physics of matter, from atoms to molecules to solids, including elements of statistical mechanics. The adiabatic separation of the motion of electrons and nuclei in matter and its spectroscopic implications are outlined for molecules and recalled regularly in the study of the dynamics of gases and solids. Numerous experiments are described and more than 160 figures give a clear visual impression of the main concepts. Sufficient detail of mathematical derivations is provided to enable students to follow easily. The focus is on present-day understanding and especially on phenomena fitting various independent-particle models. The historical development of this understanding, and phenomena such as magnetism and superconductivity, where interparticle interactions and nonadiabatic effects play a crucial role, are mostly omitted. A final outlook section stimulates the curiosity of the reader to pursue the study of such advanced topics in gra...

  5. Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

    Science.gov (United States)

    Hajilar, Shahin; Shafei, Behrouz

    2016-12-01

    The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanical properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates.

  6. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology.

    Science.gov (United States)

    van der Kamp, Marc W; Mulholland, Adrian J

    2013-04-23

    Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.

  7. Complement system part I - molecular mechanisms of activation and regulation

    Directory of Open Access Journals (Sweden)

    Nicolas eMerle

    2015-06-01

    Full Text Available Complement is a complex innate immune surveillance system, playing a key role in defense against pathogens and in host homeostasis. The complement system is initiated by conformational changes in recognition molecular complexes upon sensing danger signals. The subsequent cascade of enzymatic reactions is tightly regulated to assure that complement is activated only at specific locations requiring defense against pathogens, thus avoiding host tissue damage. Here we discuss the recent advances describing the molecular and structural basis of activation and regulation of the complement pathways and their implication on physiology and pathology. This article will review the mechanisms of activation of alternative, classical and lectin pathways, the formation of C3 and C5 convertases, the action of anaphylatoxins and the membrane attack complex. We will also discuss the importance of structure-function relationships using the example of atypical hemolytic uremic syndrome. Lastly we will discuss the development and benefits of therapies using complement inhibitors.

  8. Quantum Interactomics and Cancer Molecular Mechanisms: I. Report Outline

    CERN Document Server

    Baianu, I C

    2004-01-01

    Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...

  9. Neural tube closure: cellular, molecular and biomechanical mechanisms.

    Science.gov (United States)

    Nikolopoulou, Evanthia; Galea, Gabriel L; Rolo, Ana; Greene, Nicholas D E; Copp, Andrew J

    2017-02-15

    Neural tube closure has been studied for many decades, across a range of vertebrates, as a paradigm of embryonic morphogenesis. Neurulation is of particular interest in view of the severe congenital malformations - 'neural tube defects' - that result when closure fails. The process of neural tube closure is complex and involves cellular events such as convergent extension, apical constriction and interkinetic nuclear migration, as well as precise molecular control via the non-canonical Wnt/planar cell polarity pathway, Shh/BMP signalling, and the transcription factors Grhl2/3, Pax3, Cdx2 and Zic2. More recently, biomechanical inputs into neural tube morphogenesis have also been identified. Here, we review these cellular, molecular and biomechanical mechanisms involved in neural tube closure, based on studies of various vertebrate species, focusing on the most recent advances in the field.

  10. Cocoa phytochemicals: recent advances in molecular mechanisms on health.

    Science.gov (United States)

    Kim, Jiyoung; Kim, Jaekyoon; Shim, Jaesung; Lee, Chang Yong; Lee, Ki Won; Lee, Hyong Joo

    2014-01-01

    Recent reports on cocoa are appealing in that a food commonly consumed for pure pleasure might also bring tangible benefits for human health. Cocoa consumption is correlated with reduced health risks of cardiovascular diseases, hypertension, atherosclerosis, and cancer, and the health-promoting effects of cocoa are mediated by cocoa-driven phytochemicals. Cocoa is rich in procyanidins, theobromine, (-)-epicatechin, catechins, and caffeine. Among the phytochemicals present in consumed cocoa, theobromine is most available in human plasma, followed by caffeine, (-)-epicatechin, catechin, and procyanidins. It has been reported that cocoa phytochemicals specifically modulate or interact with specific molecular targets linked to the pathogenesis of chronic human diseases, including cardiovascular diseases, cancer, neurodegenerative diseases, obesity, diabetes, and skin aging. This review summarizes comprehensive recent findings on the beneficial actions of cocoa-driven phytochemicals in molecular mechanisms of human health.

  11. Mechanisms of Helicobacter pylori antibiotic resistance and molecular testing

    Directory of Open Access Journals (Sweden)

    Toshihiro eNishizawa

    2014-10-01

    Full Text Available Antibiotic resistance in Helicobacter pylori (H. pylori is the main factor affecting the efficacy of current treatment methods against infection caused by this organism. The traditional culture methods for testing bacterial susceptibility to antibiotics are expensive and require 10 to 14 days. Since resistance to clarithromycin, fluoroquinolone, and tetracycline seems to be exclusively caused by specific mutations in a small region of the responsible gene, molecular methods offer an attractive alternative to the above-mentioned techniques. The technique of polymerase chain reaction (PCR is an accurate and rapid method for the detection of mutations that confer antibiotic resistance. This review highlights the mechanisms of antibiotic resistance in H. pylori and the molecular methods for antibiotic susceptibility testing.

  12. The molecular mechanism and physiological role of cytoplasmic streaming.

    Science.gov (United States)

    Tominaga, Motoki; Ito, Kohji

    2015-10-01

    Cytoplasmic streaming occurs widely in plants ranging from algae to angiosperms. However, the molecular mechanism and physiological role of cytoplasmic streaming have long remained unelucidated. Recent molecular genetic approaches have identified specific myosin members (XI-2 and XI-K as major and XI-1, XI-B, and XI-I as minor motive forces) for the generation of cytoplasmic streaming among 13 myosin XIs in Arabidopsis thaliana. Simultaneous knockout of these myosin XI members led to a reduced velocity of cytoplasmic streaming and marked defects of plant development. Furthermore, the artificial modifications of myosin XI-2 velocity changed plant and cell sizes along with the velocity of cytoplasmic streaming. Therefore, we assume that cytoplasmic streaming is one of the key regulators in determining plant size.

  13. Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra

    CERN Document Server

    Charnock, G T P; Kuprov, Ilya

    2011-01-01

    An attempt is made to bypass spectral analysis and fit internal coordinates of radicals directly to experimental liquid- and solid-state electron spin resonance (ESR) spectra. We take advantage of the recently introduced large-scale spin dynamics simulation algorithms and of the fact that the accuracy of quantum mechanical calculations of ESR parameters has improved to the point of quantitative correctness. Partial solutions are offered to the local minimum problem in spectral fitting and to the problem of spin interaction parameters (hyperfine couplings, chemical shifts, etc.) being very sensitive to distortions in molecular geometry.

  14. Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

    Science.gov (United States)

    Yong, Chin W

    2016-08-22

    DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

  15. Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies.

    Science.gov (United States)

    Xiao, X; Chang, H; Li, M

    2017-01-03

    Recent large-scale genetic approaches such as genome-wide association studies have allowed the identification of common genetic variations that contribute to risk architectures of psychiatric disorders. However, most of these susceptibility variants are located in noncoding genomic regions that usually span multiple genes. As a result, pinpointing the precise variant(s) and biological mechanisms accounting for the risk remains challenging. By reviewing recent progresses in genetics, functional genomics and neurobiology of psychiatric disorders, as well as gene expression analyses of brain tissues, here we propose a roadmap to characterize the roles of noncoding risk loci in the pathogenesis of psychiatric illnesses (that is, identifying the underlying molecular mechanisms explaining the genetic risk conferred by those genomic loci, and recognizing putative functional causative variants). This roadmap involves integration of transcriptomic data, epidemiological and bioinformatic methods, as well as in vitro and in vivo experimental approaches. These tools will promote the translation of genetic discoveries to physiological mechanisms, and ultimately guide the development of preventive, therapeutic and prognostic measures for psychiatric disorders.Molecular Psychiatry advance online publication, 3 January 2017; doi:10.1038/mp.2016.241.

  16. Mapping molecular adhesion sites inside SMIL coated capillaries using atomic force microscopy recognition imaging

    Energy Technology Data Exchange (ETDEWEB)

    Leitner, Michael [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Stock, Lorenz G. [Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Traxler, Lukas [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria); Leclercq, Laurent [Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier (France); Bonazza, Klaus; Friedbacher, Gernot [Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Vienna (Austria); Cottet, Hervé [Institut des Biomolécules Max Mousseron (IBMM, UMR 5247, CNRS, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier), Place Eugène Bataillon, CC 1706, 34095 Montpellier (France); Stutz, Hanno [Division of Chemistry and Bioanalytics, Department of Molecular Biology, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Christian Doppler Laboratory for Innovative Tools for the Characterization of Biosimilars, University Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg (Austria); Ebner, Andreas, E-mail: andreas.ebner@jku.at [Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz (Austria)

    2016-08-03

    Capillary zone electrophoresis (CZE) is a powerful analytical technique for fast and efficient separation of different analytes ranging from small inorganic ions to large proteins. However electrophoretic resolution significantly depends on the coating of the inner capillary surface. High technical efforts like Successive Multiple Ionic Polymer Layer (SMIL) generation have been taken to develop stable coatings with switchable surface charges fulfilling the requirements needed for optimal separation. Although the performance can be easily proven in normalized test runs, characterization of the coating itself remains challenging. Atomic force microscopy (AFM) allows for topographical investigation of biological and analytical relevant surfaces with nanometer resolution and yields information about the surface roughness and homogeneity. Upgrading the scanning tip to a molecular biosensor by adhesive molecules (like partly inverted charged molecules) allows for performing topography and recognition imaging (TREC). As a result, simultaneously acquired sample topography and adhesion maps can be recorded. We optimized this technique for electrophoresis capillaries and investigated the charge distribution of differently composed and treated SMIL coatings. By using the positively charged protein avidin as a single molecule sensor, we compared these SMIL coatings with respect to negative charges, resulting in adhesion maps with nanometer resolution. The capability of TREC as a functional investigation technique at the nanoscale was successfully demonstrated. - Highlights: • SMIL coating allows generation of homogeneous ultra-flat surfaces. • Molecular electrostatic adhesion forces can be determined in the inner wall of CZE capillary with picoNewton accuracy. • Topographical images and simultaneously acquired adhesion maps yield morphological and chemical information at the nanoscale.

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

    CERN Document Server

    Tscherbul, T V; Yu, H -G; Dalgarno, A; Klos, Jacek; Ma, Lifang; Alexander, Millard H; 10.1063/1.4748258

    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 calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH2(X)] with He atoms. To this end, two highly accurate three-dimensional potential energy surfaces (PESs) of the He-CH2(X) complex are developed using the state-of-the-art CCSD(T) method and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occu...

  18. Surface chemistry of copper metal and copper oxide atomic layer deposition from copper(ii) acetylacetonate: a combined first-principles and reactive molecular dynamics study.

    Science.gov (United States)

    Hu, Xiao; Schuster, Jörg; Schulz, Stefan E; Gessner, Thomas

    2015-10-28

    Atomistic mechanisms for the atomic layer deposition using the Cu(acac)2 (acac = acetylacetonate) precursor are studied using first-principles calculations and reactive molecular dynamics simulations. The results show that Cu(acac)2 chemisorbs on the hollow site of the Cu(110) surface and decomposes easily into a Cu atom and the acac-ligands. A sequential dissociation and reduction of the Cu precursor [Cu(acac)2 → Cu(acac) → Cu] are observed. Further decomposition of the acac-ligand is unfavorable on the Cu surface. Thus additional adsorption of the precursors may be blocked by adsorbed ligands. Molecular hydrogen is found to be nonreactive towards Cu(acac)2 on Cu(110), whereas individual H atoms easily lead to bond breaking in the Cu precursor upon impact, and thus release the surface ligands into the gas-phase. On the other hand, water reacts with Cu(acac)2 on a Cu2O substrate through a ligand-exchange reaction, which produces gaseous H(acac) and surface OH species. Combustion reactions with the main by-products CO2 and H2O are observed during the reaction between Cu(acac)2 and ozone on the CuO surface. The reactivity of different co-reactants toward Cu(acac)2 follows the order H > O3 > H2O.

  19. Molecular mechanisms in autoimmune type 1 diabetes: a critical review.

    Science.gov (United States)

    Xie, Zhiguo; Chang, Christopher; Zhou, Zhiguang

    2014-10-01

    Autoimmune type 1 diabetes is characterized by selective destruction of insulin-secreting beta cells in the pancreas of genetically susceptible individuals. The mechanisms underlying the development of type 1 diabetes are not fully understood. However, a widely accepted point is that type 1 diabetes is caused by a combination of genetic and environmental factors. Although most type 1 diabetes patients do not have a family history, genetic susceptibility does play a vital role in beta cell autoimmunity and destruction. Human leukocyte antigen (HLA) regions are the strongest genetic determinants, which can contribute 40-50 % of the genetic risk to type 1 diabetes. Other genes, including INS also contribute to disease risk. The mechanisms of the susceptible genes in type 1 diabetes may relate to their respective roles in antigen presentation, beta cell autoimmunity, immune tolerance, and autoreactive T cell response. Environmental susceptibility factors also contribute to the risk of developing type 1 diabetes. From an epigenetic standpoint, the pathologic mechanisms involved in the development of type 1 diabetes may include DNA methylation, histone modification, microRNA, and molecular mimicry. These mechanisms may act through regulating of gene expression, thereby affecting the immune system response toward islet beta cells. One of the characteristics of type 1 diabetes is the recognition of islet autoantigens by autoreactive CD4(+) and CD8(+) T cells and autoantibodies. Autoantibodies against islet autoantigens are involved in autoantigen processing and presentation by HLA molecules. This review will mainly focus on the molecular mechanism by which genetic, epigenetic, and environmental factors contribute to the risk of type 1 diabetes.

  20. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

    Science.gov (United States)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H

    2016-11-07

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.