Science.gov

Sample records for molecular collision processes

  1. Atomic and molecular collision processes

    SciTech Connect

    Norcross, D.W.

    1991-04-03

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

  2. Semiclassical theory of electronically nonadiabatic transitions in molecular collision processes

    NASA Technical Reports Server (NTRS)

    Lam, K. S.; George, T. F.

    1979-01-01

    An introductory account of the semiclassical theory of the S-matrix for molecular collision processes is presented, with special emphasis on electronically nonadiabatic transitions. This theory is based on the incorporation of classical mechanics with quantum superposition, and in practice makes use of the analytic continuation of classical mechanics into the complex space of time domain. The relevant concepts of molecular scattering theory and related dynamical models are described and the formalism is developed and illustrated with simple examples - collinear collision of the A+BC type. The theory is then extended to include the effects of laser-induced nonadiabatic transitions. Two bound continuum processes collisional ionization and collision-induced emission also amenable to the same general semiclassical treatment are discussed.

  3. The role of atomic and molecular collision processes in plasmas - and vice versa

    NASA Astrophysics Data System (ADS)

    Gans, Timo

    2008-10-01

    A broad base of accurate data of atomic and molecular collision processes is essential for reliable modelling, simulation, and diagnostics of plasmas. This is particularly important for plasmas at elevated pressures close to atmosphere. This regime attracts rapidly growing attention due to both - promising innovative technological applications as well as new fundamental scientific phenomena. The collision dominated environment and decreasing dimensions down to microscale plasmas with extremely high surface to volume ratios significantly increase the demand for collisional deactivation and surface interaction processes. Cross sections for collisional deactivation can be determined from the effective lifetime of excited states. Direct excitation using short pulse laser systems are most reliable however limited by optical selection rules and available photon energies. Recently improved understanding of the dynamics of electron impact excitation in radio-frequency discharges allows alternative strategies using space and phase resolved optical emission spectroscopy measurements coupled with careful modelling of the population dynamics of excited states. This method based on electron impact excitation is not limited by optical selection rules and also provides access to high energetic electronic states which are not accessible with common laser systems. Data for surface interactions is inherently delicate since it strongly depends on surface properties such as coverage and temperature. Nevertheless, reliable data for recombination of radicals and metastable states, and coefficients for secondary electron emission are highly desirable for consistent modelling and simulation. An alternative approach is the active implementation of experimentally measured surface sensitive parameters such as atomic radical densities and excitation structures caused by secondary electrons. These experimentally accessible quantities can be used as fixed input parameters in improved self-consistent modelling.

  4. Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo.

    PubMed

    Parsons, Neal; Levin, Deborah A; van Duin, Adri C T; Zhu, Tong

    2014-12-21

    The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(Σg+1)-N2(Σg+1) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections. PMID:25527935

  5. Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo

    SciTech Connect

    Parsons, Neal Levin, Deborah A.; Duin, Adri C. T. van; Zhu, Tong

    2014-12-21

    The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N{sub 2}({sup 1}Σ{sub g}{sup +})-N{sub 2}({sup 1}Σ{sub g}{sup +}) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

  6. Modeling of molecular nitrogen collisions and dissociation processes for direct simulation Monte Carlo

    NASA Astrophysics Data System (ADS)

    Parsons, Neal; Levin, Deborah A.; van Duin, Adri C. T.; Zhu, Tong

    2014-12-01

    The Direct Simulation Monte Carlo (DSMC) method typically used for simulating hypersonic Earth re-entry flows requires accurate total collision cross sections and reaction probabilities. However, total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, so their reliability is unknown for the high temperatures observed in hypersonic flows. Existing DSMC reaction models accurately reproduce experimental equilibrium reaction rates, but the applicability of these rates to the strong thermal nonequilibrium observed in hypersonic shocks is unknown. For hypersonic flows, these modeling issues are particularly relevant for nitrogen, the dominant species of air. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method is used to accurately compute collision and reaction cross sections for the N2(^1Σ _g+)-N2(^1Σ _g+) collision pair for conditions expected in hypersonic shocks using a new potential energy surface developed using a ReaxFF fit to recent advanced ab initio calculations. The MD/QCT-computed reaction probabilities were found to exhibit better physical behavior and predict less dissociation than the baseline total collision energy reaction model for strong nonequilibrium conditions expected in a shock. The MD/QCT reaction model compared well with computed equilibrium reaction rates and shock-tube data. In addition, the MD/QCT-computed total cross sections were found to agree well with established variable hard sphere total cross sections.

  7. Numerical simulation of flows from free molecular regime to continuum regime by a DVM with streaming and collision processes

    NASA Astrophysics Data System (ADS)

    Yang, L. M.; Shu, C.; Wu, J.; Wang, Y.

    2016-02-01

    A discrete velocity method (DVM) with streaming and collision processes is presented in this work for simulation of flows from free molecular regime to continuum regime. The present scheme can be considered as a semi-Lagrangian like scheme. At first, we follow the conventional DVM to discretize the phase velocity space by a number of discrete velocities. Then, for each discrete velocity, the kinetic equation with BGK-Shakhov model is integrated in space and time within one time step. As a result, a simple algebraic formulation can be obtained, and its solution can be marched in time by the streaming and collision processes. However, differently from the conventional semi-Lagrangian scheme, the present scheme uses the MUSCL approach with van Albada limiter in the process of reconstructing the distribution function at the surrounding points of the cell center, and the transport distance is controlled in order to avoid extrapolation. This makes the present scheme be capable of simulating the hypersonic rarefied flows. In addition, as compared to the unified gas kinetic scheme (UGKS), the present scheme is simpler and easier for implementation. Thus, the computational efficiency can be improved accordingly. To validate the proposed numerical scheme, test examples from free molecular regime to continuum regime are simulated. Numerical results showed that the present scheme can predict the flow properties accurately even for hypersonic rarefied flows.

  8. Theoretical studies of molecular collisions

    NASA Technical Reports Server (NTRS)

    Kouri, Donald J.

    1991-01-01

    The following subject areas are covered: (1) total integral reactive cross sections and vibrationally resolved reaction probabilities for F + H2 = HF + H; (2) a theoretical study of inelastic O + N2 collisions; (3) body frame close coupling wave packet approach to gas phase atom-rigit rotor inelastic collisions; (4) wave packet study of gas phase atom-rigit motor scattering; (5) the application of optical potentials for reactive scattering; (6) time dependent, three dimensional body frame quantal wave packet treatment of the H + H2 exchange reaction; (7) a time dependent wave packet approach to atom-diatom reactive collision probabilities; (8) time dependent wave packet for the complete determination of s-matrix elements for reactive molecular collisions in three dimensions; (9) a comparison of three time dependent wave packet methods for calculating electron-atom elastic scattering cross sections; and (10) a numerically exact full wave packet approach to molecule-surface scattering.

  9. Atomic and Molecular Collisions at Liquid Surfaces.

    PubMed

    Tesa-Serrate, Maria A; Smoll, Eric J; Minton, Timothy K; McKendrick, Kenneth G

    2016-05-27

    The gas-liquid interface remains one of the least explored, but nevertheless most practically important, environments in which molecular collisions take place. These molecular-level processes underlie many bulk phenomena of fundamental and applied interest, spanning evaporation, respiration, multiphase catalysis, and atmospheric chemistry. We review here the research that has, during the past decade or so, been unraveling the molecular-level mechanisms of inelastic and reactive collisions at the gas-liquid interface. Armed with the knowledge that such collisions with the outer layers of the interfacial region can be unambiguously distinguished, we show that the scattering of gas-phase projectiles is a promising new tool for the interrogation of liquid surfaces with extreme surface sensitivity. Especially for reactive scattering, this method also offers absolute chemical selectivity for the groups that react to produce a specific observed product. PMID:27090845

  10. Collisions of antiprotons with hydrogen molecular ions

    NASA Astrophysics Data System (ADS)

    Lühr, Armin; Saenz, Alejandro

    2009-08-01

    Time-dependent close-coupling calculations of the ionization and excitation cross section for antiproton collisions with molecular hydrogen ions are performed in an impact energy range from 0.5 keV to 10 MeV. The Born-Oppenheimer and Franck-Condon approximations as well as the impact parameter method are applied in order to describe the target molecule and the collision process. It is shown that three perpendicular orientations of the molecular axis with respect to the trajectory are sufficient to accurately reproduce the ionization cross section calculated by Sakimoto [Phys. Rev. A 71, 062704 (2005)] reducing the numerical effort drastically. The independent-event model is employed to approximate the cross section for double ionization and H+ production in antiproton collisions with H2 .

  11. Ion-Ion Collision Processes: Experiment

    NASA Astrophysics Data System (ADS)

    Bruning, H.; Salzborn, E.

    2005-05-01

    Collisions between ions belong to the elementary processes occuring in all plasmas. Experimental data, measured by the crossed beams technique, for charge transfer in ion-ion collisions at keV energies are reviewed. One-electron and quasi-one-electron collision systems are discussed, which provide an ideal testing ground for theory. First ever measurements of angular differential as well as state selective electron capture cross sections are presented. Data on homo-nuclear collisions between heavy ions are also shown, as they are relevant to beam intensity losses in modern accelerator and storage rings. Finally, current studies involving molecular ions are reviewed.

  12. Electron-ion collision processes

    NASA Astrophysics Data System (ADS)

    Dunn, Gordon H.

    1996-07-01

    Almost by definition, electron-ion collisions are critically important in neutral plasmas, and one must have a quantitative knowledge of these collisions to model and understand non-LTE plasmas. Experimental studies of such processes have been carried out for more than 30 years now, giving necessary input and feedback to theoretical studies so that ultimately plasmas ranging through those in astrophysical bodies, to those in controlled fusion devices, planetary atmospheres, flames, lasers, plasma generators and lighting devices can be modelled and understood. The challenge is a huge one for both the experimental and theoretical workers, since the number of processes is large: including elastic scattering, excitation, ionization and recombination for atomic ions. One has found that for each of these there are generally a number of mechanisms operative to lead to the final state. The processes are often referred to as ``direct'' and ``indirect'' processes. For molecular ions the multiplicities of mechanisms and parameters increases almost discouragingly; since the effects of internuclear motions can enter prominently into both the target and product states. It goes without saying that the number of species is essentially limitless. Thus, despite the long time of study and much progress, there remains much to be done to achieve the quest. The author in this brief space tries to give some indication of the status of a number of processes by describing some of the forefront experimental work presently going on and indicating some problems remaining to be overcome. There is no attempt to review all data and work in the literature.

  13. Tight-binding molecular-dynamics simulation of buckyball collisions

    SciTech Connect

    Zhang, B.L.; Wang, C.Z.; Chan, C.T.; Ho, K.M. )

    1993-04-01

    The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several specific energies and orientations produce interesting novel molecules, such as small baby cages, caps, and even a Russian-Doll molecule in which a small cage is trapped in a bigger one. 28 refs., 5 figs., 2 tabs.

  14. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

    The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientifically developing countries. For example, it has been a tradition of the DMC meeting to offer of order 40 scholarships for students & postdocs to defray registration & travel costs. The benefits of increased graduate student & post doctoral attendance at the meeting cannot be over emphasized. First, these young scientists have the opportunity to present their work by means of the poster session & to a gathering of experts in their field. Secondly the limited size of the meeting allows student & young postdocs to meet & interact directly with experts in their area, to network with their peers at other institutions & become aware of career opportunities. Graduate students & post doctoral fellows are the life blood of our field. Support of their attendance at this & other similar meetings will ensure a continued flow of young talent into many areas of research represented by the DMC meeting & important to DOE.

  15. Giant Molecular Cloud Collisions as Triggers of Star Formation

    NASA Astrophysics Data System (ADS)

    Wu, Benjamin; Tan, Jonathan C.; Van Loo, Sven; nakamura, fumitaka; Bruderer, Simon

    2016-01-01

    We investigate a potentially dominant mechanism for galactic star formation: triggering via collisions between giant molecular clouds (GMCs). We create detailed numerical simulations of this process, utilizing the Enzo code with magnetohydrodynamics (MHD), including non-ideal effects, and adaptive mesh refinement (AMR) to explore how cloud collisions trigger formation of dense filaments, clumps and stars. We implement photo-dissociation region (PDR) based density/temperature/extinction-dependent heating and cooling functions that span the atomic to molecular transition and can return detailed diagnostic information. We first carried out a parameter space study via a suite of 2D simulations, which track the fate of an initially stable clump embedded within one of the clouds. We have then extended these calculations to 3D, including introduction of initial turbulence into the clouds and magnetically-regulated sub-grid models for star formation. Different magnetic field strengths and orientations are considered, as is the role of cloud collisions at various velocities and impact parameters. We examine the effects of including ambipolar diffusion. Between isolated and colliding cases, the density and kinematic structure are visualized and characterized, in addition to magnetic field configuration. We discuss observational diagnostics of cloud collisions, focusing on 13CO(J=2-1), 13CO(J=3-2), and 12CO(J=8-7) integrated intensity maps and spectra, which we synthesize from our simulation outputs. We find the ratio of J=8-7 to lower-J emission to be a powerful diagnostic probe of GMC collisions. We also analyze magnetic field orientation relative to filamentary structure, comparing to observations within the Galaxy. Finally, we examine the level of star formation activity that is induced by collisions and distinguishing kinematic properties of the stars that form by this mechanism.

  16. Division XII / Commission 14 / Working Group Collision Processes

    NASA Astrophysics Data System (ADS)

    Peach, Gillian; Dimitrijevic, Milan S.

    2012-04-01

    Research in atomic and molecular collision processes and spectral line broadening has been very active since our last report, Peach, Dimitrijević & Stancil 2009. Given the large volume of the published literature and the limited space available, we have attempted to identify work most relevant to astrophysics. Since our report can not be comprehensive, additional publications can be found in the databases at the web addresses listed in the final section. Elastic and inelastic collisions among electrons, atoms, ions, and molecules are included and charge transfer can be very important in collisions between heavy particles.

  17. Molecular processes in comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1993-01-01

    Classical trajectory calculations of the cross sections for vibrational and rotational energy exchange in direct and reactive collisions of hydrogen atoms and hydrogen molecules have been carried out. To test the sensitivity, three potential energy surfaces have been used. For the exchange transitions which occur at small internuclear distances, the rate coefficients for the three surfaces agree quite well. For the direct transitions, there are significant differences for the pure rotational transitions from j=0 to 2 and from j=1 to j=3 in which there is no change in vibration. For higher j the differences tend to disappear, suggesting that the rotational angular momentum can couple to the orbital angular momentum to overcome the centrifugal barrier. Complete numerically exact quantum mechanical calculations for the process in which vJ changes have been performed. Dr. M. A'Hearn has provided data on the fluorescent population of the NH rotational and fine-structure levels from which we should be able to predict accurate photodissociation lifetimes. The distribution rate of C2 is being investigated. A review of H3(+) in terrestrial and extraterrestrial environments was prepared for a volume of Advances in Atomic, Molecular and Optical Physics.

  18. Continuum and molecular-dynamics simulation of nanodroplet collisions

    NASA Astrophysics Data System (ADS)

    Bardia, Raunak; Liang, Zhi; Keblinski, Pawel; Trujillo, Mario F.

    2016-05-01

    The extent to which the continuum treatment holds in binary droplet collisions is examined in the present work by using a continuum-based implicit surface capturing strategy (volume-of-fluid coupled to Navier-Stokes) and a molecular dynamics methodology. The droplet pairs are arranged in a head-on-collision configuration with an initial separation distance of 5.3 nm and a velocity of 3 ms-1. The size of droplets ranges from 10-50 nm. Inspecting the results, the collision process can be described as consisting of two periods: a preimpact phase that ends with the initial contact of both droplets, and a postimpact phase characterized by the merging, deformation, and coalescence of the droplets. The largest difference between the continuum and molecular dynamics (MD) predictions is observed in the preimpact period, where the continuum-based viscous and pressure drag forces significantly overestimate the MD predictions. Due to large value of Knudsen number in the gas (Kngas=1.972 ), this behavior is expected. Besides the differences between continuum and MD, it is also observed that the continuum simulations do not converge for the set of grid sizes considered. This is shown to be directly related to the initial velocity profile and the minute size of the nanodroplets. For instance, for micrometer-size droplets, this numerical sensitivity is not an issue. During the postimpact period, both MD and continuum-based simulations are strikingly similar, with only a moderate difference in the peak kinetic energy recorded during the collision process. With values for the Knudsen number in the liquid (Knliquid=0.01 for D =36 nm ) much closer to the continuum regime, this behavior is expected. The 50 nm droplet case is sufficiently large to be predicted reasonably well with the continuum treatment. However, for droplets smaller than approximately 36 nm, the departure from continuum behavior becomes noticeably pronounced, and becomes drastically different for the 10 nm droplets.

  19. Division XII / Commission 14 / Working Group Collision Processes

    NASA Astrophysics Data System (ADS)

    Peach, Gillian; Dimitrijevic, Milan S.; Stancil, Phillip C.

    Research in atomic and molecular collision processes and spectral line broadening has been very active since our last report (Schultz & Stancil 2007, Allard & Peach 2007). Given the large volume of the published literature and the limited space available, we have attempted to identify work most relevant to astrophysics. Since our report is not comprehensive, additional publications can be found in the databases at the web addresses listed in the final section. Elastic and inelastic collisions among electrons, atoms, ions, and molecules are included and reactive processes are also considered, but except for charge exchange, they receive only sparse coverage.

  20. Molecular vibrational states during a collision

    NASA Technical Reports Server (NTRS)

    Recamier, Jose A.; Jauregui, Rocio

    1995-01-01

    Alternative algebraic techniques to approximate a given Hamiltonian by a harmonic oscillator are described both for time-independent and time-dependent systems. We apply them to the description of a one dimensional atom-diatom collision. From the resulting evolution operator, we evaluate vibrational transition probabilities as well as other time-dependent properties. As expected, the ground vibrational state becomes a squeezed state during the collision.

  1. Universal reaction rates for ultracold molecular collisions

    NASA Astrophysics Data System (ADS)

    Julienne, Paul; Idziaszek, Zbigniew

    2010-03-01

    We offer a simple yet general model of reactive collisions using a quantum defect framework based on the separation of the collision dynamics into long-range and a short-range parts [1]. Two dimensionless quantum defect parameters s and y are used to characterize the S-matrix for a given entrance channel; s represents a phase parameter and y the probability of short-range reaction. The simple analytic expressions we obtain give universal values for s-wave and p-wave collision rates for a van der Waals potential when y approaches unity. In this limit, reaction rates are governed entirely by the threshold laws governing the quantum transmission of the long range potential and depend only on the van der Waals coefficient. The universal rate constants explain the magnitude of the observed rate constants for reactive collisions of fermionic KRb + KRb or K + KRb [2]. In contrast, reaction rates will be non-universal and depend strongly on the phase parameter s if the short range reaction probability is low, y << 1. [1] Z. Idziaszek and P. S. Julienne, arXiv:0912.0370. [2] S. Ospelkaus, K.-K. Ni, D. Wang, M. H. G. de Miranda, B. Neyenhuis, G. Qu'em'ener, P. S. Julienne, J. L. Bohn, D. S. Jin, and J. Ye, arXiv:0912.3854.

  2. Merged-beams for slow molecular collision experiments

    NASA Astrophysics Data System (ADS)

    Wei, Qi; Lyuksyutov, Igor; Herschbach, Dudley

    2012-08-01

    Molecular collisions can be studied at very low relative kinetic energies, in the milliKelvin range, by merging codirectional beams with much higher translational energies, extending even to the kiloKelvin range, provided that the beam speeds can be closely matched. This technique provides far more intensity and wider chemical scope than methods that require slowing both collision partners. Previously, at far higher energies, merged beams have been widely used with ions and/or neutrals formed by charge transfer. Here, we assess for neutral, thermal molecular beams the range and resolution of collision energy that now appears attainable, determined chiefly by velocity spreads within the merged beams. Our treatment deals both with velocity distributions familiar for molecular beams formed by effusion or supersonic expansion, and an unorthodox variant produced by a rotating supersonic source capable of scanning the lab beam velocity over a wide range.

  3. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

    Describes a molecular dynamics simulator that employs ping-pong balls as the atoms or molecules and is suitable for either large lecture halls or small classrooms. Discusses its use in illustrating many of the fundamental concepts related to molecular motion and dynamics and providing a three-dimensional perspective of molecular motion. (JRH)

  4. Molecular Processes in Comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1998-01-01

    The research focused on molecular hydrogen and its response to ultraviolet radiation, photoelectron impact excitation and X-ray radiation and on the interpretation of the ultraviolet spectra of the Jupiter dayglow and auroras. A systematic effort was made to obtain reliable rate coefficients for rovibrational energy transfer of H2, particularly in collisions with hydrogen atoms. We carried out elaborate quantum-mechanical calculations of the scattering of H and H2 on what had been characterized as a reliable potential energy surface of the H3 molecular system. These calculations took into account reactive channels and rate coefficients for ortho-para transitions were obtained. Quantal calculations are too complex to be applied to all the possible rovibrational transitions and we turned to a semi-classical method. With it we calculated rate coefficients for transitions, reactive and non-reactive, for all the rovibrational levels. We carried out the calculations for three of the available H3 potential energy surfaces. We discovered an unexpected sensitivity of the rate coefficients for the non-reactive channels to the potential energy surface. This discovery stimulated more thorough investigations of the potential energy surface elsewhere and to the construction of a new surface. We have used it in further semi-classical calculations in work that will shortly be 2 completed and which, together with new quantum-mechanical calculations should comprise a set of reliable rate coefficients that can be used in discussions of H2 on the Jovian planets. We carried out a detailed study of the Jovian ultraviolet dayglow. There has been a long-running argument about the dayglow on Jupiter. There are two sources of excitation: fluorescence and photoelectron impact excitation. It had been argued that a third source "the electron glow" was needed to bring theory and observation into agreement. We believe we have shown conclusively that the third source is unnecessary. We have achieved a close quantitative agreement between the predicted spectrum arising from fluorescence and photoelectrons and the measured spectrum. We also demonstrated a method by which the presence of HD could be established observationary. Similar calculations were carried out of the ultraviolet spectra of the Jovian auroras. We again found close agreement. Indeed, the agreement was so detailed we were able to derive the temperature of the atmosphere. We found, contrary to the standard model of the time, a high temperature between 400 K and 600 K and established the presence of a significant temperature gradient. A large temperature gradient was indeed found by direct sampling with the Jupiter probe.

  5. Long-range forces and the collisions of free-molecular and transition regime aerosols

    SciTech Connect

    Marlow, W.H.

    1988-12-31

    An aerosol here is understood to be a two-component system comprised of gaseous and condensed phases with the characteristic that the condensed phase is not an equilibrium subsystem. In contrast to the usual definitions based upon geometrical or mechanical variables, this quasi-thermodynamic formulation is framed to emphasize the dynamical behavior of aerosols by allowing for coagulation and other aerosol evolutionary processes as natural consequences of the interactions and state variables appropriate to the system. As will become clear later, it also provides a point of departure for distinguishing aerosol particles from unstable gas-phase cluster systems. The question of accommodation in particle collisions must be addressed as a prelude to the discussion of the role of long-range forces. Microscopic reversibility is frequently assumed for molecular collisions with either molecules or solid surfaces. In the case of aerosol collisions, the implication of this assumption is that collisions are elastic, which is contrary to the evidence from coagulation experiments and the conventional operational assumption of sticking upon collision. Gay and Berne have performed computer simulations of the collision of two clusters consisting of a total of 135 molecules interacting via Lennard-Jones potentials. That work showed that complete accommodation, accompanied by overall heating of the unified cluster, occurred. Since heating represents an irreversible degradation of the kinetic energy of the collision, the hamiltonian of the two-cluster system should be considered as dissipative and therefore microscopic reversibility does not apply.

  6. Molecular (Feshbach) treatment of charge exchange Li/sup 3 +/+He collisions. I. Energies and couplings

    SciTech Connect

    Martin, F.; Riera, A.; Yanez, M.

    1986-05-15

    We point out a fundamental difference between the molecular treatment of charge exchange X/sup n/++H(1s) and X/sup n/++He(1s/sup 2/) collisions, which is that the latter process involves molecular states that are formally autoionizing. Then standard ab initio methods do not, in general, yield the relevant wave functions that are needed in the collision treatment, irrespective of whether quasimolecular autoionization be significant or not during the collision. We implement a particularly simple and useful form of the Feshbach formalism to calculate the energies of those two electron systems, and a method to evaluate the corresponding dynamical couplings is presented for the first time. Our implementation of this formalism together with the new computational techniques involved are presented in detail.

  7. Optimal separable bases and molecular collisions

    SciTech Connect

    Poirier, L W

    1997-12-01

    A new methodology is proposed for the efficient determination of Green`s functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. The primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR`s) and iterative sparse matrix methods commonly employed in such calculations. State to state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H{sub 2} {yields} H{sub 2} + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes.

  8. Optimal separable bases and molecular collisions

    NASA Astrophysics Data System (ADS)

    Poirier, Lionel William

    A new methodology is proposed for the efficient determination of Green's functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. Our primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR's) and iterative sparse matrix methods commonly employed in such calculations. State-to-state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H2 /to H2 + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes. The method is also applied to three-body systems in two different ways. First, numerical results are obtained for zero total angular momentum using optimized preconditioning. The J /not= 0 results are then estimated using helicity-conserving and J-shifting approximations, after minimizing the coriolis coupling via another application of the optimal basis method. An 'effective potential' interpretation of the helicity- conserving approximation is employed, which leads to an improved J-shifting scheme that automatically incorporates centrifugal distortion and other effects. Fixed-energy cumulative reaction probabilities and thermal rate constants are presented for the O + HCl → OH + Cl reactive scattering system.

  9. Shielding 2Σ ultracold dipolar molecular collisions with electric fields

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Bohn, John L.

    2016-01-01

    The prospects for shielding ultracold, paramagnetic, dipolar molecules from inelastic and chemical collisions are investigated. Molecules placed in their first rotationally excited states are found to exhibit effective long-range repulsion for applied electric fields above a certain critical value, as previously shown for nonparamagnetic molecules. This repulsion can safely allow the molecules to scatter while reducing the risk of inelastic or chemically reactive collisions. Several molecular species of 2Σ molecules of experimental interest—RbSr, SrF, BaF, and YO—are considered, and all are shown to exhibit orders of magnitude suppression in quenching rates in a sufficiently strong laboratory electric field. It is further shown that, for these molecules described by Hund's coupling case (b), electronic and nuclear spins play the role of spectator with respect to the shielding.

  10. Atomic Collision Processes for Astrophysical and Laboratory Plasmas

    NASA Astrophysics Data System (ADS)

    Pindzola, M. S.; Loch, S. D.; Ballance, C. P.; Abdel-Naby, Sh A.; Lee, T. G.; Colgan, J.; Fontes, C. J.; Badnell, N. R.; O'Mullane, M. G.

    2014-11-01

    An accurate knowledge of atomic collision processes is important for a better understanding of many astrophysical and laboratory plasmas. Collision databases which contain electron-impact excitation, ionization, and recombination cross sections and temperature dependent rate coefficients have been constructed using perturbative distorted-wave methods and non-perturbative R-matrix pseudo-states and time-dependent close-coupling methods. We present recent atomic collision results.

  11. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

    The Direct Simulation Monte Carlo (DSMC) method typically used to model thermochemical nonequilibrium rarefied gases requires accurate total collision cross sections, reaction probabilities, and molecular internal energy exchange models. However, the baseline total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, reaction probabilities are defined such that experimentally determined equilibrium reaction rates are replicated, and internal energy relaxation models are phenomenological in nature. Therefore, these models have questionable validity in modeling strongly nonequilibrium gases with temperatures greater than those possible in experimental test facilities. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method can be used to accurately compute total collision cross sections, reaction probabilities, and internal energy exchange models based on first principles for hypervelocity collision conditions. In this thesis, MD/QCT-based models were used to improve simulations of two unique nonequilibrium rarefied gas systems: the Ionian atmosphere and hypersonic shocks in Earth's atmosphere. The Jovian plasma torus flows over Io at ≈ 57 km/s, inducing high-speed collisions between atmospheric SO2 and the hypervelocity plasma's O atoms and ions. The DSMC method is well-suited to model the rarefied atmosphere, so MD/QCT studies are therefore conducted to improve DSMC collision models of the critical SO2-O collision pair. The MD/QCT trajectory simulations employed a new potential energy surface that was developed using a ReaxFF fit to a set of ab initio calculations. Compared to the MD/QCT results, the baseline DSMC models are found to significantly under-predict total cross sections, use reaction probabilities that are unrealistically high, and give unphysical internal energies above the dissociation energy for non-reacting inelastic collisions and under-predicts post-dissociation SO internal energy. Implemented into DSMC, the MD/QCT-based models had a significant effect on simulations of simple, thermal nonequilibrium heat bath and 2D counterflow cases approximating the upper atmospheric conditions of Io. In high-fidelity 1D simulations of the atmosphere of Io, the MD/QCT models predicted approximately half the SO2 atmospheric dissociation due to O and O+ bombardment and a temperature rise due to plasma heating further from the Ionian surface than the existing baseline methodologies. Hypersonic spacecraftre-entering Earth's atmosphere experience significant heating from the post-shock gas. The DSMC method is used to model hypersonic shocks during the early stages of re-entry because of the rarefied nature of the atmosphere at high altitudes. Improved modeling of the N-N 2 and N2-N 2 collision pairs are thus generated with MD/QCT. For the N-N2 pair, a potential energy surface developed at NASA Ames is used and, for the N2-N2 pair, a new potential energy surface is developed using a ReaxFF fit to recent advanced ab initio computations. The MD/QCT-computed total cross sections agreed well with the baseline models, but the MD/QCT reaction probabilities exhibited better physical behavior, a stronger dependence on initial molecular internal energy, and were generally lower than the baseline DSMC chemistry models for strong nonequilibrium conditions, but higher for equilibrium conditions. Furthermore, the MD/QCT results predicted faster rotational-translational energy relaxation for the N-N2 pair and faster vibrational-translational energy relaxation for the N2-N2 pair. The MD/QCT models were tested in DSMC simulations of 2D axisymmetric hypersonic flow over a blunt body and thermal nonequilibrium heat bath cases. The MD/QCT models led to increased post-shock N2 dissociation and faster rates of internal energy relaxation, each of which led to corresponding decreases in translational temperature.

  12. Elementary processes during collisions of ions with tryptophan molecules

    NASA Astrophysics Data System (ADS)

    Afrosimov, V. V.; Basalaev, A. A.; Kuz'michev, V. V.; Panov, M. N.; Smirnov, O. V.

    2016-03-01

    The relative cross sections of elementary processes occurring in single collisions of tryptophan molecules in the gaseous phase with He2+ ions with energy 4 keV/u are measured using time-of-flight mass spectrometry for studying the mechanism of radiation damage of amino acid molecules. The fragmentation channels for intermediate singly and doubly charged tryptophan molecular ions formed during one-electron capture, two-electron capture, and electron capture with ionization are investigated. Significant difference is observed in the mass spectra of fragmentation of intermediate doubly charged ions formed during the capture with ionization and double capture, which is associated with different energies of excitation of {C11H12N2O2}2+* ions.

  13. Molecular treatment of He/sup +/+H collisions

    SciTech Connect

    Macias, A.; Riera, A.; Yanez, M.

    1981-06-01

    Total cross sections for the reactions /sup 4/He/sup +/(1s)+H(1s)..-->../sup 4/He/sup +/(1s)+H(2p), /sup 4/He/sup +/(1s) + H(1s)..-->../sup 4/He(1s2p /sup 1,3/P)+H/sup +/ are calculated in an impact-parameter formalism, for collision energies 0.5--30 keV, using a molecular approach. The molecular energies are calculated at large internuclear distances by a configuration-interaction method, and at short distances by a block-diagonalization method. The radial couplings between the molecular wave functions are evaluated exactly, and turn out to depend strongly on the choice of origin of electronic coordinates; as a consequence, the cross sections also depend on this choice. The effect of the anomalous rotational couplings which decrease like R/sup -1/ is shown to be negligible, and a method to integrate them is proposed in the Appendix. Choosing the center of mass as origin of electronic coordinates, we obtain good agreement with experimental data, but we find no a priori reason to favor this choice. As an important conclusion, the main effect of the so-called momentum-transfer problem, which is the origin dependence of the cross sections, is due to the form of the molecular wave functions at short internuclear distances.

  14. Collision Induced Dissociation and Energy Transfer in Molecular Hydroge

    NASA Astrophysics Data System (ADS)

    Mandy, Margot E.

    2006-06-01

    Molecular hydrogen is a significant constituent in giant molecular clouds in the interstellar medium. Shocks in these clouds are associated with star formation. The cooling of the shocks is governed by competition of collisional energy transfer and dissociation with radiative cooling by quadrupole emission. Thus a detailed understanding of collisional behaviour of molecular hydrogen is needed. Work in this group has examined energy transfer and dissociation in molecular energy transfer as the result of collisions with H, D, He, and H2. Using quasiclassical trajectories and chemically accurate ab initio potentials state-to-state rate coefficients have been determined. The uncertainties of the cross sections are propagated rigourously to give uncertainties of the rate coefficients and the rate coefficients are parameterized as a function of temperature. Comparisons with quantum calculations are discussed and the proposed website is described.This work was supported by a grant from the Natural Sciences and Engineering Research Council of Canada. The calculations were carried out using the high performance computing facility jointly supported by the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund, and Silicon Graphics at the University of Northern British Columbia.

  15. Calculation of total cross sections for charge exchange in molecular collisions

    NASA Technical Reports Server (NTRS)

    Ioup, J.

    1979-01-01

    Areas of investigation summarized include nitrogen ion-nitrogen molecule collisions; molecular collisions with surfaces; molecular identification from analysis of cracking patterns of selected gases; computer modelling of a quadrupole mass spectrometer; study of space charge in a quadrupole; transmission of the 127 deg cylindrical electrostatic analyzer; and mass spectrometer data deconvolution.

  16. Single and double charge transfer in Be/sup 4+/+He collisions: A molecular (Feshbach) approach

    SciTech Connect

    Martin, F.; Riera, A.; Yaez, M.

    1986-12-01

    In recent articles, we pointed out the fundamental difference between the molecular treatment of processes involving a multicharged ion and hydrogen or helium atoms, which is the (formal) autoionizing character of the molecular channels, and we reported a (new) implementation of the Feshbach method to calculate the molecular energies and couplings. In the present work we use the wave functions calculated with this Feshbach method for the BeHe/sup 4+/ quasimolecule, introduce a common translation factor in the formalism, and calculate the single and double charge-exchange cross sections in Be/sup 4+/+He(1s/sup 2/) collisions for impact energies 0.2--20 keV/amu. The mechanisms of the processes are discussed in detail.

  17. Excitation and charge transfer in He/sup +/ + H collisions. A molecular approach including two-electron translation factors

    SciTech Connect

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

    1983-06-01

    In a previous paper we have pointed out that the common-translation-factor (CTF) method is the only one which, at present, and within the framework of the molecular model of atomic collisions, can be shown to be both convergent and computationally fast, even for many-electron systems. In this Communication we check that this second statement is correct, presenting, for the first time, a molecular calculation involving two-electron translation factors, for He/sup +/ + H collisions. A careful study of the sensitivity of the calculated cross sections to the choice of the CTF is performed, and conclusions on that sensitivity are drawn, for several types of processes.

  18. ``Reaction Microscopes": New Frontiers in Atomic and Molecular Collisions

    NASA Astrophysics Data System (ADS)

    Ullrich, Joachim

    2005-05-01

    ``Reaction Microscopes'' -- the ``cloud chambers'' of atomic and molecular physics -- are based on novel many-particle imaging methods combined with cooling techniques for the preparation of the target. Determining in coincidence the complete vector momenta of several electrons and ions after the fragmentation of atoms, molecules or clusters, they allow to explore, for the first time, quantum dynamics at its very basic, thus fundamental and still unresolved level of a few interacting quantum particles on ultra-short time scales of atto- to femtoseconds (10-18 s -- 10-15 s). In a unique combination, large solid angles close to 4π and superior momentum resolutions around a few percent of an atomic unit are reached corresponding to energy resolution of sub-μeV for ions and meV for electrons. Hence, so-far unreachable frontiers in atomic and molecular many-particle quantum dynamics have become accessible! In the talk the working principle as well as the performance of newest machines will be highlighted. Forefront-experiments will be presented which image the complete final-state many-particle momentum-state for electron, ion and ultra-short laser pulse impact. For charged-particle induced single ionisation, such measurements have revealed troubling discrepancies between experimental results and state-of-the-art predictions. For electron-impact double-ionization of He, the strongly correlated four-particle Coulomb continuum has been explored, just 24 eV above threshold. Simultaneous ionisation and excitation was investigated in a first kinematically complete experiment and laser-assisted electron collisions have become accessible. Laser-assisted collisions, laser driven wave packets recolliding with their parent ions along with ultra-short pump-probe techniques point into the future direction where one might envision controlling quantum motion on an attosecond time scale.

  19. Laser-enhanced dynamics in molecular rate processes

    NASA Technical Reports Server (NTRS)

    George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.

    1978-01-01

    The present discussion deals with some theoretical aspects associated with the description of molecular rate processes in the presence of intense laser radiation, where the radiation actually interacts with the molecular dynamics. Whereas for weak and even moderately intense radiation, the absorption and stimulated emission of photons by a molecular system can be described by perturbative methods, for intense radiation, perturbation theory is usually not adequate. Limiting the analysis to the gas phase, an attempt is made to describe nonperturbative approaches applicable to the description of such processes (in the presence of intense laser radiation) as electronic energy transfer in molecular (in particular atom-atom) collisions; collision-induced ionization and emission; and unimolecular dissociation.

  20. Molecular dynamics based chemistry models of hypervelocity collisions of O(3P) + SO2(X, 1A1) in DSMC.

    PubMed

    Parsons, Neal; Levin, Deborah A; van Duin, Adri C T

    2013-01-28

    A significant process in the formation of the unique atmosphere of Io, a Jovian moon, is collision-induced dissociation of sulfur dioxide. The direct simulation Monte Carlo method (DSMC) is used to model the rarefied gas dynamics of the Ionian atmosphere. However, there is a lack of reliable reaction and collision cross sections needed for hypervelocity conditions. In this work, collisions between SO(2) and O were studied using molecular dynamics/quasi-classical trajectories methods with the potential of Murrell and a force field for reactive systems (ReaxFF). Dissociation to SO was found to be the significant reacting process, but at higher collision energies, complete atomization of SO(2) was found to frequently occur. In contrast, dissociation to O(2) was found to be mostly negligible and formation of SO(3) occurred only at low impact velocities. The chemistry and collision models developed from the Murrell and ReaxFF methods were implemented in DSMC simulations and compared to the baseline DSMC collision and reaction models. It was found that the selection of both the dissociation reaction cross section and the non-reactive collision model has a significant effect on the counterflow, shock gas dynamic structure. PMID:23387593

  1. Multiple-electron processes in fast ion-atom collisions

    SciTech Connect

    Schlachter, A.S.

    1989-03-01

    Research in atomic physics at the Lawrence Berkeley Laboratory Super-HILAC and Bevalac accelerators on multiple-electron processes in fast ion-atom collisions is described. Experiments have studied various aspects of the charge-transfer, ionization, and excitation processes. Examples of processes in which electron correlation plays a role are resonant transfer and excitation and Auger-electron emission. Processes in which electron behavior can generally be described as uncorrelated include ionization and charge transfer in high-energy ion-atom collisions. A variety of experiments and results for energies from 1 MeV/u to 420 MeV/u are presented. 20 refs., 15 figs.

  2. Inelastic processes in collisions of Na+, K+, Rb+ ions with He and Ar atoms

    NASA Astrophysics Data System (ADS)

    Kezerashvili, R. Ya.; Lomsadze, R. A.; Gochitashvili, M. R.; Mosulishvili, N. O.

    2015-05-01

    Absolute cross sections for charge-exchange, ionization, stripping and excitation for Na+ - Ar, K+ - He and Rb+ - Ar collisions were measured in the energy range 0.7- 7.0 keV. The experimental techniques include a condenser-plate method, angle-and-energy - dependent collision of product ions, energy loss and optical spectroscopy were used for an accurate determination of the structure of inelastic cross sections for these collisions. The experimental data are used to draw certain conclusions related to mechanisms of the corresponding processes. A correlation diagram of the adiabatic quasimolecular terms of these systems has been employed to discuss the mechanisms for these processes. It is shown that charge exchange in K+- He as well as in Rb+ - Ar collisions mostly occur through the channel resulting from the capture of the electron to the ground state of the atoms in regions of pseudo-crossing of the potential curves of 1 Σ symmetry. The primary ionization mechanism for all colliding pairs is investigated. Stripping in K+- He collisions (stripping in case of Na+, Rb+ - Ar were not observed) occurs via a mechanism involving a transition of adiabatic term into the continuum in the region of nonadiabatic interaction of molecular orbits with orbital angular moments which are identical in the limit of the united atom. The excitation mechanisms of collision partners are established.

  3. Attosecond timing the ultrafast charge-transfer process in atomic collisions

    SciTech Connect

    Hu, S. X.

    2011-04-15

    By solving the three-dimensional, time-dependent Schroedinger equation, we have demonstrated that the ultrafast charge-transfer process in ion-atom collisions can be mapped out with attosecond extreme uv (xuv) pulses. During the dynamic-charge transfer from the target atom to the projectile ion, the electron coherently populates the two sites of both nuclei, which can be viewed as a 'short-lived' molecular state. A probing attosecond xuv pulse can instantly unleash the delocalized electron from such a ''transient molecule,'' so that the resulting photoelectron may exhibit a ''double-slit'' interference. On the contrary, either reduced or no photoelectron interference will occur if the attosecond xuv pulse strikes well before or after the collision. Therefore, by monitoring the photoelectron interference visibility, one can precisely time the ultrafast charge-transfer process in atomic collisions with time-delayed attosecond xuv pulses.

  4. Rotational Cooling of HD+ Molecular Ions by Superelastic Collisions with Electrons

    NASA Astrophysics Data System (ADS)

    Shafir, D.; Novotny, S.; Buhr, H.; Altevogt, S.; Faure, A.; Grieser, M.; Harvey, A. G.; Heber, O.; Hoffmann, J.; Kreckel, H.; Lammich, L.; Nevo, I.; Pedersen, H. B.; Rubinstein, H.; Schneider, I. F.; Schwalm, D.; Tennyson, J.; Wolf, A.; Zajfman, D.

    2009-06-01

    Merging an HD+ beam with velocity matched electrons in a heavy ion storage ring we observed rapid cooling of the rotational excitations of the HD+ ions by superelastic collisions (SEC) with the electrons. The cooling process is well described using theoretical SEC rate coefficients obtained by combining the molecular R-matrix approach with the adiabatic nuclei rotation approximation. We verify the ΔJ=-2 SEC rate coefficients, which are predicted to be dominant as opposed to the ΔJ=-1 rates and to amount to (1-2)×10-6cm3s-1 for initial angular momentum states with J≤7, to within 30%.

  5. Computer simulations of solute exchange using micelles by a collision-driven fusion process.

    PubMed

    Li, Shuangyang; Zhang, Xianren; Dong, Wei; Wang, Wenchuan

    2008-09-01

    In this work, the kinetic process of collision-driven solute exchange in an aqueous phase in which micelles are used as solute carriers is investigated by dissipative particle dynamics simulations. Here, we try to answer two questions about the exchange process of hydrophobic solute molecules: How the solute molecules are exchanged and what factors affect the process. For the first question, the simulation results indicate that, after a stage of intermittent collision between two neighboring aggregates, there are roughly three sequential events in a coalescence stage: (1) molecular contact, (2) neck formation, and (3) neck growth. The coalescence stage is followed by a stage of solute transfer and diffusion. It is found that there are two rate-limiting steps in the whole process of solute exchange, i.e., the break of the water film between two neighboring aggregates and the nucleation of a pore between two surfactant films. For the second question, the effects of the collision velocity, the surface tension, the repulsive interaction between the surfactant films of the colliding aggregates, as well as the steric repulsion are examined. For example, the simulation results show that the depletion force plays an important role during the coalescence stage, while the initial collision velocity basically does not change the fusion ratio. The results also demonstrate that the surface tension and interaction show different effects on the different stages of a solute exchange process. PMID:18671419

  6. Wall-collision line broadening of molecular oxygen within nanoporous materials

    SciTech Connect

    Xu, Can T.; Lewander, Maerta; Andersson-Engels, Stefan; Svensson, Tomas; Svanberg, Sune; Adolfsson, Erik

    2011-10-15

    Wall-collision broadening of near-infrared absorption lines of molecular oxygen confined in nanoporous zirconia is studied by employing high-resolution diode-laser spectroscopy. The broadening is studied for pores of different sizes under a range of pressures, providing new insights on how wall collisions and intermolecular collisions influence the total spectroscopic line profile. The pressure series show that wall-collision broadening is relatively more prominent under reduced pressures, enabling sensitive means to probe pore sizes of porous materials. In addition, we show that the total wall-collision-broadened profile strongly deviates from a Voigt profile and that wall-collision broadening exhibits an additive-like behavior to the pressure and Doppler broadening.

  7. Electron-Nitrogen Collision Processes Relevant to Planetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Johnson, Paul

    2011-06-01

    Electron-N2 collisions play an important role in the nitrogen-rich upper atmospheres of Titan, Triton, and Earth. Modeling these processes requires accurate laboratory data. Despite the recognized importance of such data, there remained an unsatisfactory degree of consensus among much of the available laboratory collision cross section data. To address this situation, our group has devoted considerable effort over the past decade to improve the status of low energy electron collision data. In doing so, we have measured direct excitation cross sections for at least 17 electronic states of neutral N2 and a variety of key UV emission cross sections. Here we review the result of this effort, highlighting how the picture of electron collision processes has evolved, where consensus has been reached and where discrepancies still exist. New electron energy-loss measurements will be presented for excitation of the valence states, with finely spaced (<1eV) impact energy increments in the threshold-to-peak region where excitation is not in proportion to the Franck-Condon factors. These data are novel in that they include measurements at fixed electron scattering angles, differential in impact energy over a range of scattering angle. Also, new near-threshold integral cross sections are provided and compared to existing data.

  8. FORMATION OF MASSIVE MOLECULAR CLOUD CORES BY CLOUD-CLOUD COLLISION

    SciTech Connect

    Inoue, Tsuyoshi; Fukui, Yasuo

    2013-09-10

    Recent observations of molecular clouds around rich massive star clusters including NGC 3603, Westerlund 2, and M20 revealed that the formation of massive stars could be triggered by a cloud-cloud collision. By using three-dimensional, isothermal, magnetohydrodynamics simulations with the effect of self-gravity, we demonstrate that massive, gravitationally unstable, molecular cloud cores are formed behind the strong shock waves induced by cloud-cloud collision. We find that the massive molecular cloud cores have large effective Jeans mass owing to the enhancement of the magnetic field strength by shock compression and turbulence in the compressed layer. Our results predict that massive molecular cloud cores formed by the cloud-cloud collision are filamentary and threaded by magnetic fields perpendicular to the filament.

  9. Metastability of isoformyl ions in collisions with helium and hydrogen. [in interstellar molecular clouds

    NASA Technical Reports Server (NTRS)

    Green, S.

    1984-01-01

    The stability of HOC(+) ions under conditions in interstellar molecular clouds is considered. In particular, the possibility that collisions with helium or hydrogen will induce isomerization to the stable HCO(+) form is examined theoretically. Portions of the electronic potential energy surfaces for interaction with He and H atoms are obtained from standard quantum mechanical calculations. Collisions with He atoms are found to be totally ineffective for inducing isomerization. Collisions with H atoms are found to be ineffective at low interstellar temperatures owing to a small (about 500 K) barrier in the entrance channel; at higher temperatures where this barrier can be overcome, however, collisions with hydrogen atoms do result in conversion to the stable HCO(+) form. Although detailed calculations are not presented, it is argued that low-energy collisions with H2 molecules are also ineffective in destroying the metastable ion.

  10. Molecular dynamics simulation of energy exchanges during hydrogen collision with graphite sheets

    SciTech Connect

    Sun Jizhong; Li Shouyang; Wang Dezhen; Stirner, Thomas; Chen Junlin

    2010-06-15

    Experiments show that the energy of particles incident on divertor plates in fusion devices seldom exceeds 100 eV. Trim code and its variants are not suitable to predict the sputtering yield of carbon-based divertor plates for this energy range and, therefore, a dynamic model, taking into account the C-H bond formation and breaking, and the structure of carbon, is needed. In this paper, the molecular dynamics method is employed to investigate collision processes between incident hydrogen atoms and a graphene sheet. The simulation results demonstrate that the collision processes cannot be adequately described by a simple binary approximation. The energy transfer from the projectile to the graphite sheet exhibits a very complicated behavior when the kinetic energy of the incident hydrogen atom is below 30 eV, strongly depending on the impact position. When its kinetic energy is lower than 0.35 eV, the incident hydrogen is always reflected back from the single, perfect graphite sheet; when its kinetic energy is higher than 0.35 eV, then whether the incident particle penetrates the graphite sheet, is reflected back or is adsorbed depends on the impact position. In certain areas of the graphite sheet, either adsorption or reflection of an incident hydrogen atom can occur in two different energy ranges.

  11. The relationship between continental collision process and metamorphic pattern in the Himalayan collision belts

    NASA Astrophysics Data System (ADS)

    Oh, Chang-Whan

    2015-04-01

    Both UHP and HP eclogites are reported from the Kaghan Valley and Tso Morari Massif in the western part of the Himalayan collision belt (Ghazanfar and Chaudhry, 1987; Thakur, 1983). UHP eclogites in the Kaghan record peak metamorphic conditions of 770 °C and 30 kbar (O'Brien et al., 2001) and was retrograded into the epidote-amphibolite or blueschist (580-610 °C, 10-13 kbar; Lombardo and Rolfo, 2000). Sensitive high-resolution ion microprobe dating of zircon reveals that the UHP eclogite formed at ca. 46 Ma (Kaneko et al., 2003; Parrish et al., 2006). The Tso Morari UHP eclogite had formed at 750 °C, > 39 kbar (Mukheerjee et al., 2003; Bundy, 1980) and underwent amphibolite facies retro-grade metamorphism (580 °C, 11 kbar) during uplift (Guillot et al., 2008). Peak metamorphism of the Tso Morari Massif was dated at ca. 53-55 Ma (Leech et al., 2005). Only HP eclogites have been reported from the mid-eastern part of the Himalayan collision belt (Lombardo and Rolfo, 2000; Corrie et al., 2010). The HP eclogite in the mid-eastern part may have formed at ca. > 780 °C and 20 kbar and was overprinted by high-pressure granulite facies metamorphism (780-750°C, 12-10 kbar) at ca. 30 Ma (Groppo et al. 2007; Corrie et al., 2010). HP granulite (890 °C, 17-18 kbar) is reported from the NBS, at the eastern terminus of the Himalayan collision belt; the granulite was subjected to retrograde metamorphism to produce lower-pressure granulite (875-850°C, 10-5 kbar), representing near-isothermal decompression (Liu and Zhong, 1997). The HP granulite metamorphism may have occurred at ca. 22-25 Ma. Along the Himalayan collision belt, peak metamorphism changes eastward from UHP eclogite facies through HP eclogite facies to high-pressure granulite facies, indicating a progressive eastwards decrease in the depth of subduction of continental crust and an eastwards increase in the geothermal gradient. The peak metamorphic ages also decrease from 53-46 Ma in the west to 22-25 Ma in the east indicating propagation of collision towards east. The following collision model of the Himalayan collision belt is proposed based on data published in previous studies. Collision between the Indian and Asian blocks started in the west before ca. 55 Ma. In the western part, the amount of oceanic slab subducted prior to continent collision was enough to pull the continental crust down to the depths of UHP metamorphism, as a wide ocean existed between the Asian and Indian blocks prior to collision. Following UHP metamorphism, oceanic slab break-off started at ca. 55~46 Ma in the west due to the very strong buoyancy of the deeply subducted continental block. In contrast, the subduction of continental crust continued at this time in the middle and eastern parts of the belt. The zone of break-off migrated eastward, initiating a change from steep- to low-angle subduction. Final break-off may have occurred in the easternmost part of the belt at ca. 22-25 Ma. The depth of slab break-off decreased toward the east due to the westward decrease of the amount of subducted oceanic crust along the Himalayan collision belt, resulting eastwards decrease of an uplifting rate due to a decrease in buoyancy of the continental slab. The slower uplift resulted in a longer period of thermal relaxation and a higher geothermal gradient. In the west, the high rate of uplift resulted the epidote amphibolite facies (580-610°C) retrograde metamorphic overprint on the UHP eclogites, whereas the relatively slow uplift in the mid-eastern part caused high-grade granulites (850°C) retrograde metamorphic overprint on the HP eclogites. The study indicates that the metamorphic pattern along the collision belt is strongly related to the amount of subducted oceanic crust between continents before collision and the depth of slab break-off. Therefore metamorphic pattern can be used to interpret both the disappeared and ongoing tectonic process during continental collision.

  12. Elastic Cross Sections for Electron Collisions with Molecules Relevant to Plasma Processing

    SciTech Connect

    Yoon, J.-S.; Song, M.-Y.; Kato, H.; Hoshino, M.; Tanaka, H.; Brunger, M. J.; Buckman, S. J.; Cho, H.

    2010-09-15

    Absolute electron-impact cross sections for molecular targets, including their radicals, are important in developing plasma reactors and testing various plasma processing gases. Low-energy electron collision data for these gases are sparse and only the limited cross section data are available. In this report, elastic cross sections for electron-polyatomic molecule collisions are compiled and reviewed for 17 molecules relevant to plasma processing. Elastic cross sections are essential for the absolute scale conversion of inelastic cross sections, as well as for testing computational methods. Data are collected and reviewed for elastic differential, integral, and momentum transfer cross sections and, for each molecule, the recommended values of the cross section are presented. The literature has been surveyed through early 2010.

  13. Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

    NASA Astrophysics Data System (ADS)

    Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

    2016-05-01

    At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

  14. Charge transfer in collisions between diatomic molecular ions and atomic hydrogen using merged beams

    SciTech Connect

    Andrianarijaona, V. M.; Draganic, I. N.; Havener, C. C.; Seely, D. G.

    2011-12-15

    A merged-beam technique is used to measure charge transfer (CT) cross sections for the (O{sub 2}{sup +},D) and (CO{sup +},D) systems over a wide range of collision energy from 20 eV/u to 2 keV/u. At the higher energies where the collision is rovibrationally frozen and the differences in the Q values of the CT process can be neglected, the cross sections all converge to (7.5{+-}0.5)x10{sup -16} cm{sup 2} at 2 keV/u and are consistent with a rovibrational frozen (H{sub 2}{sup +},H) calculation. Toward lower velocities, (O{sub 2}{sup +},D) and (CO{sup +},D) have consistently similar cross sections but diverge below 60 eV/u. In contrast, previously reported merged-beam measurements for (D{sub 2}{sup +},H), a system with fewer electrons on the molecular core, no electronic excited states, and relatively fewer charge transfer channels, shows a decreasing cross section toward lower energies. These different trends are compared to previous merged-beam measurements of charge transfer with H for several atomic 4+ ions (Si{sup 4+}, Ne{sup 4+}, N{sup 4+}, and C{sup 4+}) which have a variety of electrons on the core.

  15. Desorption induced by atomic and molecular ion collisions on LiF

    SciTech Connect

    Pereira, J. A. M.; Silveira, E. F. da

    1999-06-10

    Atomic and molecular nitrogen ion beams, produced by the PUC-Rio Van de Graaff accelerator, were used to bombard lithium fluoride thin films. Desorption of secondary ions was measured by means of a time-of-flight mass spectrometer equipped with a double grid acceleration system. The outputs of the experiment are the axial kinetic energy distribution and the desorption yield of the emitted ions. This information allowed determination of the relative contribution to desorption due to collision cascades (nuclear sputtering) and to electronic excitation (electronic sputtering). It was observed that F{sup -} ions are desorbed as a result of collision cascades and that the F{sup -} ion yields depends linearly on the number of constuents in the projectile, i.e., Y(N{sub 2}{sup +})=2Y(N{sup +}). The emission of clusters such as (LiF)Li{sup +} was found to be caused by electronic excitation and the (LiF)Li{sup +} yield revealed a nonlinear dependence: Y(N{sub 2}{sup +})>2Y(N{sup +}). Both processes were found to contribute to Li{sup +} desorption. These effects are discussed in terms of the density of deposited energy which depends on the projectile velocity and on the electronic stopping power.

  16. Collision dynamics of methyl radicals and highly vibrationally excited molecules using crossed molecular beams

    SciTech Connect

    Chu, P.M.Y.

    1991-10-01

    The vibrational to translational (V{yields}T) energy transfer in collisions between large highly vibrationally excited polyatomics and rare gases was investigated by time-of-flight techniques. Two different methods, UV excitation followed by intemal conversion and infrared multiphoton excitation (IRMPE), were used to form vibrationally excited molecular beams of hexafluorobenzene and sulfur hexafluoride, respectively. The product translational energy was found to be independent of the vibrational excitation. These results indicate that the probability distribution function for V{yields}T energy transfer is peaked at zero. The collisional relaxation of large polyatomic molecules with rare gases most likely occurs through a rotationally mediated process. Photodissociation of nitrobenzene in a molecular beam was studied at 266 nm. Two primary dissociation channels were identified including simple bond rupture to produce nitrogen dioxide and phenyl radical and isomerization to form nitric oxide and phenoxy radical. The time-of-flight spectra indicate that simple bond rupture and isomerization occurs via two different mechanisms. Secondary dissociation of the phenoxy radicals to carbon monoxide and cyclopentadienyl radicals was observed as well as secondary photodissociation of phenyl radical to give H atom and benzyne. A supersonic methyl radical beam source is developed. The beam source configuration and conditions were optimized for CH{sub 3} production from the thermal decomposition of azomethane. Elastic scattering of methyl radical and neon was used to differentiate between the methyl radicals and the residual azomethane in the molecular beam.

  17. Atomic collision processes for modelling cool star spectra

    NASA Astrophysics Data System (ADS)

    Barklem, Paul

    2015-05-01

    The abundances of chemical elements in cool stars are very important in many problems in modern astrophysics. They provide unique insight into the chemical and dynamical evolution of the Galaxy, stellar processes such as mixing and gravitational settling, the Sun and its place in the Galaxy, and planet formation, to name a just few examples. Modern telescopes and spectrographs measure stellar spectral lines with precision of order 1 per cent, and planned surveys will provide such spectra for millions of stars. However, systematic errors in the interpretation of observed spectral lines leads to abundances with uncertainties greater than 20 per cent. Greater precision in the interpreted abundances should reasonably be expected to lead to significant discoveries, and improvements in atomic data used in stellar atmosphere models play a key role in achieving such advances in precision. In particular, departures from the classical assumption of local thermodynamic equilibrium (LTE) represent a significant uncertainty in the modelling of stellar spectra and thus derived chemical abundances. Non-LTE modelling requires large amounts of radiative and collisional data for the atomic species of interest. I will focus on inelastic collision processes due to electron and hydrogen atom impacts, the important perturbers in cool stars, and the progress that has been made. I will discuss the impact on non-LTE modelling, and what the modelling tells us about the types of collision processes that are important and the accuracy required. More specifically, processes of fundamentally quantum mechanical nature such as spin-changing collisions and charge transfer have been found to be very important in the non-LTE modelling of spectral lines of lithium, oxygen, sodium and magnesium.

  18. Non-equilibrium fission processes in intermediate energy nuclear collisions

    SciTech Connect

    Loveland, W.; Casey, C.; Xu, Z.; Seaborg, G.T.; Aleklett, K.; Sihver, L.

    1989-04-01

    We have measured the target fragment yields, angular and energy distributions for the interaction of 12-16 MeV/A/sup 32/S with /sup 165/Ho and /sup 197/Au and for the interaction of 32 and 44 MeV/A /sup 40/Ar with /sup 197/Au. The Au fission fragments associated with the peripheral collision peak in the folding angle distribution originate in a normal, ''slow'' fission process in which statistical equilibrium has been established. At the two lowest projectile energies, the Au fission fragments associated with the central collision peak in the folding angle distribution originate in part from ''fast'' (/tau//approximately//sup /minus/23/s), non-equilibrium processes. Most of the Ho fission fragments originate in non- equilibrium processes. The fast, non-equilibrium process giving rise to these fragments has many of the characteristics of ''fast fission'', but the cross sections associated with these fragments are larger than one would expect from current theories of ''fast fission. '' 14 refs., 8 figs.

  19. Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision.

    PubMed

    Li, Ying; Kalia, Rajiv K; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

    2016-05-14

    At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. PMID:27110831

  20. Parallelization of a Molecular Dynamics Simulation of AN Ion-Surface Collision System:

    NASA Astrophysics Data System (ADS)

    Atiş, Murat; Özdoğan, Cem; Güvenç, Ziya B.

    Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar-Ni(100) collision system and calculated physical quantities are presented.

  1. Mountain building processes during continent continent collision in the Uralides

    NASA Astrophysics Data System (ADS)

    Brown, D.; Juhlin, C.; Ayala, C.; Tryggvason, A.; Bea, F.; Alvarez-Marron, J.; Carbonell, R.; Seward, D.; Glasmacher, U.; Puchkov, V.; Perez-Estaun, A.

    2008-08-01

    Since the early 1990's the Paleozoic Uralide Orogen of Russia has been the target of a significant research initiative as part of EUROPROBE and GEODE, both European Science Foundation programmes. One of the main objectives of these research programmes was the determination of the tectonic processes that went into the formation of the orogen. In this review paper we focus on the Late Paleozoic continent-continent collision that took place between Laurussia and Kazakhstania. Research in the Uralides was concentrated around two deep seismic profiles crossing the orogen. These were accompanied by geological, geophysical, geochronological, geochemical, and low-temperature thermochronological studies. The seismic profiles demonstrate that the Uralides has an overall bivergent structural architecture, but with significantly different reflectivity characteristics from one tectonic zone to another. The integration of other types of data sets with the seismic data allows us to interpret what tectonic processes where responsible for the formation of the structural architecture, and when they were active. On the basis of these data, we suggest that the changes in the crustal-scale structural architecture indicate that there was significant partitioning of tectonothermal conditions and deformation from zone to zone across major fault systems, and between the lower and upper crust. Also, a number of the structural features revealed in the bivergent architecture of the orogen formed either in the Neoproterozoic or in the Paleozoic, prior to continent-continent collision. From the end of continent-continent collision to the present, low-temperature thermochronology suggests that the evolution of the Uralides has been dominated by erosion and slow exhumation. Despite some evidence for more recent topographic uplift, it has so far proven difficult to quantify it.

  2. Exclusive diffractive processes in electron-ion collisions

    NASA Astrophysics Data System (ADS)

    Toll, Tobias; Ullrich, Thomas

    2013-02-01

    We present a new technique to calculate the cross section for diffractive vector meson production and deeply virtual Compton scattering (DVCS) in electron-ion collisions based on the dipole model. The measurement of these processes can provide valuable information on nonlinear QCD phenomena, such as gluon saturation, and is the the only known way to gain insight into the spatial distribution of gluons in nuclei. We present predictions of differential cross-section distribution dσ/dQ2 and dσ/dt for J/ψ and ϕ meson production for diffractive processes of heavy nuclei, and demonstrate the feasibility of extracting the gluon source distribution of heavy nuclei, F(b), from coherent diffraction. We briefly introduce a new event generator based on our method that can be used for studying exclusive diffractive processes at a future electron-ion collider.

  3. Generalization of the Hartree-Fock approach to collision processes

    SciTech Connect

    Hahn, Y.

    1997-06-01

    The conventional Hartree and Hartree-Fock approaches for bound states are generalized to treat atomic collision processes. All the single-particle orbitals, for both bound and scattering states, are determined simultaneously by requiring full self-consistency. This generalization is achieved by introducing two {ital Ans{umlt a}tze}: (a) the weak asymptotic boundary condition, which maintains the correct scattering energy and target orbitals with correct number of nodes, and (b) square integrable amputated scattering functions to generate self-consistent field (SCF) potentials for the target orbitals. The exact initial target and final-state asymptotic wave functions are not required and thus need not be specified {ital a priori}, as they are determined simultaneously by the SCF iterations. To check the asymptotic behavior of the solution, the theory is applied to elastic electron-hydrogen scattering at low energies. The solution is found to be stable and the weak asymptotic condition is sufficient to produce the correct scattering amplitudes. The SCF potential for the target orbital shows the strong penetration by the projectile electron during the collision, but the exchange term tends to restore the original form. Potential applicabilities of this extension are discussed, including the treatment of ionization and shake-off processes. {copyright} {ital 1997} {ital The American Physical Society}

  4. Generalization of the Hartree-Fock approach to collision processes

    NASA Astrophysics Data System (ADS)

    Hahn, Yukap

    1997-06-01

    The conventional Hartree and Hartree-Fock approaches for bound states are generalized to treat atomic collision processes. All the single-particle orbitals, for both bound and scattering states, are determined simultaneously by requiring full self-consistency. This generalization is achieved by introducing two Ansäauttze: (a) the weak asymptotic boundary condition, which maintains the correct scattering energy and target orbitals with correct number of nodes, and (b) square integrable amputated scattering functions to generate self-consistent field (SCF) potentials for the target orbitals. The exact initial target and final-state asymptotic wave functions are not required and thus need not be specified a priori, as they are determined simultaneously by the SCF iterations. To check the asymptotic behavior of the solution, the theory is applied to elastic electron-hydrogen scattering at low energies. The solution is found to be stable and the weak asymptotic condition is sufficient to produce the correct scattering amplitudes. The SCF potential for the target orbital shows the strong penetration by the projectile electron during the collision, but the exchange term tends to restore the original form. Potential applicabilities of this extension are discussed, including the treatment of ionization and shake-off processes.

  5. Collision-induced vibrational absorption in molecular hydrogens

    SciTech Connect

    Reddy, S.P.

    1993-05-01

    Collision induced absorption (CIA) spectra of the first overtone bands of H{sub 2}, D{sub 2}, and HD have been recorded for gas densities up to 500 amagat at 77-300 K. Analyses of these spectra reveal that (1) contrary to the observations in the fundamental bands, the contribution of the isotropic overlap interaction to the first overtone bands is negligible, (2) the squares of the matrix elements B{sub 32}(R)/ea{sub o} [= {lambda}{sub 32} exp(-(R-{sigma})/{rho}{sub 32}) + 3 (R/a{sub o}){sup -4}] where the subscripts 3 and 2 represent L and {lambda}, respectively, account for the absorption intensity of the bands and (3) the mixed term, 2,3 {lambda}{sub 32} exp (-(R-{sigma})/{rho}{sub 32}) <{vert_bar}Q{vert_bar}> <{alpha}> (R/a){sup -4}, gives a negative contribution. In the CIA spectra of H{sub 2} in its second overtone region recorded at 77, 201 and 298 K for gas densities up to 1000 amagat, a dip in the Q branch with characteristic Q{sub p} and Q{sub R} components has been observed. The analysis of the absorption profiles reveals, in addition to the previously known effects, the occurrence of the triple-collision transitions of H{sub 2} of the type Q{sub 1}(J) + Q{sub 1}(J) + Q{sub 1}(J) for the first time. From the profile analysis the absorption coefficient of these transitions is obtained.

  6. Many-electron aspects of molecular promotion in ion-atom collisions - Production of core-excited states of Li in Li/+/-He collisions

    NASA Technical Reports Server (NTRS)

    Elston, S. B.; Vane, C. R.; Schumann, S.

    1979-01-01

    Production of core-excited autoionizing states of neutral Li having configurations of the form 1snln(prime)l(prime) has been observed over the impact-energy range from 10-50 keV. Although the results for production of all such states is remarkably consistent with a quasi-molecular-excitation model proposed by Stolterfoht and Leithaeuser (1976), production of individual lines in the observed spectra exhibits collision-velocity dependencies indicative of considerably more complex processes, including processes which appear to be inherently two-electron in nature. Excitation functions are presented for (1s2s/2/)/2/S, 1s(2s2p/3/P)/2/P, 1s(2s2p/1/P)/2/P, and (1s2p/2/)/2/D core-excited state of Li and for total core excitation.

  7. Shattering dissociation in high-energy molecular collisions between nitrate esters

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor V.; Dunlap, Brett I.

    2011-09-01

    We present ab initio molecular dynamics simulations of head-on collisions between ethyl nitrate molecules at collisional energies from 200 to 1200 kJ/mol. Above a threshold energy, an increasing fraction of the collisions led to rapid dissociation on impact—"shattering." The probability of the shattering dissociation was derived from the quasiclassical trajectories sampling the initial vibrational motion at Tvib = 300 K. Even for the zero impact parameter and a fixed orientation considered, the observed dissociation probability exhibited a wide spread (much larger than kTvib) as a function of the collision energy. This is attributed to variations in the initial vibrational phase. We propose a closed-form expression for the energy-dependent dissociation probability that captures the dependence on the phase and use it to analyze the probability of the shattering dissociation of a larger nitrate ester, pentaerythritol tetranitrate.

  8. Exclusive processes with a leading neutron in e p collisions

    NASA Astrophysics Data System (ADS)

    Gonçalves, V. P.; Navarra, F. S.; Spiering, D.

    2016-03-01

    In this paper we extend the color dipole formalism to the study of exclusive processes associated with a leading neutron in e p collisions at high energies. The exclusive ρ , ϕ and J /Ψ production, as well as the deeply virtual Compton scattering, are analyzed assuming a diffractive interaction between the color dipole and the pion emitted by the incident proton. We compare our predictions with the HERA data on ρ production and estimate the magnitude of the absorption corrections. We show that the color dipole formalism is able to describe the current data. Finally, we present our estimate for the exclusive cross sections which can be studied at HERA and in future electron-proton colliders.

  9. Molecular processes in a high temperature shock layer

    NASA Technical Reports Server (NTRS)

    Guberman, S. L.

    1984-01-01

    Models of the shock layer encountered by an Aeroassisted Orbital Transfer Vehicle require as input accurate cross sections and rate constants for the atomic and molecular processes that characterize the shock radiation. From the estimated atomic and molecular densities in the shock layer and the expected residence time of 1 m/s, it can be expected that electron-ion collision processes will be important in the shock model. Electron capture by molecular ions followed by dissociation, e.g., O2(+) + e(-) yields 0 + 0, can be expected to be of major importance since these processes are known to have high rates (e.g., 10 to the -7th power cu/cm/sec) at room temperature. However, there have been no experimental measurements of dissociative recombination (DR) at temperatures ( 12000K) that are expected to characterize the shock layer. Indeed, even at room temperature, it is often difficult to perform experiments that determine the dependence of the translational energy and quantum yields of the product atoms on the electronic and vibrational state of the reactant molecular ions. Presented are ab initio quantum chemical studies of DR for molecular ions that are likely to be important in the atmospheric shock layer.

  10. Indene formation under single-collision conditions from the reaction of phenyl radicals with allene and methylacetylene--a crossed molecular beam and ab initio study.

    PubMed

    Parker, Dorian S N; Zhang, Fangtong; Kaiser, Ralf I; Kislov, Vadim V; Mebel, Alexander M

    2011-11-01

    Polycyclic aromatic hydrocarbons (PAHs) are regarded as key intermediates in the molecular growth process that forms soot from incomplete fossil fuel combustion. Although heavily researched, the reaction mechanisms for PAH formation have only been investigated through bulk experiments; therefore, current models remain conjectural. We report the first observation of a directed synthesis of a PAH under single-collision conditions. By using a crossed-molecular-beam apparatus, phenyl radicals react with C(3)H(4) isomers, methylacetylene and allene, to form indene at collision energies of 45 kJ mol(-1). The reaction dynamics supported by theoretical calculations show that both isomers decay through the same collision complex, are indirect, have long lifetimes, and form indene in high yields. Through the use of deuterium-substituted reactants, we were able to identify the reaction pathway to indene. PMID:21956874

  11. Theoretical investigation of electron transfer and detachment processes in low energy H- + Li and Li- + H collisions

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Lin, X. H.; Yan, B.; Wang, J. G.; Janev, R. K.

    2016-02-01

    The charge exchange and collisional detachment processes in H- + Li and Li- + H collisions have been studied by using the quantal molecular orbital close-coupling (QMOCC) method in the energy ranges of about 0.12-1000 eV u-1 and 0.1 meV-1000 eV, respectively, and the inelastic collision cross sections and rate coefficients have been computed and presented. It is found that the electron transfer process in the H- + Li and Li- + H collisions is due to the Demkov coupling between the 12Σ+ and 22Σ+ states at internuclear distances of about 15a0. The collisional electron detachment in the considered collision system is due to the excitation of the remaining six states, which are all unstable against autodetachment. These states are populated through a series of Landau-Zener couplings of the 22Σ+ state with upper 2Σ+ states and by the rotational 2Σ+-2Π couplings at small internuclear distances. The cross sections for electron transfer in H- + Li and Li- + H collisions in the energy range of 10-1000 eV u-1 attain values in the range of 10-16-10-15 cm2 (reaching their maximum values of about 5 × 10-15 cm2 at 500-600 eV u-1), while the values of the corresponding electron detachment cross sections in this energy range attain generally smaller values.

  12. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  13. Charge Transfer in Collisions between Diatomic Molecular Ions and Atomic Hydrogen Using Merged Beams

    SciTech Connect

    Andrianarijaona, V. M.; Draganic, Ilija N; Seely, D. G.; Havener, Charles C

    2011-01-01

    A merged-beams technique is used to measure charge transfer (CT) cross sections for the (O2+,D) and (CO+,D) systems from 2 keV/u to 20 eV/u, which covers a wide range of energy: high energies where the collision is ro-vibrationally frozen to low energies where ro-vibrational modes become important. At high energies where the differences in the Q-values of the CT process can be neglected, the cross sections all converge to (7.5 0.5) x 10-16 cm2 at 2 keV/u and are consistent with a H2+ + H calculation which assumes the ro-vibrational modes are frozen. Toward lower velocities, (O2+,D) and (CO+,D) have consistently similar cross sections, as one might expect from the comparison of their characteristic vibrational time, but diverge below 60eV/u. In contrast, previously reported merged-beams measurements for (D2+,H), a system with fewer electrons on the molecular core, no electronic excited states and with relatively less charge transfer channels, shows a decreasing cross section toward lower energies. These different trends are compared to merged-beams measurements of charge transfer for several 4+ atomic ions that have a different number of electrons on the core.

  14. Quantum chemistry and molecular processes

    SciTech Connect

    Head-Gordon, M.

    1996-08-01

    This article gives an overview of modern electronic structure theory, which is the development of approximate quantum mechanical methods for calculating the ground and excited electronic states of molecules. A series of seven topics are discussed which have contributed to the present state of the field and that illustrate in a general way some of the essential physical models and approximations that underpin electronic structure calculations. These topics begin from the definition of theoretical model chemistries and the treatment of electron correlation by wave function-based techniques and density functional theory, for both molecular energies and a range of molecular properties. Beyond these main theoretical issues, questions of chemical interpretation, computational algorithms, and the modeling of surrounding environment are also discussed. Collectively these topics define many of the classes of chemical problems which can be reliably and feasibly solved by such calculations at present, and conversely they also serve to define a number of unresolved challenges for the future. 77 refs., 3 figs.

  15. Estimates of Collisional Cooling and Quenching Rates for Atomic and Molecular Ion Collisions with Ultracold Atoms.

    NASA Astrophysics Data System (ADS)

    Smith, Winthrop; Wells, James

    2009-05-01

    Translational cross sections and rate coefficients for cold ion-neutral elastic and charge-exchange collisions (either atomic or molecular) are >> larger (˜10^6 a.u.) than neutral-neutral collisions at the same CM energy. This is due to the long range polarization potential V(R) = -C4/R^4, where C4 is proportional to the polarizability of the neutral partner. Thus collisions between ultracold alkali atoms (trapped in a magneto-optic trap or MOT) and low-energy ions can be used for sympathetic cooling experiments. We are building a prototype hybrid-trap apparatus [1] that applies these principles to collisions of Ca^+ ions (which can be laser pre-cooled) with MOT-trapped ultracold Na atoms. Some calculations on this system and other related ion-neutral systems have been published [2] and some initial experiments on other ion-neutral species have begun [3]. Estimates of cooling and quenching rates in the low K-mK CM energy range for Ca+ on Na and other cases will be presented and possible experiments described. [1] Winthrop W. Smith, Oleg P. Makarov and Jian Lin, J. Modern Optics 52, 2253 (2005). [2] R. Côt'e and A. Dalgarno, Phys. Rev. A 62, 012709 (2000); R. Côt'e, Phys. Rev. Lett. 85, 5316 (2000). [3] A. Grier, M. Cetina, F.Orucevic, and V. Vuletic, ArXiv atom-ph/0808.3620.

  16. Quantifying Plasma Collision Processes in Xenon Powered Electric Propulsion Systems

    NASA Astrophysics Data System (ADS)

    Dressler, Rainer A.; Chiu, Yu-hui

    2011-05-01

    The use of xenon plasma electrostatic space propulsion systems for low-thrust applications is growing rapidly due to the significant propellant mass savings associated with the high specific impulse of the engines. The high expense of the propellant drives the cost of ground-based testing, which lacks many attributes of in-space conditions. The cost-effective performance and integration optimization of these propulsion systems, consequently, is highly dependent on models that correctly render the static plasma properties and its outflow from the engine at arbitrary conditions. A primary impediment to the accuracy of models is quantitative data such as energy dependent cross sections for a multitude of collision processes that govern the plasma properties. We present a review of theoretical and experimental advances in determining vital cross sections and their implementation in models of electrostatic thruster plasmas. Experimentally validated theoretical charge exchange and xenon ion differential scattering cross sections have led to improved modeling of the angular distribution of Hall Effect thruster plume ion currents. New cross sections for inelastic electron and xenon ion scattering on xenon atoms, including atoms in the 5p56s J = 2 metastable state, have led to the development of a collisional radiative model that predicts local electron temperatures from near-infrared spectral intensities.

  17. Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

    PubMed

    Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

    2011-12-29

    Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. PMID:22082054

  18. The Accuracy of Molecular Processes

    NASA Astrophysics Data System (ADS)

    Stavans, Joel

    Recombination is arguably one of the most fundamental mechanisms driving genetic diversity during evolution. Recombination takes place in one way or another from viruses such as HIV and polio, to bacteria, and finally to man. In both prokaryotes and eukaryotes, homologous recombination is assisted by enzymes, recombinases, that promote the exchange of strands between two segments of DNA, thereby creating new genetic combinations. In bacteria, homologous recombination takes place as a pathway for the repair of DNA lesions and also during horizontal or lateral gene transfer processes, in which cells take in exogenous pieces of DNA. This allows bacteria to evolve rapidly by acquiring large sequences of DNA, a process which would take too long by gene duplications and single mutations. I will survey recent results on the fidelity of homologous recombination as catalyzed by the bacterial recombinase RecA. These results show discrimination up to the level of single base mismatches, during the initial stages of the recombination process. A cascaded kinetic proofreading process is proposed to explain this high discrimination. Kinetic proofreading ideas are also reviewed.

  19. Analyzing collision processes with the smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2014-02-01

    It has been illustrated several times how the built-in acceleration sensors of smartphones can be used gainfully for quantitative experiments in school and university settings (see the overview in Ref. 1). The physical issues in that case are manifold and apply, for example, to free fall,2 radial acceleration,3 several pendula, or the exploitation of everyday contexts.6 This paper supplements these applications and presents an experiment to study elastic and inelastic collisions. In addition to the masses of the two impact partners, their velocities before and after the collision are of importance, and these velocities can be determined by numerical integration of the measured acceleration profile.

  20. Molecular Dynamics Simulation of Defect Production in Collision Cascades in Zircon

    SciTech Connect

    Devanathan, Ram; Corrales, Louis R.; Weber, William J.; Chartier, Alain; Meis, Constantin

    2005-01-01

    Defect production in collision cascades in zircon has been examined by molecular dynamics simulations using a partial charge model combined with the Ziegler-Biersack-Littmark potential. U, Zr, Si and O recoils with energies ranging from 250 eV to 5 keV were simulated in the NVE ensemble. To obtain good statistics, 5-10 cascades in randomly chosen directions were simulated for each ion and energy. The damage consists of mainly Si and O Frenkel pairs, a smaller number of Zr Frenkel pairs, and Zr on Si antisite defects. Defect production, interstitial clustering, ion beam mixing and Si-O-Si polymerization increase with PKA mass and energy.

  1. Comparison of binary collision approximation and molecular dynamics for displacement cascades in GaAs.

    SciTech Connect

    Foiles, Stephen Martin

    2011-10-01

    The predictions of binary collision approximation (BCA) and molecular dynamics (MD) simulations of displacement cascades in GaAs are compared. There are three issues addressed in this work. The first is the optimal choice of the effective displacement threshold to use in the BCA calculations to obtain the best agreement with MD results. Second, the spatial correlations of point defects are compared. This is related to the level of clustering that occurs for different types of radiation. Finally, the size and structure of amorphous zones seen in the MD simulations is summarized. BCA simulations are not able to predict the formation of amorphous material.

  2. Overview on collision processes of highly charged ions with atoms present status and problems

    SciTech Connect

    Janev, R.K.

    1983-05-01

    This paper provides a brief discussion on the present status of the collision physics of highly charged ions with atoms. The emphasis is on the main achievements in understanding and describing the most important collision processes, and as charge transfer, ionization and Auger-type processes, and even more on those open problems which, due either to their scientific or practical importance, represent challenges to current research in this field. The paper concentrates on general ideas and problems whose development and solutions have advanced or will advance our basic understanding of the collision dynamics of multiply charged ions with atoms.

  3. A Investigation of a Possible Molecular Effect in Ion Atom Collision Using a Gaseous Argon Target

    NASA Astrophysics Data System (ADS)

    Arora, Sanjeev

    1992-01-01

    The present work deals with an investigation of the molecular effect, which is defined as the difference in experimental results using isotachic atomic ion and molecular ion beams in ion atom collisions. Previous studies have dealt almost exclusively with total cross section measurements. This thesis explores the idea that the molecular effect may be more pronounced in the differential ionization probability of the target atoms. Also, a gaseous argon target of sufficiently low density was used in order to ensure that the two correlated protons in the H _2^{+} beam did not interact with two adjacent target atoms simultaneously. We report that, contrary to the expectations noted above, the molecular effect in the K shell differential ionization probability of argon for scattering angles up to 90^circ appears to be no more than the molecular effect in the total ionization probability. The uncertainity in our results is statistical in nature and can be improved upon by running the experiment for a longer duration of time.

  4. Bibliography of atomic and molecular processes, 1983

    SciTech Connect

    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.

    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.

  5. 1982 bibliography of atomic and molecular processes

    SciTech Connect

    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.

    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.

  6. 1985 bibliography of atomic and molecular processes

    SciTech Connect

    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.

    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.

  7. 1984 Bibliography of atomic and molecular processes

    SciTech Connect

    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.

    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. Towards the simulation of molecular collisions with a superconducting quantum computer

    NASA Astrophysics Data System (ADS)

    Geller, Michael

    2013-05-01

    I will discuss the prospects for the use of large-scale, error-corrected quantum computers to simulate complex quantum dynamics such as molecular collisions. This will likely require millions qubits. I will also discuss an alternative approach [M. R. Geller et al., arXiv:1210.5260] that is ideally suited for today's superconducting circuits, which uses the single-excitation subspace (SES) of a system of n tunably coupled qubits. The SES method allows many operations in the unitary group SU(n) to be implemented in a single step, bypassing the need for elementary gates, thereby making large computations possible without error correction. The method enables universal quantum simulation, including simulation of the time-dependent Schrodinger equation, and we argue that a 1000-qubit SES processor should be capable of achieving quantum speedup relative to a petaflop supercomputer. We speculate on the utility and practicality of such a simulator for atomic and molecular collision physics. Work supported by the US National Science Foundation CDI program.

  9. The effects of molecular collisions between the mobile phase and the solute in gas-solid chromatography.

    PubMed

    Zhang, Dali; Ke, Jiajun; Lu, Lizhu

    2015-10-01

    In chromatographic processes, molecular collisions between the mobile phase and the solute result in the transfer of kinetic energy. Based on these interactions, the relationship between the gauge pressure of the carrier gas at the column inlet and the partition frequency of the solute is derived; consequently, the relationship between the column temperature and partition frequency can be obtained. These relationships have been experimentally validated. The change in the peak shape described herein has been successfully explained using this relationship: the partition frequency was calculated from the theoretical plate number of a tailing peak. We propose a new mechanism for peak tailing using plate theory, which states that as the number of plates increases, the symmetry of the peak increases. PMID:26227076

  10. STAR FORMATION IN DISK GALAXIES. I. FORMATION AND EVOLUTION OF GIANT MOLECULAR CLOUDS VIA GRAVITATIONAL INSTABILITY AND CLOUD COLLISIONS

    SciTech Connect

    Tasker, Elizabeth J.; Tan, Jonathan C.

    2009-07-20

    We investigate the formation and evolution of giant molecular clouds (GMCs) in a Milky-Way-like disk galaxy with a flat rotation curve. We perform a series of three-dimensional adaptive mesh refinement numerical simulations that follow both the global evolution on scales of {approx}20 kpc and resolve down to scales {approx}<10 pc with a multiphase atomic interstellar medium. In this first study, we omit star formation and feedback, and focus on the processes of gravitational instability and cloud collisions and interactions. We define clouds as regions with n {sub H} {>=} 100 cm{sup -3} and track the evolution of individual clouds as they orbit through the galaxy from their birth to their eventual destruction via merger or via destructive collision with another cloud. After {approx}140 Myr a large fraction of the gas in the disk has fragmented into clouds with masses {approx}10{sup 6} M {sub sun} and a mass spectrum similar to that of Galactic GMCs. The disk settles into a quasi-steady-state in which gravitational scattering of clouds keeps the disk near the threshold of global gravitational instability. The cloud collision time is found to be a small fraction, {approx}1/5, of the orbital time, and this is an efficient mechanism to inject turbulence into the clouds. This helps to keep clouds only moderately gravitationally bound, with virial parameters of order unity. Many other observed GMC properties, such as mass surface density, angular momentum, velocity dispersion, and vertical distribution, can be accounted for in this simple model with no stellar feedback.

  11. Resource Paper: Molecular Excited State Relaxation Processes.

    ERIC Educational Resources Information Center

    Rhodes, William

    1979-01-01

    Develops the concept of oscillatory v dissipative limits as it applies to electronic excited state processes in molecular systems. Main emphasis is placed on the radiative and nonradiative dynamics of the excited state of a molecule prepared by interaction with light or some other excitation source. (BT)

  12. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K.; Brinker, Charles Jeffrey

    1998-01-01

    A process for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film.

  13. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K.; Brinker, Charles Jeffrey

    1999-01-01

    A process for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film.

  14. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, N.K.; Brinker, C.J.

    1999-08-10

    A process is described for producing a molecular sieve silica membrane comprising depositing a hybrid organic-inorganic polymer comprising at least one organic constituent and at least one inorganic constituent on a porous substrate material and removing at least a portion of the at least one organic constituent of the hybrid organic-inorganic polymer, forming a porous film. 11 figs.

  15. Quasi-molecular processes in dense plasmas

    SciTech Connect

    Younger, S.M.

    1991-01-01

    Quasi-molecular phenomena occur in dense plasmas when the interatomic spacing is comparable to the characteristic wavelength of the electrons. If the electronic states are bound, covalent orbitals arise with different excitation energies, radiative rates, and collisional rates than for isolated ions. For continuum electrons, charge localization near transient clusters of nuclei can influence many scattering and transport processes. We identify several novel consequences of quasi-molecular phenomena in plasmas and give a possible explanation of high energy features associated with helium-like emissions lines observed in recent inertial fusion experiments. 7 refs.

  16. Cloud-cloud collision in the Galactic center 50 km s-1 molecular cloud

    NASA Astrophysics Data System (ADS)

    Tsuboi, Masato; Miyazaki, Atsushi; Uehara, Kenta

    2015-12-01

    We performed a search of star-forming sites influenced by external factors, such as SNRs, H II regions, and cloud-cloud collisions (CCCs), to understand the star-forming activity in the Galactic center region using the NRO Galactic Center Survey in SiO v = 0, J = 2-1, H13CO+J = 1-0, and CS J = 1-0 emission lines obtained with the Nobeyama 45 m telescope. We found a half-shell-like feature (HSF) with a high integrated line intensity ratio of ∫TB(SiO v = 0, J = 2-1)dv/∫TB(H13CO+J = 1-0)dv ˜ 6-8 in the 50 km s-1 molecular cloud; the HSF is a most conspicuous molecular cloud in the region and harbors an active star-forming site where several compact H II regions can be seen. The high ratio in the HSF indicates that the cloud contains huge shocked molecular gas. The HSF can be also seen as a half-shell feature in the position-velocity diagram. A hypothesis explaining the chemical and kinetic properties of the HSF is that the feature originates from a CCC. We analyzed the CS J = 1-0 emission line data obtained with the Nobeyama Millimeter Array to reveal the relation between the HSF and the molecular cloud cores in the cloud. We made a cumulative core mass function (CMF) of the molecular cloud cores within the HSF. The CMF in the CCC region is not truncated at least up to ˜2500 M⊙, although the CMF of the non-CCC region reaches the upper limit of ˜1500 M⊙. Most massive molecular cores with Mgas > 750 M⊙ are located only around the ridge of the HSF and adjoin the compact H II region. These may be a sign of massive star formation induced by CCCs in the Galactic center region.

  17. Formation of giant molecular clouds in global spiral structures: The role of orbital dynamics and cloud-cloud collisions

    NASA Technical Reports Server (NTRS)

    Roberts, W. W., Jr.; Stewart, G. R.

    1987-01-01

    The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.

  18. Phase-index problem in the semiclassical description of molecular collisions

    NASA Astrophysics Data System (ADS)

    Bonnet, L.; Crespos, C.

    2008-12-01

    Semiclassical approaches of molecular collisions as proposed by Miller and Marcus involve phase indices, related to focal and turning points along trajectories contributing to S matrix elements. The main purpose of the work is to revisit the previous approaches in the case of two degrees of freedom rotationally inelastic collisions so as to make phase indices explicitly appear from first principles. Classical S matrix theory (CSMT) and three semiclassical initial value representation (SCIVR) treatments, respectively involving simple, double, and triple integrals, are considered. The phase index is either the Maslov index of the classical configuration space Green function (CSMT and the first two SCIVR methods), or the Maslov index of the Van Vleck-Gutzwiller space-time propagator (third SCIVR method). In order to assess the validity of the four previous approaches, their predictions are compared with exact quantum scattering results for interaction potentials leading to strong quantum interferences. The Gaussian weighting procedure, recently introduced in the quasiclassical trajectory method, is used here for practical CSMT calculations. We finally discuss the standard application of CSMT in the light of the previous developments and results.

  19. Understanding molecular scale effects during photoresist processing

    NASA Astrophysics Data System (ADS)

    Schmid, Gerard Michael

    2003-06-01

    The dimensional tolerances of photoresist features are now at the nanometer scale, where effects of individual molecules are important. In recognition of the industrial need for a molecular-scale understanding of photoresist performance, mechanistic models have been developed for each of the several photolithography processes that are used with positive-tone, chemically amplified photoresists: film creation, exposure, post exposure bake, and development. These models are based on experimental studies that have clarified details of photoresist function including the photochemical quantum efficiency of photoresist exposure, the reaction-diffusion properties of exposure photoproducts, and the complex dissolution behavior of phenolic homopolymers and copolymers in aqueous base. A dynamic Monte Carlo simulation has been developed to test the experimentally derived models and further examine the underlying physical processes relevant to photoresist patterning. This mesoscale simulation consists of distinct modules for each processing step, each of which captures the appropriate chemical and physical phenomena at the molecular scale. The several simulation modules have yielded results that are qualitatively correct for every major resist processing step. The inputs to the simulation are fundamental and measurable material and processing parameters and empirical calibrations are not required. The chemical detail included in the models enables investigation of the wide formulation variable space. Furthermore, the mesoscale nature of the simulation offers the unique ability to study the stochastic processes that contribute to resist feature roughness. This simulation thus provides a useful predictive tool to guide the rational design of new photoresist materials and the optimization of photolithography processes.

  20. Recommended direct simulation Monte Carlo collision model parameters for modeling ionized air transport processes

    NASA Astrophysics Data System (ADS)

    Swaminathan-Gopalan, Krishnan; Stephani, Kelly A.

    2016-02-01

    A systematic approach for calibrating the direct simulation Monte Carlo (DSMC) collision model parameters to achieve consistency in the transport processes is presented. The DSMC collision cross section model parameters are calibrated for high temperature atmospheric conditions by matching the collision integrals from DSMC against ab initio based collision integrals that are currently employed in the Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) and Data Parallel Line Relaxation (DPLR) high temperature computational fluid dynamics solvers. The DSMC parameter values are computed for the widely used Variable Hard Sphere (VHS) and the Variable Soft Sphere (VSS) models using the collision-specific pairing approach. The recommended best-fit VHS/VSS parameter values are provided over a temperature range of 1000-20 000 K for a thirteen-species ionized air mixture. Use of the VSS model is necessary to achieve consistency in transport processes of ionized gases. The agreement of the VSS model transport properties with the transport properties as determined by the ab initio collision integral fits was found to be within 6% in the entire temperature range, regardless of the composition of the mixture. The recommended model parameter values can be readily applied to any gas mixture involving binary collisional interactions between the chemical species presented for the specified temperature range.

  1. Inelastic processes in Ne+ and Ar+ collisions with Mg and Y surfaces leading to scattered-ion fractions and vacuum-ultraviolet photon emission

    NASA Astrophysics Data System (ADS)

    Rabalais, J. Wayne; Chen, Jie-Nan; Kumar, Ranjit

    1985-09-01

    Collisions of kiloelectronvolt Ne+ on Mg and Ar+ on Y yield scattered-ion fractions as high as 70% and 38%, respectively, and 1,3P--> 1S resonance radiation from the excited neutral projectile atoms in the vacuum ultraviolet range 30-200 nm. These data, along with that from the oxidized and hydroxylated surfaces, show that electron promotions within the molecular orbitals of the quasidiatomic molecule formed during the close encounter are a significant, if not dominating, process in kiloelectronvolt ion-surface collisions.

  2. Angular dependent post-collision interaction in Auger processes

    NASA Astrophysics Data System (ADS)

    van der Straten, P.; Morgenstern, R.; Niehaus, A.

    1988-03-01

    We have reformulated the theory of post-collision interaction (PCI) for Auger-decay following inner-shell photoionisation in order to take the time into account with the Auger-electron need to overtake the slow electron. The energy-shift of the Auger-electron due to PCI is calculated by solving in a reasonable approximation the classical equation of motion for the Auger electron. In contrast to the theory of Russek and Mehlhorn we derive analytical expressions for the transition amplitude, the line shape and the line shift of the Auger-electrons. If in our model the Auger electron and the slow electron are treated uncorrelated in direction our analytical expressions agree well with the numerical results of Russek and Mehlhorn. However if we account for directional electron-electron correlations, we show that deviations from the theory of Russek and Mehlhorn are to be expected. The possibility of detecting these deviations is discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    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 wave function. 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 [CH_2(tilde{X}^3B_1)] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH_2(tilde{X}^3B_1) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations 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 occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH_2(tilde{X}^3B_1) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.

  4. Theory of molecular rate processes in the presence of intense laser radiation

    NASA Technical Reports Server (NTRS)

    George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.; Lin, J.-T.

    1979-01-01

    The present paper deals with the influence of intense laser radiation on gas-phase molecular rate processes. Representations of the radiation field, the particle system, and the interaction involving these two entities are discussed from a general rather than abstract point of view. The theoretical methods applied are outlined, and the formalism employed is illustrated by application to a variety of specific processes. Quantum mechanical and semiclassical treatments of representative atom-atom and atom-diatom collision processes in the presence of a field are examined, and examples of bound-continuum processes and heterogeneous catalysis are discussed within the framework of both quantum-mechanical and semiclassical theories.

  5. Molecular-state treatment of collisions between protons and He/sup +/ ions

    SciTech Connect

    Winter, T.G.; Hatton, G.J.; Lane, N.F.

    1980-09-01

    Cross sections have been calculated for electron transfer into all states of H in collisions of protons and /sup 4/He/sup +/ ions at center-of-mass energies from 1.6 to 14 keV. Excitation of the 2s, 2p/sub 0/, and 2p/sub 1/ states of He/sup +/ has also been considered. The coupled-molecular-state calculations incorporate matrix elements and potential curves determined previously for up to ten molecular states 1ssigma, 2ssigma, ..., 3ddelta and up to 22 states 1ssigma, 2ssigma, ..., 4fphi 5gsigma, 5g..pi.. in treatments with and without plane-wave translational factors, respectively. The departure from rectilinear trajectories has been estimated to affect the electron-transfer cross sections by less than 7% at energies above 1.6 keV. The present results show very good agreement with the magnitude and structure of a recent experimental cross-section curve.

  6. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  7. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

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

    SciTech Connect

    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 role 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 role 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 via ion-induced dipole collisions with the bound electrons. The ions are thus important in randomising and equilibrating the velocity distribution of atomic products of molecular dissociation.

  9. Ab-initio molecular treatment of the symmetric Mg2+-Mg charge transfer process

    NASA Astrophysics Data System (ADS)

    Amami, M.; Moussa, A.; Zaidi, A.; Lahmar, S.; Bacchus-Montabonel, M. C.

    2016-02-01

    Potential energy curves of the MgMg2+ molecular system in the lowest electronic states as well as radial and rotational couplings between these states are obtained from ab-initio calculations at the CASSCF/MRCI level of theory using large basis sets. These data are used to investigate, via the semi-classical molecular close coupling method, the single symmetric charge transfer processes of Mg2+-Mg collisions in the [1.0-650] keV laboratory energy range. Total and partial cross sections for the expected capture channels are calculated and compared with the available experimental and theoretical results.

  10. Laboratory studies of atomic collision processes of importance in planetary atmospheres

    NASA Technical Reports Server (NTRS)

    Stebbings, R. F.; Smith, K.

    1985-01-01

    A series of differential cross sections for angular scattering and charge transfer was measured. These studies employ position-sensitive detectors (PSD's) to collect collision products scattered over a wide range of angles; and the research program includes investigation of differential cross sections for total angular scattering, charge transfer, stripping, and other collisions. All of these processes can be studied with the same basic apparatus, but minor modifications in the equipment details and in the data acquisition programs and techniques are required for each individual experiment.

  11. Double pendulum model for a tennis stroke including a collision process

    NASA Astrophysics Data System (ADS)

    Youn, Sun-Hyun

    2015-10-01

    By means of adding a collision process between the ball and racket in the double pendulum model, we analyzed the tennis stroke. The ball and the racket system may be accelerated during the collision time; thus, the speed of the rebound ball does not simply depend on the angular velocity of the racket. A higher angular velocity sometimes gives a lower rebound ball speed. We numerically showed that the proper time-lagged racket rotation increased the speed of the rebound ball by 20%. We also showed that the elbow should move in the proper direction in order to add the angular velocity of the racket.

  12. Quantum theory of molecular collisions in a magnetic field: Efficient calculations based on the total angular momentum representation

    NASA Astrophysics Data System (ADS)

    Tscherbul, T. V.; Dalgarno, A.

    2010-11-01

    An efficient method is presented for rigorous quantum calculations of atom-molecule and molecule-molecule collisions in a magnetic field. The method is based on the expansion of the wave function of the collision complex in basis functions with well-defined total angular momentum in the body-fixed coordinate frame. We outline the general theory of the method for collisions of diatomic molecules in the ?2 and ?3 electronic states with structureless atoms and with unlike ?2 and ?3 molecules. The cross sections for elastic scattering and Zeeman relaxation in low-temperature collisions of CaH(?+2) and NH(?-3) molecules with H3e atoms converge quickly with respect to the number of total angular momentum states included in the basis set, leading to a dramatic (>10-fold) enhancement in computational efficiency compared to the previously used methods [A. Volpi and J. L. Bohn, Phys. Rev. A 65, 052712 (2002); R. V. Krems and A. Dalgarno, J. Chem. Phys. 120, 2296 (2004)]. Our approach is thus well suited for theoretical studies of strongly anisotropic molecular collisions in the presence of external electromagnetic fields.

  13. Effects of molecular rotation in low-energy electron collisions of H3+.

    PubMed

    Wolf, Andreas; Kreckel, H; Lammich, L; Strasser, D; Mikosch, J; Glosík, J; Plasil, R; Altevogt, S; Andrianarijaona, V; Buhr, H; Hoffmann, J; Lestinsky, M; Nevo, I; Novotny, S; Orlov, D A; Pedersen, H B; Terekhov, A S; Toker, J; Wester, R; Gerlich, D; Schwalm, D; Zajfman, D

    2006-11-15

    Measurements on the energetic structure of the dissociative recombination rate coefficient in the millielectronvolt range are described for H3+ ions produced in the lowest rotational levels by collisional cooling and stored as a fast beam in the magnetic storage ring TSR (Test Storage Ring). The observed resonant structure is consistent with that found previously at the storage ring facility CRYRING in Stockholm, Sweden; theoretical predictions yield good agreement on the overall size of the rate coefficient, but do not reproduce the detailed structure. First studies on the nuclear spin symmetry influencing the lowest level populations show a small effect different from the theoretical predictions. Heating processes in the residual gas and by collisions with energetic electrons, as well as cooling owing to interaction with cold electrons, were observed in long-time storage experiments, using the low-energy dissociative recombination rate coefficient as a probe, and their consistency with the recent cold H3+ measurements is discussed. PMID:17015371

  14. Final Report. The 2015 Conference on the Dynamics of Molecular Collisions

    SciTech Connect

    Suits, Arthur G.

    2015-08-31

    The 25th The Conference on the Dynamics of Molecular Collisions (DMC) was held from July 12-17, 2015. The Conference provides a unique platform and focal point for the gathering of experimentalists and theoreticians in the field of chemical dynamics. Since its inauguration in 1965, it has played an irreplaceable role in the development of this field and of many distinguished careers. This 25th meeting was highly successful. We held ten oral sessions and four poster sessions. Nobel Laureate Yuan T. Lee presented the keynote lecture. At this meeting, celebrating 50 years of chemical reaction dynamics, one hundred thirty-seven attendees participated, forty-two talks were presented as well as fifty-nine posters.Many attendees remarked that it was the “best meeting of the year.” Results from the meeting and other contributions were collected in a special issue of the Journal of Physical Chemistry A, published December 17, 2015. With this proposal we sought support for students, post-doctoral researchers and junior scientists who needed financial support. The Department of Energy has a large program in gas phase chemistry and many of the speakers and session chairs at the meeting are presently supported by DOE, including Professor Millard Alexander and Carl Lineberger, the recipents of the 2015 Herschbach Prizes that were awarded at the meeting. Funds were used to supplement registration fees for students and post-docs and to cover registration fees for the six selected “hot topic” presentations.

  15. Molecular Visualization of the Spreading Process

    NASA Astrophysics Data System (ADS)

    Xu, Hui; Beers, Kathryn; Matyjaszewski, Krzysztof; Rubinstein, Michael

    2005-03-01

    We carried out atomic force microscopy studies of a polymer melt spontaneously spreading on a solid substrate with molecular resolution. Along with the position of the contact line, AFM enabled clear visualization of the molecules at every stage of the spreading process. Thus, one obtained direct information about (i) the position of the center of mass, (ii) orientation, and (iii) the local curvature for every individual molecule in its unique environment. Three characteristic rates, i.e. the spreading rate of the precursor film Dspread=(3.9±0.2)x10^ 3 nm^2/s, the flow-induced diffusion rate of molecules within the film Dinduced=1.3±0.1 nm^2/s, and the thermal diffusion coefficient of single molecules Dtherm<=0.10±0.03 nm^2/s, were independently measured. Since Dspread>>Dinduced, plug flow of polymer chains was identified as the main mass-transport mechanism of spreading with insignificant contribution from the molecular diffusion.

  16. The Theory of High Energy Collision Processes - Final Report DOE/ER/40158-1

    SciTech Connect

    Wu, Tai, T.

    2011-09-15

    In 1984, DOE awarded Harvard University a new Grant DE-FG02-84ER40158 to continue their support of Tai Tsun Wu as Principal Investigator of research on the theory of high energy collision processes. This Grant was renewed and remained active continuously from June 1, 1984 through November 30, 2007. Topics of interest during the 23-year duration of this Grant include: the theory and phenomenology of collision and production processes at ever higher energies; helicity methods of QED and QCD; neutrino oscillations and masses; Yang-Mills gauge theory; Beamstrahlung; Fermi pseudopotentials; magnetic monopoles and dyons; cosmology; classical confinement; mass relations; Bose-Einstein condensation; and large-momentum-transfer scattering processes. This Final Report describes the research carried out on Grant DE-FG02-84ER40158 for the period June 1, 1984 through November 30, 2007. Two books resulted from this project and a total of 125 publications.

  17. Initial results of a full kinetic simulation of RF H{sup −} source including Coulomb collision process

    SciTech Connect

    Mochizuki, S.; Shibata, T.; Nishida, K.; Hatayama, A.; Mattei, S.; Lettry, J.

    2015-04-08

    In order to evaluate Electron Energy Distribution Function (EEDF) more correctly for radio frequency inductively coupled plasma (RF-ICP) in hydrogen negative ion sources, the Electromagnetic Particle-In-Cell (EM-PIC) simulation code has been improved by taking into account electron-electron Coulomb collision. Binary collision model is employed to model Coulomb collision process and we have successfully modeled it. The preliminary calculation including Coulomb collision has been done and it is shown that Coulomb collision doesn’t have significant effects under the condition: electron density n{sub e} ∼ 10{sup 18} m{sup −3} and high gas pressure p{sub H{sub 2}} = 3 Pa, while it is necessary to include Coulomb collision under high electron density and low gas pressure conditions.

  18. Statistical kinetics of processive molecular motors

    NASA Astrophysics Data System (ADS)

    Schnitzer, Mark Jacob

    1999-10-01

    We describe new theoretical and experimental tools for studying biological motor proteins at the single molecule scale. These tools enable measurements of molecular fuel economies, thereby providing insight into the pathways for conversion of biochemical energy into mechanical work. Kinesin is an ATP-dependent motor that moves processively along microtubules in discrete steps of 8 nm. How many molecules of ATP are hydrolysed per step? To determine this coupling ratio, we develop a fluctuation analysis, which relates the variance in records of mechanical displacement to the number of rate-limiting biochemical transitions in the engine cycle. Using fluctuation analysis and optical trapping interferometry, we determine that near zero load, single molecules of kinesin hydrolyse one ATP nucleotide per 8-nm step. To study kinesin behavior under load, we use a molecular force clamp, capable of maintaining constant loads on single kinesin motors moving processively. Analysis of records of motion under variable ATP concentrations and loads reveals that kinesin is a `tightly- coupled' motor, maintaining the 1:1 coupling ratio up to loads of ~ 5 pN. Moreover, a Michaelis-Menten analysis of velocity shows that the kinesin cycle contains at least two load- dependent transitions. The rate of one of these transitions affects ATP affinity, while the other does not. Therefore, the kinesin stall force must depend on the ATP concentration, as is demonstrated experimentally. These findings rule out existing theoretical models of kinesin motility. We develop a simple theoretical formalism describing a tightly-coupled mechanism for movement. This `energy-landscape' formalism quantitatively accounts for motile properties of RNA polymerase (RNAP), the enzyme that transcribes DNA into RNA. The shapes of RNAP force-velocity curves indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling suggests that high loads may halt RNAP by promoting a structural change which moves all or part of the enzyme backwards along the DNA through a distance of 5-10 base pairs. Using the energy landscape formalism, we also propose a model for kinesin. The model incorporates both the ATP-dependent and the ATP-independent mechanical transitions in the motor cycle and explains experimental measurements of kinesin velocity.

  19. Angle and energy resolved studies of the collision-induced dissociation of polyatomic molecular ions: Baseline studies of CH[sub 4][sup +] and C[sub 3]H[sub 8][sup +

    SciTech Connect

    Anderson, S.G.

    1992-01-01

    A deeper fundamental understanding of the collision process and subsequent dissociation for polyatomic ions is essential to optimize future studies of collision induced dissociation (CID). An instrument was developed with an unique system of electrostatic lenses that allows CID to be observed in the energy range from a few tenths of an eV to several thousand eV. The instrument permits daughter ion distributions to be mapped in angle and energy. The CID spectra of methane and propane were investigated at keV energies using a commercial tandem mass spectrometer. The relative abundances of the daughter ions, the energy deposition, and kinetic energy release were determined as a function of collision gas was also investigated and interpreted in terms of center of mass (CM) collision energy and the Massey adiabatic criterion most probable energy deposition. The daughter ion abundance, kinetic energy transfer, and kinetic energy release were observed as a function of collision gas, CM collision energy and attenuation of the primary ion beam. A simple model is proposed to describe the effect of multiple collisions on the CID process. Propane molecular ion CID was investigated with the new instrument at laboratory energies ranging from 18 eV to 1 keV and CM collision energies ranging from 1.5 eV to 450 eV. The daughter ion distributions obtained from these experiments show that there is no change in mechanism between CID observed in quadrupole instruments at eV energies and CID observed in sector instruments at keV lab energies. The energy and angular distribution of CID daughter ions is close to the CM with large CM scattering angles at low energy and shifts to near the elastic scattering circle and small CM scattering angles at high lab energies.

  20. Electron Transfer Processes to Continuum in Near-Relativistic Ion-Atom Collisions

    SciTech Connect

    Hagmann, S.; Stoehlker, Th.; Fritzsche, S.; Surzhykov, A.; Jakubassa-Amundsen, D.; Najjari, B.; Voitkiv, A.; Ullrich, J.; Moshammer, R.; Kozhuharov, C.; Gumberidze, A.; Spillmann, U.; Reuschl, R.; Hess, S.; Trotsenko, S.; Bosch, F.; Liesen, D.; Nofal, M.; Doerner, R.; Rothard, H.

    2009-03-10

    Theories for electron transfer to the continuum have encountered considerable difficulties to take into account the intrinsic many-electron processes in the capture channel. This may partially be attributed to large momentum transfers involved and thus collision systems are mostly not in the realm of first order perturbation theories. For this reason we have studied collision systems where simultaneously distinct competing electron transfer processes are found to be active, like radiative (RECC) and non-radiative electron capture to continuum (ECC) in the relativistic domain where one or two even active electrons are involved; here another, though distinct, transfer process, the projectile electron loss to continuum (ELC), permits additionally to study the dynamics of ionization very close to threshold. We have studied these electron transfer processes simultaneously in forward electron emission in two systems of different projectile Compton profile, U{sup 88+}+N{sub 2} and Sn{sup 47+}+N{sub 2} collisions using the forward electron spectrometer at the supersonic jet-target of the ESR storage ring. We report first results and compare with theory.

  1. Molecular beam studies of elementary chemical processes.

    PubMed

    Lee, Y T

    1987-05-15

    The experimental investigation of elementary chemical reactions is presently in a very exciting period. The advance in modern microscopic experimental methods, especially crossed molecular beams and laser technology, has made it possible to explore the dynamics and mechanisms of important elementary chemical reactions in great detail. Through the continued accumulation of detailed and reliable knowledge about elementary reactions, we will be in a better position to understand, predict, and control many time-dependent macroscopic chemical processes that are important in nature or to human society. In addition, because of recent improvements in the accuracy of theoretical predictions based on large-scale ab initio quantum mechanical calculations, meaningful comparisons between theoretical and experimental findings have become possible. In the remaining years of the 20th century, there is no doubt that the experimental investigation of the dynamics and mechanisms of elementary chemical reactions will play a very important role in bridging the gap between the basic laws of mechanics and the real world of chemistry. PMID:17777849

  2. Formation of the phenyl radical [C6H5(X(2)A1)] under single collision conditions: a crossed molecular beam and ab initio study.

    PubMed

    Zhang, Fangtong; Jones, Brant; Maksyutenko, Pavlo; Kaiser, Ralf I; Chin, Christine; Kislov, Vadim V; Mebel, Alexander M

    2010-03-01

    Reactions of dicarbon molecules (C(2)) with C(4)H(6) isomers such as 1,3-butadiene represent a potential, but hitherto unnoticed, route to synthesize the first aromatic C(6) ring in hydrocarbon flames and in the interstellar medium where concentrations of dicarbon transient species are significant. Here, crossed molecular beams experiments of dicarbon molecules in their X(1)Sigma(g)(+) electronic ground state and in the first electronically excited a(3)Pi(u) state have been conducted with 1,3-butadiene and two partially deuterated counterparts (1,1,4,4-D4-1,3-butadiene and 2,3-D2-1,3-butadiene) at two collision energies of 12.7 and 33.7 kJ mol(-1). Combining these scattering experiments with electronic structure and RRKM calculations on the singlet and triplet C(6)H(6) surfaces, our investigation reveals that the aromatic phenyl radical is formed predominantly on the triplet surface via indirect scattering dynamics through a long-lived reaction intermediate. Initiated by a barrierless addition of triplet dicarbon to one of the terminal carbon atoms of 1,3-butadiene, the collision complex undergoes trans-cis isomerization followed by ring closure and hydrogen migration prior to hydrogen atom elimination, ultimately forming the phenyl radical. The latter step emits the hydrogen atom almost perpendicularly to the rotational plane of the decomposing intermediate and almost parallel to the total angular momentum vector. On the singlet surface, smaller contributions of phenyl radical could not be excluded; experiments with partially deuterated 1,3-butadiene indicate the formation of the thermodynamically less stable acyclic H(2)CCHCCCCH(2) isomer. This study presents the very first experimental evidence, contemplated by theoretical studies, that under single collision conditions an aromatic hydrocarbon molecule can be formed in a bimolecular gas-phase reaction via reaction of two acyclic molecules involving cyclization processes at collision energies highly relevant to combustion flames. PMID:20136077

  3. A wind tunnel study of the effects of collision processes on the shape and oscillation for moderate-size raindrops

    NASA Astrophysics Data System (ADS)

    Szakáll, Miklós; Kessler, Simon; Diehl, Karoline; Mitra, Subir K.; Borrmann, Stephan

    2014-06-01

    Drop-drop collision experiments were carried out at the Mainz vertical wind tunnel. Water drops of 2.5 mm diameter were freely floated at their terminal velocities in a vertical air stream and collided with 0.5 mm diameter droplets. The collisions were recorded with a high speed digital video camera at a frame rate of 1000 per second. Altogether 116 collision events were observed, 75 of which ended with coalescence, and the rest with filament type breakup. The coalescence efficiency and its dependence on the Weber number and on the eccentricity of the colliding drops showed good agreement with earlier numerical studies. Thirty-six recorded collisions were further analyzed in order to characterize the oscillation behavior of large drops after a collisional excitation. Besides the introduction of the experimental method for studying the raindrop collisions, the study primarily focused on the characterization of the average value and the amplitude of the axis ratio variation, the active oscillation modes and their frequencies, and the decay of the oscillations excited by the collision. In spite of the fact that the amplitude of the axis ratio variation increased up to 4 to 6 times of its value before collision - depending on whether the collision ended with coalescence or breakup -, the average axis ratios increased by less than 1%. Since the sizes of largest drops after collision remained practically unchanged during the collision process, the frequencies of the active fundamental (n = 2) oscillation modes of the drops did not change significantly either. Instantaneously after collision the transverse oscillation mode and the whole body rotation dominated, while at a later instant the oblate-prolate mode determined again the drop shape alteration. It was further found that the damping of the oscillation after collision can be adequately described by the viscous decay of a liquid spherical drop.

  4. Molecular Processing of Polymers with Cyclodextrins

    NASA Astrophysics Data System (ADS)

    Tonelli, Alan E.

    We summarize our recent studies employing the cyclic starch derivatives called cyclodextrins (CDs) to both nanostructure and functionalize polymers. Two important structural characteristics of CDs are taken advantage of to achieve these goals. First the ability of CDs to form noncovalent inclusion complexes (ICs) with a variety of guest molecules, including many polymers, by threading and inclusion into their relatively hydrophobic interior cavities, which are roughly cylindrical with diameters of ˜ 0.5 - 1.0 nm. α-, β-, and γ-CD contain six, seven, and eight α-1,4-linked glucose units, respectively. Warm water washing of polymer-CD-ICs containing polymer guests insoluble in water or treatment with amylase enzymes serves to remove the host CDs and results in the coalescence of the guest polymers into solid samples. When guest polymers are coalesced from the CD-ICs by removing their host CDs, they are observed to solidify with structures, morphologies, and even conformations that are distinct from bulk samples made from their solutions and melts. Molecularly mixed, intimate blends of two or more polymers that are normally immiscible can be obtained from their common CD-ICs, and the phase segregation of incompatible blocks can be controlled (suppressed or increased) in CD-IC coalesced block copolymers. In addition, additives may be more effectively delivered to polymers in the form of their crystalline CD-ICs or soluble CD-rotaxanes. Secondly, the many hydroxyl groups attached to the exterior rims of CDs, in addition to conferring water solubility, provide an opportunity to covalently bond them to polymers either during their syntheses or via postpolymerization reactions. Polymers containing CDs in their backbones or attached to their side chains are observed to more readily accept and retain additives, such as dyes and fragrances. Processing with CDs can serve to both nanostructure and functionalize polymers, leading to greater understanding of their behaviors and to new properties and applications.

  5. Time-to-Collision estimation from motion based on primate visual processing.

    PubMed

    Galbraith, John M; Kenyon, Garrett T; Ziolkowski, Richard W

    2005-08-01

    A population coded algorithm, built on established models of motion processing in the primate visual system, computes the time-to-collision of a mobile robot to real-world environmental objects from video imagery. A set of four transformations starts with motion energy, a spatiotemporal frequency based computation of motion features. The following processing stages extract image velocity features similar to, but distinct from, optic flow; "translation" features, which account for velocity errors including those resulting from the aperture problem; and finally, estimate the time-to-collision. Biologically motivated population coding distinguishes this approach from previous methods based on optic flow. A comparison of the population coded approach with the popular optic flow algorithm of Lucas and Kanade against three types of approaching objects shows that the proposed method produces more robust time-to-collision information from a real world input stimulus in the presence of the aperture problem and other noise sources. The improved performance comes with increased computational cost, which would ideally be mitigated by special purpose hardware architectures. PMID:16119266

  6. Electron Capture and Loss Processes in Forward Electron Emission in Fast Ion-atom Collisions

    SciTech Connect

    Toth, G.; Tanis, J. A.; Zavodszky, P. A.

    2009-03-10

    Forward-going continuum electron emission has been investigated in 0.4-2 MeV/u O{sup 7+} and O{sup 8+}+He collisions. The one and two-electron processes of electron capture to the continuum (ECC), electron loss to the continuum (ELC), and transfer ionization (TI) have been separated by detecting cusp electrons in coincidence with the outgoing charge states of the projectile ions. The data are compared to earlier results of Zhu et al. for the O{sup 7+}+Ar collision system. The relative importance of the different contributions to forward electron emission and the role of the electron-electron interaction are discussed. The relationships of these results to recent studies of radiative-electron-capture-to-the continuum (RECC) are discussed.

  7. Theoretical investigation of the electron capture and loss processes in the collisions of He2+ + Ne

    NASA Astrophysics Data System (ADS)

    Hong, Xuhai; Wang, Feng; Jiao, Yalong; Su, Wenyong; Wang, Jianguo; Gou, Bingcong

    2013-08-01

    Based on the time-dependent density functional theory, a method is developed to study ion-atom collision dynamics, which self-consistently couples the quantum mechanical description of electron dynamics with the classical treatment of the ion motion. Employing real-time and real-space method, the coordinate space translation technique is introduced to allow one to focus on the region of target or projectile depending on the actual concerned process. The benchmark calculations are performed for the collisions of He2+ + Ne, and the time evolution of electron density distribution is monitored, which provides interesting details of the interaction dynamics between the electrons and ion cores. The cross sections of single and many electron capture and loss have been calculated in the energy range of 1-1000 keV/amu, and the results show a good agreement with the available experiments over a wide range of impact energies.

  8. Theoretical investigation of the electron capture and loss processes in the collisions of He2+ + Ne.

    PubMed

    Hong, Xuhai; Wang, Feng; Jiao, Yalong; Su, Wenyong; Wang, Jianguo; Gou, Bingcong

    2013-08-28

    Based on the time-dependent density functional theory, a method is developed to study ion-atom collision dynamics, which self-consistently couples the quantum mechanical description of electron dynamics with the classical treatment of the ion motion. Employing real-time and real-space method, the coordinate space translation technique is introduced to allow one to focus on the region of target or projectile depending on the actual concerned process. The benchmark calculations are performed for the collisions of He(2+) + Ne, and the time evolution of electron density distribution is monitored, which provides interesting details of the interaction dynamics between the electrons and ion cores. The cross sections of single and many electron capture and loss have been calculated in the energy range of 1-1000 keV/amu, and the results show a good agreement with the available experiments over a wide range of impact energies. PMID:24007011

  9. Electromagnetic processes in nucleus-nucleus collisions relating to space radiation research

    NASA Technical Reports Server (NTRS)

    Norbury, John W.

    1992-01-01

    Most of the papers within this report deal with electromagnetic processes in nucleus-nucleus collisions which are of concern in the space radiation program. In particular, the removal of one and two nucleons via both electromagnetic and strong interaction processes has been extensively investigated. The theory of relativistic Coulomb fission has also been developed. Several papers on quark models also appear. Finally, note that the theoretical methods developed in this work have been directly applied to the task of radiation protection of astronauts. This has been done by parameterizing the theoretical formalism in such a fashion that it can be used in cosmic ray transport codes.

  10. Ionization of Na(3P) atoms by collisions with vibrationally excited nitrogen molecules in crossed molecular beams

    NASA Astrophysics Data System (ADS)

    De Jong, A. A.; Kircz, J. G.; Alkemade, C. Th. J.; van der Valk, F.

    1981-06-01

    A crossed molecular beam experiment is described in which the rate of ionization of Na(3P) atoms in collision with vibrationally excited N 2 molecul has been measured as a function of the N 2 temperature up to 3050 K. The activation energy in the experiment appears to be close to the ionization energy of the 3P level. An ionization cross section of about 100 »A 2 (excluding the activation energy factor) is derived with the help of a theoretical model. The limitations of the experiments as well as of the model are discussed.

  11. Molecular treatment of the ion-pair formation reaction in H(1s) + H(1s) collisions

    SciTech Connect

    Borondo, F.; Martin, F.; Yaez, M.

    1987-01-01

    All the available theoretical calculations of the cross section for the ion-pair formation reaction H(1s)+H(1s)..-->..H/sup +/H/sup -/(1s/sup 2/) have been performed using methods that are only valid at high collision energies. They get good agreement with the experiments for impact energies greater than 25 keV, but fail completely at smaller energies. In this work we report the cross section for this reaction at impact energies less than 10 keV, calculated in the framework of the impact-parameter approximation and using the molecular method with a common translation factor.

  12. H(D) ? D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects

    PubMed Central

    Vurdu, Can D.; Gven, Ziya B.

    2011-01-01

    All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified LondonEyringPolanyiSato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

  13. Ion-Neutral Collisions in the Interstellar Medium: Wave Damping and Elimination of Collisionless Processes

    NASA Astrophysics Data System (ADS)

    Spangler, Steven R.; Savage, Allison H.; Redfield, Seth

    2011-09-01

    Most phases of the interstellar medium contain neutral atoms in addition to ions and electrons. This introduces differences in plasma physics processes in those media relative to the solar corona and the solar wind at a heliocentric distance of 1 astronomical unit. In this paper, we consider two well-diagnosed, partially-ionized interstellar plasmas. The first is the Warm Ionized Medium (WIM) which is probably the most extensive phase in terms of volume. The second is the gas of the Local Clouds of the Very Local Interstellar Medium (VLISM). Ion-neutral interactions seem to be important in both media. In the WIM, ion-neutral collisions are relatively rare, but sufficiently frequent to damp magnetohydrodynamic (MHD) waves (as well as propagating MHD eddies) within less than a parsec of the site of generation. This result raises interesting questions about the sources of turbulence in the WIM. In the case of the VLISM, the ion-neutral collision frequency is higher than that in the WIM, because the hydrogen is partially neutral rather than fully ionized. We present results showing that prominent features of coronal and solar wind turbulence seem to be absent in VLISM turbulence. For example, ion temperature does not depend on ion mass. This difference may be due to ion-neutral collisions, which distribute power from more effectively heated massive ions such as iron to other ion species and neutral atoms.

  14. Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Haug, Kenneth; Zhao, Meishan; Truhlar, Donald G.; Sun, Yan

    1988-01-01

    The quantum mechanical problem of reactive or nonreactive scattering of atoms and molecules is formulated in terms of square-integrable basis sets with variational expressions for the reactance matrix. Several formulations involving expansions of the wave function (the Schwinger variational principle) or amplitude density (a generalization of the Newton variational principle), single-channel or multichannel distortion potentials, and primitive or contracted basis functions are presented and tested. The test results, for inelastic and reactive atom-diatom collisions, suggest that the methods may be useful for a variety of collision calculations and may allow the accurate quantal treatment of systems for which other available methods would be prohibitively expensive.

  15. Collision tectonics

    SciTech Connect

    Coward, M.P.; Ries, A.C.

    1985-01-01

    The motions of lithospheric plates have produced most existing mountain ranges, but structures produced as a result of, and following the collision of continental plates need to be distinguished from those produced before by subduction. If subduction is normally only stopped when collision occurs, then most geologically ancient fold belts must be collisional, so it is essential to recognize and understand the effects of the collision process. This book consists of papers that review collision tectonics, covering tectonics, structure, geochemistry, paleomagnetism, metamorphism, and magmatism.

  16. Orientation and alignment effects for one-electron transfer processes in ion-atom collisions involving an optically prepared target

    NASA Astrophysics Data System (ADS)

    Dowek, D.; Houver, J. C.

    1997-04-01

    Recent aspects in the study of the role of electronic orbital alignment and orientation in one-electron transfer processes induced in atomic collisions are reviewed. We focus on the study of collisions involving a laser prepared target, in the range where the collision velocity ?c and the velocity of the active electron ?e are of comparable magnitude. Results obtained in the recent years, both for total electron capture cross sections and for angular scattering analysis, are presented and discussed in terms of simple models.

  17. State-Specific Collision Dynamics of Molecular Super Rotors with Oriented Angular Momentum.

    PubMed

    Murray, Matthew J; Ogden, Hannah M; Toro, Carlos; Liu, Qingnan; Burns, David A; Alexander, Millard H; Mullin, Amy S

    2015-12-17

    An optical centrifuge pulse drives carbon dioxide molecules into ultrahigh rotational states with rotational frequencies of ? ? 32 THz based on the centrifuge frequency at the full width at half-maximum of the spectral chirp. High-resolution transient IR absorption spectroscopy is used to measure the time-evolution of translational and rotational energy for a number of states in the range of J = 0-100 at a sample pressure of 5-10 Torr. Transient Doppler profiles show that the products of super rotor collisions contain substantial amounts of translational energy, with J-dependent energies correlating to a range of ?J propensities. The transient population in J = 100 is short-lived, indicating rapid relaxation of high J states; populations in J = 36, 54, and 76 increase overall as the super rotor energy is redistributed. Transient line profiles for J = 0 and 36 are consistently narrower than the initial ambient sample temperature, showing that collision cross sections for super rotors increase with decreasing collision energy. Quantum scattering calculations on Ar-CO2(j) collisions are used to interpret the qualitative features of the experimental results. The results of this study provide the groundwork for developing a more complete understanding of super rotor dynamics. PMID:26469322

  18. Time-of-Flight Experiments in Molecular Motion and Electron-Atom Collision Kinematics

    ERIC Educational Resources Information Center

    Donnelly, Denis P.; And Others

    1971-01-01

    Describes a set of experiments for an undergraduate laboratory which demonstrates the relationship between velocity, mass, and temperature in a gas. The experimental method involves time-of-flight measurements on atoms excited to metastable states by electron impact. Effects resulting from recoil in the electron-atom collision can also be…

  19. Inelastic processes in ion/surface collisions: Scattered ion fractions and VUV photon emission for Ne + and Ar + collisions with Mg and Y surfaces

    NASA Astrophysics Data System (ADS)

    Rabalais, J. Wayne; Chen, Jie-Nan; Kumar, R.; Narayana, M.

    1985-12-01

    Time-of-flight (TOF) scattering spectra and vacuum ultraviolet (VUV) photon emission spectra resulting from 1-10 keV Ne+ and Ar+ ions impinging on magnesium and yttrium surfaces and the corresponding oxidized and hydroxylated surfaces have been measured. Measurements of the scattered neutrals plus ions and neutrals only are used to calculate scattered ion fractions Y+ for the single scattering collisions. The Y+ values rise steeply at low ion energies E0 (˜1-2 keV), reaching values of 70% and 38% at 10 keV for Ne+/Mg and Ar+/Y, respectively, and are very sensitive to adsorbate coverage. The dominant photon emission observed from the clean metals in the VUV range 30-200 nm is 1,3P → 1S resonance radiation from the excited neutral projectile atoms; emission was also observed from excited H and O for adsorbate covered surfaces. A model is developed for electronic transitions in keV ion/surface collisions which considers Auger and resonant transitions along the ion trajectory and electron promotions in the quasidiatomic molecule of the close encounter. By making an assumption of equality in the close encounter, the model can be fitted to the experimental data, allowing determination of ionization PI and neutralization PN probabilities as a function of the distance of approach. The results show that electron promotions within MO's of the collision complex formed during encounter are significant, if not dominating, processes in keV ion surface collisions.

  20. LETTER TO THE EDITOR: Post-collision interaction in double Auger processes

    NASA Astrophysics Data System (ADS)

    Sheinerman, S. A.

    1998-04-01

    A post-collision interaction (PCI) in the inner-shell photoionization followed by a double Auger decay is considered. The general analytical expressions for an amplitude and a cross section of the process under consideration are obtained. These formulae allow for the PCI distortion and are valid for a wide range of velocities of the photoelectron except a near-threshold region. The possibility of observing the PCI effects in triple- and double-coincidence experiments is discussed. The results of our approach are applied to the case of the Xe 0953-4075/31/8/006/img1-photoionization followed by the double Auger decay.

  1. Electron Capture Processes in Ion-Atom Collisions at Intermediate Projectile Energies

    NASA Astrophysics Data System (ADS)

    Schulz, M.; Harris, A. L.; Kirchner, T.; Madison, D. H.

    2013-09-01

    Recent studies on differential cross sections for double capture as well as transfer and target excitation of intermediate energy p + He collisions are reviewed. Experimental data are compared to both perturbative and non-perturbative calculations. One of the main interests in two-electron processes in general is the role of electron-electron correlations. The comparison between experiment and theory reveals that such effects are difficult to identify in double capture and transfer and target excitation in this energy regime because they cannot be easily disentangled from features related to the projectile-residual target ion interaction.

  2. Processing energy and signals by molecular and supramolecular systems.

    PubMed

    Balzani, Vincenzo; Credi, Alberto; Venturi, Margherita

    2008-01-01

    Any kind of device or machine requires a substrate, energy, and information signals. If we wish to operate at the nanometer scale, we must use molecules as substrates. Energy- and signal-processing at a molecular level relies on cause/effect relationships between the input supplied and the kind of process obtained. We have classified energy- and signal-processing at the molecular level according to the nature of the input (electronic, photonic, or chemical) and the nature of the obtained effect (electronic, photonic, or chemical process that follows). By coupling the three kinds of inputs with the three types of resulting processes, nine types of molecular-based processes (electronic, photonic, chemionic, electrophotonic, electrochemionic, photoelectronic, photochemionic, chemiophotonic, and chemioelectronic) can be identified. In this concept article, looking at molecular transformations in an unconventional way, we have tried to give a flavor of some of the new features that project the old science of chemistry towards novel achievements. PMID:17948331

  3. Kinematics of the CS method for the treatment of molecular collisions. [Coupled State

    NASA Technical Reports Server (NTRS)

    Hahne, G. E.

    1984-01-01

    The problem of the quantum treatment of nonreactive collisions of two simple molecules or of an atom and a molecule is considered mathematically. Kinematical structure theorems analogous to the Wigner-Eckart theorem for scalar operators are derived for the transition operator (T-operator) of a two-molecule system, where, in addition to the usual conservation laws, certain additional conservation laws are presumed satisfied in a collision. The additional conservation laws were examined in order to develop a testable approximation scheme (CS method) for the specification of the kinematics of a system of two rigid diatomic molecules. The rand p-helicity basis states for a two-rigid rotor system are defined and unitary transformations established between these and conventional bases. It is found that only questionable criteria exist for testing the on-the-energy-shell matrix of a T(energy) operator for the presence of properties of two of the additional conservation laws.

  4. Sub-lithospheric small scale convection - a process for continental collision magmatism

    NASA Astrophysics Data System (ADS)

    Kaislaniemi, L.; Van Hunen, J.; Allen, M. B.; Neill, I.

    2013-12-01

    We have studied the role of sub-lithospheric small scale convection in the generation of collision zone magmatism, using combined geodynamic-petrological models. We compare the results with the collisional magmatism of the Turkish-Iranian plateau, where a number of randomly (in both space and time) distributed volcanic centres on has been produced by the active Arabia-Eurasia collision since initial plate collision at ~27-35 Ma. These volcanic rocks have a highly variable geochemical signature, but commonly point to a lithospheric mantle or asthenospheric source. Major and trace element characteristics span the range from OIB-like, to calc-alkali, shoshonitic and even ultrapotassic. We suggest these spatially, temporally and chemically diverse patterns of volcanism are caused by sub-lithospheric small scale convection (SSC), manifested as small (50 to 300 km) convection cells at the lithosphere-asthenosphere boundary and dripping of the lithospheric mantle into the asthenosphere. SSC is activated by the increased amount of water in the lithospheric and asthenospheric mantle and its rheological weakening effect. The increase in water content is caused by the subduction prior to the collision and/or continental subduction during collision. The mantle convection code CitCom, together with a parameterized melting model, is used to model the SSC process. We relate the water content to the mantle solidus and viscosity, and the amount of depletion to the viscosity and buoyancy of the mantle material. We measure the amount of magmatism taking place by assuming direct and instantaneous percolation of mantle melts to the surface. We mimic the dislocation creep mechanism with a diffusion creep mechanism using low activation energy--either one is needed for the SSC to take place under realistic conditions. Results show that SSC is able to produce small degrees (0-2 %) of melting of the mantle through dripping lithosphere, decompression melting, erosion of the overlying lithosphere, and advection of hot material into contact with the cold lithosphere. The degree of melting might be strongly controlled by the lithosphere thickness and the extent of its hydration during the past Tethyan subduction. Mantle melting leaves behind depleted, more viscous and more buoyant layers at the lithosphere-asthenosphere boundary which may take millions of years before sinking back to deeper mantle. Average volcanic layer thicknesses of hundreds of meters can be reached via the SSC process, corresponding to observations from the Turkish-Iranian plateau. By its random nature, SSC can explain why the continental collision magmatism on the Turkish-Iranian plateau does not seem to have clearly recognisable spatial or temporal patterns. The potential of the SSC to effectively mix the asthenosphere-lithosphere close to their boundary appears to offer an explanation for the geochemical heterogeneity of the observed volcanism. SSC may be related to whole mantle delamination (offering zones of weaknesses for its initiation) or slab break-off (SSC being enhanced by the break-off), but neither is a prerequisite for SSC magmatism.

  5. Coulomb explosion and binary encounter processes in collisions between slow ions and small molecules of biological interest

    SciTech Connect

    Juhasz, Z.; Sulik, B.

    2008-12-08

    In this work we study the ion impact induced fragmentation of small molecules, which are relevant for radiation damage studies in biological tissues. We present double differential ion emission yields for collisions of N{sup 6+} ions with water and methane molecules at 15 and 30 keV impact energies. The angular distribution of the fragment ions shows post-collision and nucleus-nucleus binary collision effects. In the multiple capture energy range, a strong interplay is indicated between the Coulomb explosion and the binary collision mechanisms. In the energy region, where triple capture is dominant, an unexpected angular distribution was found for water fragments, which may be attributed to orientation sensitivity of some of the capture channels. Such processes are relevant for astrophysics and radiation therapy.

  6. Molecular Thermodynamics for Chemical Process Design

    ERIC Educational Resources Information Center

    Prausnitz, J. M.

    1976-01-01

    Discusses that aspect of thermodynamics which is particularly important in chemical process design: the calculation of the equilibrium properties of fluid mixtures, especially as required in phase-separation operations. (MLH)

  7. Calculation of rotationally inelastic processes in electron collisions with CO{sub 2} molecules

    SciTech Connect

    Gianturco, F.A.; Stoeckling, T.

    1997-03-01

    The rotational excitation of the title linear polyatomic target, treated as a rigid rotor is computed using a fully {ital ab initio} interaction potential recently employed to obtain integral elastic cross sections [Gianturco and Stoecklin, J. Phys. B {bold 29}, 3933 (1996)] and to unravel several resonances in the low-energy region. The present study looks at the rotationally inelastic processes which can occur in the energy range across the long-lived shape resonance at 3.9 eV and finds that the resonant process strongly enhances the overall efficiency of the rotational excitation by the electron projectile, as shown by the computed values of the average rotational energy transfers. Angular distributions are also evaluated at different collision energies and compared with earlier calculations. {copyright} {ital 1997} {ital The American Physical Society}

  8. The influence of surface processes in modulating the deformation of the deep lithosphere during collision

    NASA Astrophysics Data System (ADS)

    Pysklywec, Russell; Gray, Robert

    2014-05-01

    The importance of climate-controlled surface processes (erosion and deposition) in influencing the tectonics of plate collision and orogenesis has been well recognized for crustal-scale tectonics. We consider the geodynamics of coupled crust and mantle processes during such collisional events to consider how the surface processes modify the deformation of the deeper parts of the plate and lithosphere as a whole. The geodynamics are explored quantitatively using high resolution 2D thermal-mechanical numerical experiments. The model has a free surface, prescribed erosional laws (e.g., empirically derived relief- and slope-dependent erosion), and sediment deposition dependent on the amount of material eroded make up the top boundary of the model domain and allow topography to develop self consistently with the underlying tectonics. The models reveal that during the early stages of continental plate collision, the altered of crustal mass flux by surface erosion can modify the stress regime within the crust and at the crust-mantle interface and subsequently the behaviour of the underlying mantle lithosphere. For example with active surface erosion stable subduction-like plate consumption is maintained. In the absence of erosion, subduction is inhibited by accumulating crust causing the convergent plates to steepen dip, detach, and reverse consumption polarity. We also isolate the influence of sediment deposition in the collisional models. In very different ways, the surface transport and deposition of the eroded material can have a significant effect on modulating the dynamics of the whole lithosphere between various modes of deformation. Overall, the models reveal the sensitivity of the near-surface and deep continental plate boundary evolution to surface processes.

  9. Methods for Processing and Interpretation of AIS Signals Corrupted by Noise and Packet Collisions

    NASA Astrophysics Data System (ADS)

    Poļevskis, J.; Krastiņš, M.; Korāts, G.; Skorodumovs, A.; Trokšs, J.

    2012-01-01

    The authors deal with the operation of Automatic Identification System (AIS) used in the marine traffic monitoring to broadcast messages containing information about the vessel: id, payload, size, speed, destination etc., meant primarily for avoidance of ship collisions. To extend the radius of AIS operation, it is envisaged to dispose its receivers on satellites. However, in space, due to a large coverage area, interfering factors are especially pronounced - such as packet collision, Doppler's shift and noise impact on AIS message receiving, pre-processing and decoding. To assess the quality of an AIS receiver's operation, a test was carried out in which, varying automatically frequency, amplitude, noise, and other parameters, the data on the ability of the receiver's ability to decode AIS signals are collected. In the work, both hardware- and software-based AIS decoders were tested. As a result, quite satisfactory statistics has been gathered - both on the common and the differing features of such decoders when operating in space. To obtain reliable data on the software-defined radio AIS receivers, further research is envisaged.

  10. Validity of central field approximations in molecular scattering - Low energy CO-He collisions

    NASA Technical Reports Server (NTRS)

    Monchick, L.; Green, S.

    1975-01-01

    Close-coupled calculations have been carried out on collisions of helium and carbon monoxide interacting via a theoretical interaction potential which is believed to reproduce accurately the true interaction of this system. These are compared with an equivalent set of calculations for the spherical average of this potential. It is concluded that the latter approximation holds reasonably well for transport-property calculations but not for differential and total scattering cross sections. As a consequence, conservation of scattering-cross-section theorems that are based on this interaction potential do not hold well.

  11. How are particle production, nucleon emission and target fragment evaporation processes interrelated in hadron-nucleus collisions?

    NASA Technical Reports Server (NTRS)

    Strugalski, Z.

    1985-01-01

    Relations between particle production, nucleon emission, and fragment evaporation processes were searched for in hadron-nucleus collisions. It was stated that: (1) the nucleon emission and target fragment evaporation proceed independently of the particle production process; and (2) relation between multiplicities of the emitted protons and of the evaporated charged fragments is expressed by simple formula.

  12. Chemistry of molecular growth processes in flames.

    PubMed

    Smyth, K C; Miller, J H

    1987-06-19

    Chemical mechanisms of pyrolysis, growth, and oxidation processes in flames have traditionally been inferred from spatial profile measurements of species concentrations. Experimental investigations now include the detection of numerous minor species such as reactive radicals and intermediate hydrocarbons. In assessing a proposed mechanism important new constraints can be established when the detailed species profile data are combined with velocity and temperature measurements and analyzed to determine production and destruction rates for specific molecules. Recent results on hydrocarbon diffusion flames provide new information on the interplay between chemical and transport processes. These measurements have led to direct tests of proposed routes for the formation of aromatic hydrocarbons and the first, small soot particles. The inception chemistry of hydrocarbon growth reactions and initial particle formation is thought to control soot formation, flame radiation and energy transfer, and pollutant emission in combustion environments. PMID:17835737

  13. Chemistry of Molecular Growth Processes in Flames

    NASA Astrophysics Data System (ADS)

    Smyth, Kermit C.; Houston Miller, J.

    1987-06-01

    Chemical mechanisms of pyrolysis, growth, and oxidation processes in flames have traditionally been inferred from spatial profile measurements of species concentrations. Experimental investigations now include the detection of numerous minor species such as reactive radicals and intermediate hydrocarbons. In assessing a proposed mechanism important new constraints can be established when the detailed species profile data are combined with velocity and temperature measurements and analyzed to determine production and destruction rates for specific molecules. Recent results on hydrocarbon diffusion flames provide new information on the interplay between chemical and transport processes. These measurements have led to direct tests of proposed routes for the formation of aromatic hydrocarbons and the first, small soot particles. The inception chemistry of hydrocarbon growth reactions and initial particle formation is thought to control soot formation, flame radiation and energy transfer, and pollutant emission in combustion environments.

  14. Crustal processes cause adakitic chemical signatures in syn-collision magmatism from SE Iran

    NASA Astrophysics Data System (ADS)

    Allen, Mark; Kheirkhah, Monireh; Neill, Iain

    2015-04-01

    We report new elemental and Nd-Sr isotopic analyses for Late Cenozoic intrusive and extrusive rocks emplaced in SE Iran as part of the wider syn-collision magmatic province within the Turkish-Iranian Plateau. The sample sites are near the town of Dehaj in Kerman Province. Most of the rocks are from stocks and batholiths, interpreted as the roots of central volcanoes. Age controls are not precise, but the rocks are likely to be Late Miocene-Quaternary in age. Basaltic to andesitic lavas crop out nearby; their relationships to the intrusive rocks are uncertain. Geochemically, the entire range of rocks from basalt lavas through to rhyolitic intrusives ranges from 51-71 wt.% silica and isotopic signatures are similar to Bulk Earth, without any clear evidence for large-scale crustal contamination. The basaltic to andesitic lavas appear to have variable and often high La/Yb and Sr/Y such that they range from calc-alkaline arc-like rocks to adakitic compositions depending on the degree of fractionation. The intrusive rocks seem to form a separate suite, with clear indications of increasing Sr/Y and Dy/Yb with fractionation. Previous interpretations relate adakitic magmatism to Tethyan oceanic slab break-off and slab melting beneath the collision zone. However, as the 'adakitic signature' is increasingly apparent in more evolved magmas, at least in the intrusives, adakite generation is more likely to have occurred during melt evolution from an initial low Sr/Y and low La/Yb parent. This parental melt may have been similar in starting composition to proposed non-adakitic basaltic melts from elsewhere in the collision zone. The high Sr/Yb and La/Yb signatures are best explained by the suppression of plagioclase fractionation by high magmatic water contents, promoting incompatible behaviour of Sr. Conversely, Y and Yb are compatible during amphibole and garnet fractionation at crustal or uppermost mantle levels. Rather than a localised slab break-off or melting effect, the Dehaj magmatism may have developed its geochemical signature during deep fractionation as the ascent of the magmas was impeded by thick orogenic crust. The rocks may be seen as just another part of the widespread syn-collision magmatism that has affected widespread areas of Turkey, Iran, Armenia and neighbouring countries in the last ~10-15 Ma, and need not be used as markers for debateable geodynamic events such as break-off. Adakites are also present in NE Iran without any obvious association with subduction processes. We argue that magmatism across much of the plateau is linked at least in part to mantle upwelling following Miocene slab break-off, but also to small-scale convection beneath the collision zone, as predicted by numerical modelling. Particular compositions such as those at Dehaj are influenced by local sources and differentiation processes, but there is no need for independent triggers for initial melting across disparate locations.

  15. A Simple Method for Modeling Collision Processes in Plasmas with a Kappa Energy Distribution

    NASA Astrophysics Data System (ADS)

    Hahn, M.; Savin, D. W.

    2015-08-01

    We demonstrate that a nonthermal distribution of particles described by a kappa distribution can be accurately approximated by a weighted sum of Maxwell-Boltzmann distributions. We apply this method to modeling collision processes in kappa-distribution plasmas, with a particular focus on atomic processes important for solar physics. The relevant collision process rate coefficients are generated by summing appropriately weighted Maxwellian rate coefficients. This method reproduces the rate coefficients for a kappa distribution to an estimated accuracy of better than 3%. This is equal to or better than the accuracy of rate coefficients generated using “reverse-engineering” methods, which attempt to extract the needed cross sections from the published Maxwellian rate coefficient data and then reconvolve the extracted cross sections with the desired kappa distribution. Our approach of summing Maxwellian rate coefficients is easy to implement using existing spectral analysis software. Moreover, the weights in the sum of the Maxwell-Boltzmann distribution rate coefficients can be found for any value of the parameter κ, thereby enabling one to model plasmas with a time-varying κ. Tabulated Maxwellian fitting parameters are given for specific values of κ from 1.7 to 100. We also provide polynomial fits to these parameters over this entire range. Several applications of our technique are presented, including the plasma equilibrium charge state distribution (CSD), predicting line ratios, modeling the influence of electron impact multiple ionization on the equilibrium CSD of kappa-distribution plasmas, and calculating the time-varying CSD of plasmas during a solar flare.

  16. Near-threshold photoionization of hydrogenlike uranium studied in ion-atom collisions via the time-reversed process.

    PubMed

    Stöhlker, T; Ma, X; Ludziejewski, T; Beyer, H F; Bosch, F; Brinzanescu, O; Dunford, R W; Eichler, J; Hagmann, S; Ichihara, A; Kozhuharov, C; Krämer, A; Liesen, D; Mokler, P H; Stachura, Z; Swiat, P; Warczak, A

    2001-02-01

    Radiative electron capture, the time-reversed photoionization process occurring in ion-atom collisions, provides presently the only access to photoionization studies for very highly charged ions. By applying the deceleration mode of the ESR storage ring, we studied this process in low-energy collisions of bare uranium ions with low- Z target atoms. This technique allows us to extend the current information about photoionization to much lower energies than those accessible for neutral heavy elements in the direct reaction channel. The results prove that for high- Z systems, higher-order multipole contributions and magnetic corrections persist even at energies close to the threshold. PMID:11177990

  17. Nonstandard. gamma. gamma. r arrow l sup + l minus processes in relativistic heavy-ion collisions

    SciTech Connect

    Almeida, L.D.; Natale, A.A.; Novaes, S.F. ); Eboli, O.J.P. )

    1991-07-01

    We study lepton pair production in heavy-ion collisions with emphasis on nonstandard contributions to the QED subprocess {gamma}{gamma}{r arrow}{ital l}{sup +}{ital l{minus}}. The existence of compositeness of fermions and/or bosons can be tested in this reaction up to the TeV mass scale. We show that for some processes the capabilities of relativistic heavy-ion colliders to disclose new physics surpass the possibilities of {ital e}{sup +}{ital e{minus}} or {ital p{bar p}} machines. In particular, spin-zero composite particles which couple predominantly to two photons, predicted in composite models, can be studied in a broad range of masses.

  18. Nonstatistical fluctuations for deep inelastic processes in {sup 27}Al+{sup 27}Al collisions

    SciTech Connect

    Berceanu, I.; Duma, M.; Moisa, D.; Petrovici, M.; Pop, A.; Simion, V.; Zoppo, A. Del; D'Erasmo, G.; Imme, G.; Lanzano, G.; Pagano, A.; Pantaleo, A.; Raciti, G.

    2006-08-15

    The excitation functions (EFs) for different fragments produced in the {sup 27}Al+{sup 27}Al dissipative collisions have been measured in steps of 250 keV in the incident energy range 122-132 MeV. Deep inelastic processes have been selected by integrating events on a total kinetic energy loss window of 12 MeV between 20 and 32 MeV. Large fluctuations are observed in all the studied EFs. Large-channel cross-correlation coefficients confirm the nonstatistical origin of these fluctuations. The energy autocorrelation function (EAF) shows damped oscillation structure as expected when a dinuclear system with a lifetime [{tau}=(5.1{+-}2.1){center_dot}10{sup -21}s], similar with its revolution period (T=4.9{center_dot}10{sup -21}sec), is formed. From the periodicity of the EAF oscillations, information on the deformation of the {sup 27}Al+{sup 27}Al dinucleus is inferred.

  19. Electron emission and electron transfer processes in proton-naphthalene collisions at intermediate velocities

    NASA Astrophysics Data System (ADS)

    Mishra, P. M.; Rajput, J.; Safvan, C. P.; Vig, S.; Kadhane, U.

    2013-11-01

    We investigate the fragmentation and ionization of naphthalene by protons at intermediate velocities (between 1.41 and 2.68 a.u.). Relative cross sections for electron capture (EC), electron emission (EE), and capture ionization are measured. The EC cross sections decrease rapidly over the energy range under consideration (50-150 keV) and are lower than EE cross sections. The EE cross sections, on the other hand, change very slowly in this energy range. The energetics of interactions is quantified by comparing the mass spectra with the photodissociation breakdown curves from literature. In the case of single capture, resonant electron transfer to n = 1 state in H+ is seen to dominate the interaction but is shown to be accompanied by a small amount of electronic energy loss. In the EE mode, two mechanisms are shown to be active in the collision process: large impact parameter plasmon excitation mode, and closer encounters with higher amounts of electronic energy loss.

  20. Nuclear de-excitation processes following medium energy heavy ion collisions

    SciTech Connect

    Blann, M.

    1986-09-01

    As heavy ion reaction studies have progressed from beam energies below 10 MeV/nucleon to higher energies, many non-equilibrium reaction phenomena have been observed. Among these are nucleon emission with velocities in excess of the beam velocity, incomplete momentum transfer to evaporation residue and fission-like fragments, ..gamma..-rays with energies in excess of 100 MeV, and ..pi../sup 0/ production when beam energies are below the threshold for production by the nucleon-nucleon collision mechanism. Additionally, prefission neutrons have been observed in excess of numbers expected from equilibrium models. A few of the approaches which have been applied to these phenomena are as follows: Intranuclear cascade: two body collisions are assumed to mediate the equilibration. The geometry and momentum space is followed semiclassically. The approach has many successes though it may suffer in a few applications is not following holes; TDHF considers one body processes only; in the energy regime of interest, two body processes are important so that this may not be a viable approach; Boltzmann-Uehling-Uhlenbeck or Vlasov-Uehling-Uhlenbeck (BUU/VUU) equations combine both one body and two body dynamics. The spatial and momentum evolution of the reactions are followed in a mean field. These should be the Cadillacs of the models. They are computationally tedious, and sometimes significant approximations are made in order to achieve computational tract ability; models of collective deceleration. A very simple model approach is discussed to interpret these phenomena, the Boltzmann master equation (BME). The hybrid model was the first to be applied to the question of heavy ion precompound decay, and the BME second. 26 refs., 5 figs., 2 tabs.

  1. Nonthermal Lorentzian wake-field effects on collision processes in complex dusty plasmas

    SciTech Connect

    Hong, Woo-Pyo; Jung, Young-Dae

    2014-10-15

    The influence of nonthermal Lorentzian wake-field on the electron-dust grain collision is investigated in complex dusty plasmas. The Eikonal method and the effective interaction potential are applied to obtain the Eikonal scattering phase shift, the differential Eikonal collision cross section, and the total Eikonal collision cross section as functions of the collision energy, the impact parameter, the Mach number, and the spectral index of Lorentzian plasma. It is found that the nonthermal effect enhances the Eikonal scattering phase shift and, however, suppresses the Eikonal collision cross section for the electron-dust grain in Lorentzian complex dusty plasmas. It is also found that the Eikonal scattering phase shift decreases with increasing Mach number and spectral index. In addition, the Eikonal collision cross section increases with an increase of the spectral index and Mach number in Lorentzian complex dusty plasmas.

  2. Nonthermal Lorentzian wake-field effects on collision processes in complex dusty plasmas

    NASA Astrophysics Data System (ADS)

    Hong, Woo-Pyo; Jung, Young-Dae

    2014-10-01

    The influence of nonthermal Lorentzian wake-field on the electron-dust grain collision is investigated in complex dusty plasmas. The Eikonal method and the effective interaction potential are applied to obtain the Eikonal scattering phase shift, the differential Eikonal collision cross section, and the total Eikonal collision cross section as functions of the collision energy, the impact parameter, the Mach number, and the spectral index of Lorentzian plasma. It is found that the nonthermal effect enhances the Eikonal scattering phase shift and, however, suppresses the Eikonal collision cross section for the electron-dust grain in Lorentzian complex dusty plasmas. It is also found that the Eikonal scattering phase shift decreases with increasing Mach number and spectral index. In addition, the Eikonal collision cross section increases with an increase of the spectral index and Mach number in Lorentzian complex dusty plasmas.

  3. Validity of approximate methods in molecular scattering - Thermal HCl-He collisions

    NASA Technical Reports Server (NTRS)

    Green, S.; Monchick, L.

    1975-01-01

    Accurate close coupling scattering calculations are presented for thermal energy HCl-He collisions. The interaction potential is obtained from the Gordon-Kim electron gas model, adjusted to have the correct long-range multipole form. A variety of phenomenological cross sections are computed from the close coupling S matrix, and these are compared with results from several commonly employed approximate methods. In particular, it is found that the total integral, total differential, and gas kinetic cross sections are accurately predicted by the central field approximation which retains just the spherical average of the interaction. Integral inelastic cross sections are represented quite accurately by the coupled states approximation of McGuire and Kouri, but only qualitatively by the effective potential method of Rabitz.

  4. From molecular activities and processes to biological function.

    PubMed

    van Helden, J; Naim, A; Lemer, C; Mancuso, R; Eldridge, M; Wodak, S J

    2001-03-01

    This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual description of the network of interactions between molecular entities within the cell and between cells. This model is implemented in the aMAZE database that presently deals with information on metabolic pathways, gene regulation, sub- or supracellular locations, and transport. It is shown that this model constitutes a useful generalisation of data representations currently implemented in metabolic pathway databases, and that it can furthermore include multiple schemes for categorising and classifying molecular entities, activities, processes and localisations. In particular, we highlight the flexibility offered by our system in representing multiple molecular activities and their control, in viewing biological function at different levels of resolution and in updating this view as our knowledge evolves. PMID:11465065

  5. Collision processes involving heavy many-electron ions interacting with neutral atoms

    NASA Astrophysics Data System (ADS)

    Tolstikhina, Inga Yu; Shevelko, Vyacheslav P.

    2013-03-01

    An overview of experimental data and theoretical computational methods is given for effective cross sections of charge exchange (electron capture) and electron loss (projectile ionization) processes involving heavy many-electron ions (like Xe ^{q+}, Pb ^{q+}, W ^{q+}, U ^{q+}) colliding with neutral atoms (H, He, N, Ne, Ar, Kr, Xe) in the E \\approx 10 keV/u - 10 Gev/u energy range, i.e., from low up to relativistic energies. These charge-changing processes can occur with a high probability, reaching 10^{-14} - 10^{-16} cm ^2 cross-section values and, therefore, they play a key role in the kinetics of laboratory and astrophysical plasmas and influence the lifetimes of ion beams in accelerator facilities. Multielectron capture and loss processes are considered, as well, since their importance in the case of heavy atomic projectiles strongly increases, and a contribution to the total cross sections reaches more than 50%. An important aspect of the overview is a consideration of the influence of the inner-shell electrons of two colliding systems and a role of isotope effects in electron capture by very slow ions ( E \\approx 10 - 100 eV/u) from hydrogen isotopes H, D, and T. A short description of the corresponding computer codes is given for the calculation of cross sections of electron capture and electron loss processes for complex atoms and ions over a wide collision energy range.

  6. Collision Processes of Highly Charged Ions with Electrons Studied with an Electron Beam Ion Trap

    SciTech Connect

    Nakamura, Nobuyuki; Watanabe, Tsutomu; Ohtani, Shunsuke; Kavanagh, Anthony P.; Currell, Fred J.; Watanabe, Hirofumi; Sakaue, Hiroyuki A.; Kato, Daiji; Li Yueming; Tong Xiaoming

    2009-09-10

    The electron beam ion trap in Tokyo (Tokyo-EBIT)is suitable for studying relativistic effects in the collisions of highly charged heavy ions with electrons because it can produce and trap very highly charged heavy ions which interact with a mono-energetic and unidirectional relativistic electron beam with an energy of up to 200 keV. Recently, we have been studying resonant processes in ionization and recombination by measuring the charge abundance inside the EBIT at the equilibrium. The abundance ratio between adjacent charge states varies slowly with the electron energy when there is no resonant process. However, when the electron energy coincides with the resonant energy at which ionization or recombination is enhanced, the abundance ratio can drastically change. Thus, the resonant processes can be studied by measuring the abundance ratio between adjacent ions as a function of electron beam energy. In this talk, recent progress for heavy ions with very high charge states up to He-like Bi{sup 81+}, is presented. For such ions, relativistic effects significantly affect the resonant processes. For example, the generalized Breit interaction (GBI) effect, which treats the retardation in the exchange of single virtual photon between the free and orbital electrons, has been clearly observed in the DR resonant strength in Li-like Bi{sup 80+}. Recently we have also found that the GBI effect plays an important role in the interference between non-resonant and resonant recombinations. Experimental results are presented in comparison with theoretical calculations.

  7. Photochemical processes in a two-component molecular contaminant film

    NASA Astrophysics Data System (ADS)

    Luey, Kenneth T.; Coleman, Dianne J.

    2008-08-01

    Previously, significant laboratory work has been performed on the photochemical deposition and darkening of molecular contaminant films. Much of this work addresses single, purified molecular species to understand fundamental photochemical processes. However, some of this work disagrees with other studies involving mixed, real spacecraft materials. There are also points of disagreement with contaminated returned optics from the Hubble Space Telescope where mixed contaminants were found. In this paper, we describe a method for vacuum depositing a controlled, reproducible contaminant film containing two molecular species: tetramethyl-tetraphenyl trisiloxane (DC 704) and dioctyl phthalate (DOP). We use this film to show differences in photochemical processes compared to a pure film of DC 704. We show that some photopolymerization processes occur more slowly in a two-component, mixed film during accelerated exposure to vacuum ultraviolet (VUV) radiation.

  8. Modulation of Energy Conversion Processes in Carbonaceous Molecular Bearings.

    PubMed

    Hitosugi, Shunpei; Ohkubo, Kei; Kawashima, Yuki; Matsuno, Taisuke; Kamata, Sho; Nakamura, Kosuke; Kono, Hirohiko; Sato, Sota; Fukuzumi, Shunichi; Isobe, Hiroyuki

    2015-11-01

    The energetics and photodynamics of carbonaceous molecular bearings with discrete molecular structures were investigated. A series of supramolecular bearings comprising belt-persistent tubular cycloarylene and fullerene molecules accepted photonic stimuli to afford charge-separated species via a photoinduced electron transfer process. The energy conversion processes associated with the photoexcitation, however, differed depending on the molecular structure. A π-lengthened tubular molecule allowed for the emergence of an intermediary triplet excited state at the bearing, which should lead to an energy conversion to thermal energy. On the other hand, low-lying charge-separated species induced by an endohedral lithium ion in fullerene enabled back electron transfer processes to occur without involving triplet excited species. The structure-photodynamics relationship was analyzed in terms of the Marcus theory to reveal a large electronic coupling in this dynamic supramolecular system. PMID:26195132

  9. 1978 bibliography of atomic and molecular processes. [Bibliography

    SciTech Connect

    Not Available

    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.

  10. 1979 bibliography of atomic and molecular processes. [Bibliography

    SciTech Connect

    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.

  11. Spectral lineshapes of collision-induced absorption (CIA) and collision-induced light scattering (CILS) for molecular nitrogen using isotropic intermolecular potential. New insights and perspectives

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Mostafa, S. I.; Bancewicz, T.; Maroulis, G.

    2014-08-01

    The rototranslational collision-induced absorption (CIA) at different temperatures and collision-induced light scattering (CILS) at room temperature of nitrogen gas are analyzed in terms of new isotropic intermolecular potential, multipole-induced dipole functions and interaction-induced pair polarizability models, using quantum spectral lineshape computations. The irreducible spherical form for the induced operator of light scattering mechanisms was determined. The high frequency wings are discussed in terms of the collision-induced rotational Rayleigh effect and estimates for the dipole-octopole polarizability E4, is obtained and checked with the ab initio theoretical value. The quality of the present potential has been checked by comparing between calculated and experimental thermo-physical and transport properties over a wide temperature range, which are found to be in good agreement.

  12. CO-0.30-0.07: A Candidate Site of Collision-induced Massive Star Formation in the Milky Way's Central Molecular Zone

    NASA Astrophysics Data System (ADS)

    Tanaka, K.

    2016-05-01

    Cloud-cloud collision has long been claimed to be an efficient trigger of massive star formation. We present interferometric maps of a candidate site of collision-triggered star formation newly discovered at 40 pc projected distance from the Galactic center. The cloud CO- 0.3 has an extremely broad molecular line emission of a 140 km s-1 velocity width despite of absence of any known energy sources nearby and inside the cloud. Recent observations with the Atacama Large Millimeter and Submillimeter Array have unveiled that the cloud is comprised by two distinctive velocity components which appear to contact at a thin, well-defined interface layer on the plane-of-the-sky, suggesting that the extremely broad emissions originate from shocked regions created by cloud-cloud collision.

  13. Process and product development in the manufacturing of molecular therapeutics.

    PubMed

    Atkinson, E M; Christensen, J R

    1999-08-01

    In the development of molecular therapies, a great deal of attention has focused on tissue targets, gene delivery vectors, and expression cassettes. In order to become an approved therapy, however, a molecular therapeutic has to pass down the same product registration pathway as any other biological product. Moving from research into industrial production requires careful attention to regulatory, manufacturing and quality concerns. Early work on developing and characterizing robust and scaleable manufacturing processes will ultimately be rewarded by ease of implementation as the product is successful in clinical trials. Regulatory agencies require solid process and product characterization studies to demonstrate control and understanding of the molecular therapeutic. As the gene therapy industry matures, standards will continue to rise, creating an industry that is capable of producing safe, high-quality and effective therapies for many of the world's most difficult disease targets. PMID:11713755

  14. Molecular-beam Studies of Primary Photochemical Processes

    DOE R&D Accomplishments Database

    Lee, Y. T.

    1982-12-01

    Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

  15. Nonsequential double ionization of helium in IR+XUV two-color laser fields: Collision-ionization process

    NASA Astrophysics Data System (ADS)

    Jin, Facheng; Tian, Yuanye; Chen, Jing; Yang, Yujun; Liu, Xiaojun; Yan, Zong-Chao; Wang, Bingbing

    2016-04-01

    We investigate the nonsequential double ionization (NSDI) process of an atom in IR+XUV two-color intense laser fields, where the photon energy of the XUV laser is higher than the atomic ionization threshold. By using the frequency-domain theory, we consider the NSDI as a process caused by the collision-ionization mechanism and obtain the NSDI spectrum that presents a multiplateau structure. With the help of channel analysis, we find that the height of a plateau in the NSDI spectrum is determined by the number of XUV photons absorbed by the electrons. Furthermore, to explain the interference structure in the NSDI spectrum, we also compare the contributions of forward and backward collisions to the NSDI probability. We find that the forward collision dominates the contributions to the NSDI when two electrons are ejected along the same direction and both forward and backward collisions make a comparable contribution to NSDI when the two electrons are ejected along opposite directions. By applying the saddle-point approximation, we obtain an energy-circle formula, which may illustrate the formation of the NSDI spectrum structure.

  16. Ultracold ionizing collisions in metastable xenon

    NASA Astrophysics Data System (ADS)

    Orzel, Chad Ryan

    1999-10-01

    This work presents the results of a series of experiments investigating Penning and associative ionization collisions in laser-cooled samples of metastable xenon. An absolute measurement of the collisional rate coefficient for the ionizing collision process is made for an unpolarized sample of 132 Xe, and the rate coefficients for unpolarized samples of three bosonic (132Xe, 134Xe, and 136Xe) and two fermionic (129Xe and 131Xe) isotopes are found to be identical at temperatures above the p- wave centrifugal barrier. A new technique exploiting the correlations which arise between position and velocity in a ballistically expanding sample is used to measure collisional rate coefficients at ultra-low ( <= 1 μK) temperatures in spin-polarized samples. Quantum statistical effects forbid s-wave collisions for spin-polarized fermions; a factor of two reduction in the ratio of spin-polarized to unpolarized collisional rate coefficients at low temperature is observed in a sample of fermions, while the ratio for a sample of bosons increases by 50%. Optical control of ultra-cold collisions is demonstrated, exploiting the long collision time for samples at ~100 μK to increase or decrease the collision rate by laser excitation to attractive or repulsive molecular potentials during the collision process. Optical shielding is used to reduce the collisional rate coefficient by as much as a factor of 8 below its value in the absence of light, and by a factor of 30 below its value in a magneto-optical trap (MOT). This technique is used to increase the number and density of atoms in the MOT, as well as the lifetime of the trap. Optical control techniques are exploited using short (40 ns) laser pulses to study the dynamics of ultra-cold collisions in a time-resolved manner. The rate of associative ionization in excited-state collisions is estimated, and flux enhancement of the rate of ground- state collisions is observed. A simple theoretical model explains the dynamics of time-resolved optical shielding, and measurements of the collision time for optical shielding are used to extract an effective C3 coefficient for the excited-state molecular potentials. Finally, in a three-dimensional optical lattice, the dynamical effects of the optical potential on the collision process are observed. Enhancement of the collision rate over that for free atoms is observed at short times after the atoms are loaded into the lattice. After the atoms thermalize and localize into individual potential wells, the collision rate is suppressed by as much as a factor of two. From these measurements and a simple model, an estimate of the rate at which atoms ``hop'' between wells is extracted.

  17. Cenozoic Mountain Building Process in the Greater Caucasus, from Subduction to Collision

    NASA Astrophysics Data System (ADS)

    Wang, S. J.; Lee, Y. H.; Chung, S. L.; Okrostsvaridze, A.

    2014-12-01

    The Arabia-Eurasia collision propagates from south to north which results in the south Caspian Sea northward subducting and rapid exhumation in the Greater Caucasus. In this study we conduct the apatite fission track dating combing with previous thermochronolgy data to reveal the comprehensive exhumation history of the Greater Caucasus. The Greater Caucasus shows the bivegent-wedge shape and the highest metamorphic grade shows in the central axis area and decreases to northward and southward. The apatite shows in the central axis area (ca. 2-5 Ma) with highest elevation indicates the highest uplift and exhumation rate area that indicates the all the Caucasus start to rapid exhumation since the Pliocene. The apatite ages increases the ages to the east and west which indicates decreasing the exhumation. Variation the exhumation along the strike of mountain infers different convergence process. To the eastern side the transition or oceanic North Anatolia crust subduct to the Eurasia plate and North Anatolia continent crust subduct and collide with Eurasia plate that result in high exhumation rate in the central Greater Caucasus.

  18. Revisiting the reactivity of uracil during collision induced dissociation: tautomerism and charge-directed processes.

    PubMed

    Beach, Daniel G; Gabryelski, Wojciech

    2012-05-01

    In our recent work towards the nontarget identification of products of nucleic acid (NA) damage in urine, we have found previous work describing the dissociation of NA bases not adequate to fully explain their observed reactivity. Here we revisit the gas-phase chemistry of protonated uracil (U) during collision induced dissociation (CID) using two modern tandem mass spectrometry techniques; quadrupole ion trap (QIT) and quadrupole time of flight (Q-TOF). We present detailed mechanistic proposals that account for all observed products of our experiments and from previous isotope labeling data, and that are supported by previous ion spectroscopy results and theoretical work. The diverse product-ions of U cannot be explained adequately by only considering the lowest energy form of protonated U as a precursor. The tautomers adopted by U during collisional excitation make it possible to relate the complex reactivity observed to reasonable mechanistic proposals and feasible product-ion structures for this small highly conjugated heterocycle. These reactions proceed from four different stable tautomers, which are excited to a specific activated precursor from which dissociation can occur via a charge-directed process through a favorable transition state to give a stabilized product. Understanding the chemistry of uracil at this level will facilitate the identification of new modified uracil derivatives in biological samples based solely on their reactivity during CID. Our integrated approach to describing ion dissociation is widely applicable to other NA bases and similar classes of biomolecules. PMID:22351291

  19. Stopping powers and cross sections due to two-photon processes in relativistic nucleus-nucleus collision

    NASA Technical Reports Server (NTRS)

    Cheung, Wang K.; Norbury, John W.

    1992-01-01

    The radiation dose received from high energy galactic cosmic rays (GCR) is a limiting factor in the design of long duration space flights and the building of lunar and martian habitats. It is of vital importance to have an accurate understanding of the interactions of GCR in order to assess the radiation environment that the astronauts will be exposed to. Although previous studies have concentrated on the strong interaction process in GCR, there are also very large effects due to electromagnetic (EM) interactions. In this report we describe our first efforts at understanding these EM production processes due to two-photon collisions. More specifically, we shall consider particle production processes in relativistic heavy ion collisions (RHICs) through two-photon exchange.

  20. Collision cross section prediction of deprotonated phenolics in a travelling-wave ion mobility spectrometer using molecular descriptors and chemometrics.

    PubMed

    Gonzales, Gerard Bryan; Smagghe, Guy; Coelus, Sofie; Adriaenssens, Dieter; De Winter, Karel; Desmet, Tom; Raes, Katleen; Van Camp, John

    2016-06-14

    The combination of ion mobility and mass spectrometry (MS) affords significant improvements over conventional MS/MS, especially in the characterization of isomeric metabolites due to the differences in their collision cross sections (CCS). Experimentally obtained CCS values are typically matched with theoretical CCS values from Trajectory Method (TM) and/or Projection Approximation (PA) calculations. In this paper, predictive models for CCS of deprotonated phenolics were developed using molecular descriptors and chemometric tools, stepwise multiple linear regression (SMLR), principal components regression (PCR), and partial least squares regression (PLS). A total of 102 molecular descriptors were generated and reduced to 28 after employing a feature selection tool, composed of mass, topological descriptors, Jurs descriptors and shadow indices. Therefore, the generated models considered the effects of mass, 3D conformation and partial charge distribution on CCS, which are the main parameters for either TM or PA (only 3D conformation) calculations. All three techniques yielded highly predictive models for both the training (R(2)SMLR = 0.9911; R(2)PCR = 0.9917; R(2)PLS = 0.9918) and validation datasets (R(2)SMLR = 0.9489; R(2)PCR = 0.9761; R(2)PLS = 0.9760). Also, the high cross validated R(2) values indicate that the generated models are robust and highly predictive (Q(2)SMLR = 0.9859; Q(2)PCR = 0.9748; Q(2)PLS = 0.9760). The predictions were also very comparable to the results from TM calculations using modified mobcal (N2). Most importantly, this method offered a rapid (<10 min) alternative to TM calculations without compromising predictive ability. These methods could therefore be used in routine analysis and could be easily integrated to metabolite identification platforms. PMID:27181646

  1. Collision cross sectional areas from analysis of Fourier transform ion cyclotron resonance line width: a new method for characterizing molecular structure.

    PubMed

    Yang, Fan; Voelkel, Jacob E; Dearden, David V

    2012-06-01

    We demonstrate a technique for determining molecular collision cross sections via measuring the variation of Fourier transform ion cyclotron resonance (FTICR) line width with background damping gas pressure, under conditions where the length of the FTICR transient is pressure limited. Key features of our method include monoisotopic isolation of ions, the pulsed introduction of damping gas to a constant pressure using a pulsed leak valve, short excitation events to minimize collisions during the excitation, and proper choice of damping gas (Xe is superior to He). The measurements are reproducible within a few percent, which is sufficient for distinguishing between many structural possibilities and is comparable to the uncertainty in cross sections calculated from computed molecular structures. These techniques complement drift ion mobility measurements obtained on dedicated instruments. They do not require a specialized instrument, but should be easily performed on any FTICR mass spectrometer equipped with a pulsed leak valve. PMID:22540423

  2. Young-type interference in collisions between hydrogen molecular ions and helium.

    PubMed

    Schmidt, L Ph H; Schössler, S; Afaneh, F; Schöffler, M; Stiebing, K E; Schmidt-Böcking, H; Dörner, R

    2008-10-24

    The dissociative electron transfer from He into 10 keV H2+ was measured in a kinematically complete experiment by using the cold target recoil ion momentum spectroscopy imaging technique in combination with a highly resolving molecular fragment imaging technique. The electron transfer into the dissociative b(3)Sigma+_(u) state of H2 could be selected by kinematic conditions. We find a striking double slit interference pattern in the transverse momentum transfer which we can modify by selecting different internuclear distances. Compared to an optical double slit, interference minima and maxima are interchanged. The latter is the result of a phase shift in the electronic part of the wave function. PMID:18999747

  3. Theoretical analysis of dynamic processes for interacting molecular motors

    NASA Astrophysics Data System (ADS)

    Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem

    2015-02-01

    Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  4. Molecular collisions: Effect on the HD infrared spectrum and development of a Moyal quantum mechanical description

    NASA Astrophysics Data System (ADS)

    McQuarrie, Barry Robert

    1998-06-01

    Interference is possible between the allowed dipole moment of the molecule HD and the pair dipole moment induced by collision with a foreign gas atom. The resulting line shape can be described by the sum of a Lorentzian and an asymmetric profile. The mixing of rotational levels by an anisotropic interaction potential call permit components of the induced dipole moment that do not have the same symmetry of the allowed moment to interfere with it. For the rotational spectrum of HD-He and HD-Ar the effect of each component of the induced dipole moment on the line shape parameters is determined for various temperatures and transitions. For line intensity, the component with the same symmetry as the allowed moment always dominates, but the effect of the other components is shown to be significant. The line shape parameters for the vibrorotational spectrum of HD-He are calculated for P1(1),/ R1(0),/ R1(1) transitions at 77, 195, and 295 K. Moyal quantum mechanics is an alternative to Heisenberg or Schrodinger quantum mechanics. The method yields a semiclassical expansion of phase space trajectories in terms of Planck's constant, h. The Moyal correction to the classical part of the solution is found to O(h2). The first computational version of Moyal quantum mechanics to calculate average values for three dimensional systems with physically relevant parameters is developed. The system treated is the scattering of a Gaussian wave packet by the helium, neon, and argon interaction potentials. The Gaussian is squeezed in momentum so that the momentum average can be done analytically. This introduces a momentum correction and the Gaussian is taken to have a single initial velocity. We examine scattering at velocities of 300-1200 m/s. Sensitive areas of the phase space average are identified. Integrals over coordinate phase space (impact parameter and displacement y) are examined in detail. The region of phase space which produces rainbow scattering is determined to result in the largest quantum effects. The Moyal correction is found to be small for impact parameters greater than 2brainbow - bglory. The corrections to average values are examined in detail for helium at a velocity of 300 m/s. It is shown that the Moyal corrections have an asymptotic time behaviour which is the same as that of the classical part of the average, but that they may grow as t /to /infty to dominate the total average. The corrections to the average value are examined as functions of mass and velocity. The Moyal correction is seen to change sign relative to the classical part of the average in both cases. The momentum correction is shown to have a mass-2 dependence. More complex asymptotic behaviour of the Moyal correction is examined for both the mass and the velocity. Comparison between the size of the correction for the systems consisting of two helium, neon, and argon atoms is performed. (Abstract shortened by UMI.)

  5. Angular distribution and spin polarization of molecular auger processes

    NASA Astrophysics Data System (ADS)

    Lohmann, B.; Bonhoff, S.; Bonhoff, K.; Lehmann, J.; Blum, K.

    1997-02-01

    The general theory for angular distribution and spin polarization of molecular Auger electrons emitted from freely rotating diatomic molecules is discussed within the framework of a two-step model. Assuming electron impact ionization then, in contrast to a primary photoionization process, the number of independent parameters is no longer restricted by dipole selection rules. Different spin polarization states of the primary electron beam will be considered. The physical importance of a coherent excitation process is discussed within a simple example. Numerical results for the anisotropy parameters characterizing the dynamics of the Auger emission process are discussed for HF.

  6. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

    PubMed

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

    Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. PMID:21271625

  7. Non-Elastic Processes in Atom Rydberg-Atom Collisions: Review of State of Art and Problems

    NASA Astrophysics Data System (ADS)

    Mihajlov, A. A.; Srećković, V. A.; Ignjatović, Lj. M.; Klyucharev, A. N.; Dimitrijević, M. S.; Sakan, N. M.

    2015-12-01

    In our previous research, it has been demonstrated that inelastic processes in atom Rydberg-atom collisions, such as chemi-ionization and ( n- n') mixing, should be considered together. Here we will review the present state-of-the-art and the actual problems. In this context, we will consider the influence of the ( n- n')-mixing during a symmetric atom Rydberg-atom collision processes on the intensity of chemi-ionization process. It will be taken into account H(1s) + H ∗( n) collisional systems, where the principal quantum number is n>> 1. It will be demonstrated that the inclusion of ( n- n') mixing in the calculation, influences significantly on the values of chemi-ionization rate coefficients, particularly in the lower part of the block of the Rydberg states. Different possible channels of the ( n- n')-mixing influence on chemi-ionization rate coefficients will be demonstrated. The possibility of interpretation of the ( n- n')-mixing influence will be considered on the basis of two existing methods for describing the inelastic processes in symmetrical atom Rydberg-atom collisions.

  8. Preparation and characterization of two types of separate collagen nanofibers with different widths using aqueous counter collision as a gentle top-down process

    NASA Astrophysics Data System (ADS)

    Kondo, Tetsuo; Kumon, Daisuke; Mieno, Akiko; Tsujita, Yutaro; Kose, Ryota

    2014-12-01

    Two types of single collagen nanofibers with different widths were successfully prepared from native collagen fibrils using aqueous counter collision (ACC) as a top-down process. A mild collision of an aqueous suspension at a 100 MPa ejection pressure yielded nanofibers, termed CNF100, which have an inherent axial periodicity and are ˜100 nm in width and ˜10 μm in length. In contrast, ACC treatment at 200 MPa provided a non-periodic, shorter and thinner nanofiber, termed CNF10, that was ˜10 nm in width and ˜5 μm in length. Both nanofibers exhibited the inherent triple helix conformation of native collagen supramolecules. Even a medial collision that exceeded the above ACC pressures provided solely a mixture of the two nanofiber products. The two nanofiber types were well characterized, and their tensile strengths were estimated based on their sonication-induced fragmentation behaviors that related to their individual fiber morphologies. As a result, CNF10, which was found to be a critical minimum nanofibril unit, and CNF10 exhibited totally different features in sizes, morphology, tensile strength and viscoelastic properties. In particular, as the mechanical strength of the molecular scaffold affects cell differentiation, the two collagen nanofibers prepared here by ACC have the potential for controlling cell differentiation in possibly different ways, as they have different mechanical properties. This encourages the consideration of the application of CNF100 and CNF10 in the fabrication of new functional materials with unique properties such as a scaffold for tissue engineering.

  9. The role of multiple electron capture in the x-ray emission process following charge exchange collisions with neutral targets

    NASA Astrophysics Data System (ADS)

    Otranto, S.; Cariatore, N. D.; Olson, R. E.

    2015-01-01

    In this work we theoretically study photonic spectra that follow charge exchange processes between highly charged ions and neutral argon and CO targets. The range of collision energies studied is 5 eV/amu-10 keV/amu, covering typical EBIT-traps and Solar Wind energies. Our studies are based on multiple electrons schemes within the classical trajectory Monte Carlo method. Electrons are sorted with the sequential binding energies for the target under consideration. The role played by the multiple electron capture process for the different collision systems under consideration is explicitly analyzed and its contribution separated as arising from double radiative decay and autoionizing multiple capture. Present studies are stimulated by the upcoming launch of the Astro-H mission in 2015, which will provide high resolution spectra in the 0.3 keV-12keV band.

  10. Stopping powers and cross sections due to two-photon processes in relativistic nucleus-nucleus collisions

    NASA Technical Reports Server (NTRS)

    Cheung, Wang K.; Norbury, John W.

    1994-01-01

    The effects of electromagnetic-production processes due to two-photon exchange in nucleus-nucleus collisions are discussed. Feynman diagrams for two-photon exchange are evaluated using quantum electrodynamics. The total cross section and stopping power for projectile and target nuclei of identical charge are found to be significant for heavy nuclei above a few GeV per nucleon-incident energy.

  11. Experimental study of the space-time development of the particle production process in hadron-nucleon collisions, using massive target nucleus as a detector

    NASA Technical Reports Server (NTRS)

    Strugalski, Z.

    1985-01-01

    Experimental study of the space-time development of the particle production process in hadronic collisions at its initial stage was performed. Massive target nuclei have been used as fine detectors of properties of the particle production process development within time intervals smaller than 10 to the 22nd power s and spatial distances smaller than 10 to the 12th power cm. In hadron-nucleon collisions, in particular in nucleon-nucleon collisions, the particle production process goes through intermediate objects in 2 yields 2 type endoergic reactions. The objects decay into commonly observed resonances and paricles.

  12. Theoretical studies in molecular fragmentation: Processes, energetics and diagnostics

    NASA Astrophysics Data System (ADS)

    Kirby, K. P.

    1983-09-01

    This research is directed toward providing diagnostic tools with which to identify and quantify the presence of fragment species and their energy states resulting from molecular destruction processes. Ab initio methods were used to calculate potential energy curves and transition moments for excited Sigma + and 1 Pi states of CO. Vibration rotation transition probabilities for vibrationally hot CN have been obtained. Work is commencing on the excited electronic states of NH.

  13. Study of a hydrogen-bombardment process for molecular cross-linking within thin films

    SciTech Connect

    Liu, Y.; Yang, J.; Yang, D. Q.; Nie, H.-Y.; Lau, W. M.

    2011-02-21

    A low-energy hydrogen bombardment method, without using any chemical additives, has been designed for fine tuning both physical and chemical properties of molecular thin films through selectively cleaving C-H bonds and keeping other bonds intact. In the hydrogen bombardment process, carbon radicals are generated during collisions between C-H bonds and hydrogen molecules carrying {approx}10 eV kinetic energy. These carbon radicals induce cross-linking of neighboring molecular chains. In this work, we focus on the effect of hydrogen bombardment on dotriacontane (C{sub 32}H{sub 66}) thin films as growing on native SiO{sub 2} surfaces. After the hydrogen bombardment, XPS results indirectly explain that cross-linking has occurred among C{sub 32}H{sub 66} molecules, where the major chemical elements have been preserved even though the bombarded thin film is washed by organic solution such as hexane. AFM results show the height of the perpendicular phase in the thin film decreases due to the bombardment. Intriguingly, Young's modulus of the bombarded thin films can be increased up to {approx}6.5 GPa, about five times of elasticity of the virgin films. The surface roughness of the thin films can be kept as smooth as the virgin film surface after thorough bombardment. Therefore, the hydrogen bombardment method shows a great potential in the modification of morphological, mechanical, and tribological properties of organic thin films for a broad range of applications, especially in an aggressive environment.

  14. Subduction and collision processes in the Central Andes constrained by converted seismic phases.

    PubMed

    Yuan, X; Sobolev, S V; Kind, R; Oncken, O; Bock, G; Asch, G; Schurr, B; Graeber, F; Rudloff, A; Hanka, W; Wylegalla, K; Tibi, R; Haberland, C; Rietbrock, A; Giese, P; Wigger, P; Röwer, P; Zandt, G; Beck, S; Wallace, T; Pardo, M; Comte, D

    The Central Andes are the Earth's highest mountain belt formed by ocean-continent collision. Most of this uplift is thought to have occurred in the past 20 Myr, owing mainly to thickening of the continental crust, dominated by tectonic shortening. Here we use P-to-S (compressional-to-shear) converted teleseismic waves observed on several temporary networks in the Central Andes to image the deep structure associated with these tectonic processes. We find that the Moho (the Mohorovicić discontinuity--generally thought to separate crust from mantle) ranges from a depth of 75 km under the Altiplano plateau to 50 km beneath the 4-km-high Puna plateau. This relatively thin crust below such a high-elevation region indicates that thinning of the lithospheric mantle may have contributed to the uplift of the Puna plateau. We have also imaged the subducted crust of the Nazca oceanic plate down to 120 km depth, where it becomes invisible to converted teleseismic waves, probably owing to completion of the gabbro-eclogite transformation; this is direct evidence for the presence of kinetically delayed metamorphic reactions in subducting plates. Most of the intermediate-depth seismicity in the subducting plate stops at 120 km depth as well, suggesting a relation with this transformation. We see an intracrustal low-velocity zone, 10-20 km thick, below the entire Altiplano and Puna plateaux, which we interpret as a zone of continuing metamorphism and partial melting that decouples upper-crustal imbrication from lower-crustal thickening. PMID:11140679

  15. Molecular (Feshbach) treatment of charge exchange Li/sup 3 +/+He collisions. II. Cross sections

    SciTech Connect

    Errea, L.F.; Martin, F.; Mendez, L.; Riera, A.; Yanez, M.

    1986-05-15

    Using the wave functions calculated in the preceding article, and a common translation factor, the charge exchange cross section for the Li/sup 3 +/+He(1s/sup 2/) reaction is calculated, and the mechanism of the process discussed. We show how small deviations from the Landau--Zener model, which are unrelated to Nikitin's conditions for its validity, lead to a minimum of the cross section at an impact energy Eapprox. =1 keV, and to larger values of sigma at intermediate nuclear velocities.

  16. Large scale molecular dynamics modeling of materials fabrication processes

    SciTech Connect

    Belak, J.; Glosli, J.N.; Boercker, D.B.; Stowers, I.F.

    1994-02-01

    An atomistic molecular dynamics model of materials fabrication processes is presented. Several material removal processes are shown to be within the domain of this simulation method. Results are presented for orthogonal cutting of copper and silicon and for crack propagation in silica glass. Both copper and silicon show ductile behavior, but the atomistic mechanisms that allow this behavior are significantly different in the two cases. The copper chip remains crystalline while the silicon chip transforms into an amorphous state. The critical stress for crack propagation in silica glass was found to be in reasonable agreement with experiment and a novel stick-slip phenomenon was observed.

  17. Theoretical studies of molecular processes in catalysis and materials

    SciTech Connect

    Hay, P.J.

    1996-12-31

    Applications are presented of quantum chemistry approaches to molecular processes in three areas: catalysis, chemical vapor deposition and polymerization. Reactions of organic molecules at acid sites in zeolite catalysts are investigated using aluminosilicate cluster models with an aim towards understanding hydrocarbon cracking chemistry. Gradient-corrected density functional theory is employed to study the chemical processes involved in B-doped polysilicon deposition and Ci-ion etching of silicon surfaces. Finally the initiation step of base-catalyzed polymerization of siloxane polymers is examined using ab initio quantum chemistry and reaction field salvation models.

  18. Natural language processing and visualization in the molecular imaging domain.

    PubMed

    Tulipano, P Karina; Tao, Ying; Millar, William S; Zanzonico, Pat; Kolbert, Katherine; Xu, Hua; Yu, Hong; Chen, Lifeng; Lussier, Yves A; Friedman, Carol

    2007-06-01

    Molecular imaging is at the crossroads of genomic sciences and medical imaging. Information within the molecular imaging literature could be used to link to genomic and imaging information resources and to organize and index images in a way that is potentially useful to researchers. A number of natural language processing (NLP) systems are available to automatically extract information from genomic literature. One existing NLP system, known as BioMedLEE, automatically extracts biological information consisting of biomolecular substances and phenotypic data. This paper focuses on the adaptation, evaluation, and application of BioMedLEE to the molecular imaging domain. In order to adapt BioMedLEE for this domain, we extend an existing molecular imaging terminology and incorporate it into BioMedLEE. BioMedLEE's performance is assessed with a formal evaluation study. The system's performance, measured as recall and precision, is 0.74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information. PMID:17084109

  19. Primary damage in tungsten using the binary collision approximation, molecular dynamic simulations and the density functional theory

    NASA Astrophysics Data System (ADS)

    De Backer, A.; Sand, A.; Ortiz, C. J.; Domain, C.; Olsson, P.; Berthod, E.; Becquart, C. S.

    2016-02-01

    The damage produced by primary knock-on atoms (PKA) in W has been investigated from the threshold displacement energy (TDE) where it produces one self interstitial atom-vacancy pair to larger energies, up to 100 keV, where a large molten volume is formed. The TDE has been determined in different crystal directions using the Born-Oppenheimer density functional molecular dynamics (DFT-MD). A significant difference has been observed without and with the semi-core electrons. Classical MD has been used with two different empirical potentials characterized as ‘soft’ and ‘hard’ to obtain statistics on TDEs. Cascades of larger energy have been calculated, with these potentials, using a model that accounts for electronic losses (Sand et al 2013 Europhys. Lett. 103 46003). Two other sets of cascades have been produced using the binary collision approximation (BCA): a Monte Carlo BCA using SDTrimSP (Eckstein et al 2011 SDTrimSP: Version 5.00. Report IPP 12/8) (similar to SRIM www.srim.org) and MARLOWE (RSICC Home Page. (https://rsicc.ornl.gov/codes/psr/psr1/psr-137.html) (accessed May, 2014)). The comparison of these sets of cascades gave a recombination distance equal to 12 Å which is significantly larger from the one we reported in Hou et al (2010 J. Nucl. Mater. 403 89) because, here, we used bulk cascades rather than surface cascades which produce more defects (Stoller 2002 J. Nucl. Mater. 307 935, Nordlund et al 1999 Nature 398 49). Investigations on the defect clustering aspect showed that the difference between BCA and MD cascades is considerably reduced after the annealing of the cascade debris at 473 K using our Object Kinetic Monte Carlo model, LAKIMOCA (Domain et al 2004 J. Nucl. Mater. 335 121).

  20. Interstellar Processes Leading to Molecular Deuterium Enrichment and Their Detection

    NASA Technical Reports Server (NTRS)

    Sandford, Scott A.; Kliss, Mark (Technical Monitor)

    2001-01-01

    Large deuterium (D) enrichments in meteoritic materials indicate that interstellar organic materials survived incorporation into parent bodies within the forming Solar System. These enrichments are likelier due to one or more of four distinct astrochemical processes. These are (1) low temperature gas phase ion-molecule reactions; (2) low temperature gas-grain reactions; (3) gas phase unimolecular photodissociation, and (4) ultraviolet photolysis in D-enriched ice mantles. Each of these processes should be associated with molecular carriers having, distinct regiochemical signatures (D placement on the product molecules, correlation with specific chemical functionalities, etc.). These processes are reviewed and specific spectroscopic signatures for the detection of these processes in space are identified and described.

  1. Effects of adsorption and roughness upon the collision processes at the convertor surface of a plasma sputter negative ion source

    SciTech Connect

    Kenmotsu, T.; Wada, M.

    2012-02-15

    Atomic collision processes associated with surface production of negative hydrogen ions (H{sup -}) by particle reflection at molybdenum surface immersed in hydrogen plasma have been investigated. To calculate sputtering yields of Cs, as well as energy spectra and angular distributions of reflected hydrogen atoms from molybdenum surface by H{sup +} ion and Cs{sup +} ion bombardments, a Monte Carlo simulation code ACAT (Atomic Collision in Amorphous Target) was run with the corresponding surface conditions. A fractal surface model has been developed and adopted to ACAT for evaluating the effect due to roughness of target material. The results obtained with ACAT have indicated that the retention of hydrogen atoms leads to the reduction in sputtering yields of Cs, and the surface roughness does largely affect the sputtering yields of Cs.

  2. Molecular dynamic simulation of non-melt laser annealing process

    NASA Astrophysics Data System (ADS)

    Liren, Yan; Dai, Li; Wei, Zhang; Zhihong, Liu; Wei, Zhou; Quan, Wang

    2016-03-01

    Molecular dynamic simulation is performed to study the process of material annealing caused by a 266 nm pulsed laser. A micro-mechanism describing behaviors of silicon and impurity atoms during the laser annealing at a non-melt regime is proposed. After ion implantation, the surface of the Si wafer is acted by a high energy laser pulse, which loosens the material and partially frees both Si and impurity atoms. While the residual laser energy is absorbed by valence electrons, these atoms are recoiled and relocated to finally form a crystal. Energy-related movement behavior is observed by using the molecular dynamic method. The non-melt laser anneal appears to be quite sensitive to the energy density of the laser, as a small excess energy may causes a significant impurity diffusion. Such a result is also supported by our laser anneal experiment.

  3. Exclusive processes in electron-ion collisions in the dipole formalism

    SciTech Connect

    Cazaroto, E. R.; Navarra, F. S.; Carvalho, F.; Goncalves, V. P.

    2013-03-25

    We compare the predictions of two saturation models for production of vector mesons and of photons in electron-ion collisions. The models considered are the b-CGC and the rcBK. The calculations were made in the kinematical range of the LHeC and of the future eRHIC.

  4. Systematic investigation of negative Cooper-Frye contributions in heavy ion collisions using coarse-grained molecular dynamics

    NASA Astrophysics Data System (ADS)

    Oliinychenko, D.; Huovinen, P.; Petersen, H.

    2015-02-01

    In most heavy ion collision simulations involving relativistic hydrodynamics, the Cooper-Frye formula is applied to transform the hydrodynamical fields to particles. In this article the so-called negative contributions in the Cooper-Frye formula are studied using a coarse-grained transport approach. The magnitude of negative contributions is investigated as a function of hadron mass, collision energy in the range of Elab=5 -160 A GeV, collision centrality, and the energy density transition criterion defining the hypersurface. The microscopic results are compared to negative contributions expected from hydrodynamical treatment assuming local thermal equilibrium. The main conclusion is that the number of actual microscopic particles flying inward is smaller than the negative contribution one would expect in an equilibrated scenario. The largest impact of negative contributions is found to be on the pion rapidity distribution at midrapidity in central collisions. For this case negative contributions in equilibrium constitute 8-13% of positive contributions, depending on collision energy, but only 0.5-4% in cascade calculation. The dependence on the collision energy itself is found to be nonmonotonous with a maximum at 10 - 20 A GeV.

  5. Target structure-induced suppression of the ionization cross section for low-energy antiproton-molecular hydrogen collisions: theoretical confirmation.

    PubMed

    Abdurakhmanov, I B; Kadyrov, A S; Fursa, D V; Bray, I

    2013-10-25

    Theoretical confirmation of the experimentally observed phenomenon [Knudsen et al., Phys. Rev. Lett. 105, 213201 (2010)] of target structure-induced suppression of the ionization cross section for low-energy antiproton-molecular hydrogen collisions is given. To this end a novel time-dependent convergent close-coupling approach to the scattering problem that accounts for all possible orientations of the molecular target, has been developed. The approach is applied to study single ionization of molecular hydrogen on the wide energy range from 1 keV to 2 MeV with a particular emphasis on low energies. Results for the orientation-averaged total single ionization cross section are compared with available experimental data and good agreement is found at low (<20 keV) and high (>90 keV) energies. A minor discrepancy is found within a small energy gap near the maximum of the cross section. PMID:24206488

  6. Molecular Beam Studies of Kinetic Processes in Nanoscale Water Films

    NASA Astrophysics Data System (ADS)

    Smith, R. Scott; Kay, Bruce D.

    Studies of the properties of crystalline ice and amorphous solid water are the focus of considerable diverse and interdisciplinary research. The reasons include understanding heterogeneous atmospheric processes, interstellar and cometary astrophysics, cryobiology, and the physics and chemistry of liquids. In this review we summarize our recent work using nanoscale ice films to characterize the kinetic behavior of crystalline ice and amorphous solid water. The adsorption, desorption, crystallization and diffusion kinetics of the nanoscale films are studies using molecular beam and programmed desorption techniques. The results of these experiments and their implications for the physical properties of nanoscale ice films are presented.

  7. Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides

    DOEpatents

    Kozyavkin, Sergei A.; Malykh, Andrei G.; Polouchine, Nikolai N.; Slesarev, Alexei I.

    2003-04-15

    A method of inhibiting at least one molecular process in a sample, comprising administering to the sample an oligonucleotide or polynucleotide containing at least one monomeric unit having formula (I): wherein A is an organic moiety, n is at least 1, and each X is independently selected from the group consisting of --NRCOCONu, --NHCOCR.sub.2 CR.sub.2 CONu, --NHCOCR.dbd.CRCONu, and --NHCOSSCONu, wherein each R independently represents H or a substituted or unsubstituted alkyl group, and Nu represents a nucleophile, or a salt of the compound.

  8. Process for attaching molecular wires and devices to carbon nanotubes and compositions thereof

    NASA Technical Reports Server (NTRS)

    Tour, James M. (Inventor); Bahr, Jeffrey L. (Inventor); Yang, Jiping (Inventor)

    2008-01-01

    The present invention is directed towards processes for covalently attaching molecular wires and molecular electronic devices to carbon nanotubes and compositions thereof. Such processes utilize diazonium chemistry to bring about this marriage of wire-like nanotubes with molecular wires and molecular electronic devices.

  9. Application to processing system using intra-molecular BRET

    NASA Astrophysics Data System (ADS)

    Otsuji, Tomomi; Okuda-Ashitaka, Emiko; Kojima, Satoshi; Akiyama, Hidehumi; Ito, Seiji; Ohmiya, Yoshihiro

    2003-07-01

    Luciferases are used as the reporter gene for promoter activity, whereas a green fluorescent protein (GFP) is used as marker for cellular function and localization. Recently, bioluminescence resonance energy transfer (BRET) between luciferase and YFP is used for analysis of inter-molecular reaction such as ligand-receptor in the living cells. The neuropeptides nocistatin (NST) and nociceptin/orphanin FQ (Noc/OFQ) are derived from the same precursor protein, while NST exhibits antagonism against Noc/OFQ-actions. In this study, we attempt an intra-molecular BRET system for monitoring dynamic biological process of the production of NST and Noc/OFQ in the living cells. At first, we constructed a fusion protein (Rluc-GFP) covalently linking luciferase (Renilla luciferase; Rluc) to Aequorea GFP as an intra-molecular BRET partner. Furthermore, we inserted constructs of mouse NST and Noc/OFQ (Rluc-m-GFP) or bovine NST and Noc/OFQ (Rluc-b-GFP) containing a proteolytic cleavage motif (Lys-Arg) within Rluc-GFP. When these constructions were transfected into Cos7 cells, all fusion proteins had luciferase activity and specific fluorescence. Luminescence spectra of Rluc-GFP, Rluc-m-GFP and Rluc-b-GFP fusion proteins with DeepBlueC as a substrate showed two peaks centered at 400 nm and 510 nm, whereas Rluc showed one peak centered at 400 nm. These results indicate that the proteolytic cleavage motif inserted fusion proteins between luciferase and GFP are available for intra-molecular BRET systems at first step.

  10. Coordinate space translation technique for simulation of electronic process in the ion-atom collision.

    PubMed

    Wang, Feng; Hong, Xuhai; Wang, Jian; Kim, Kwang S

    2011-04-21

    Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lüdde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O((3)P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results. PMID:21513388

  11. High Speed Data Processing for Imaging MS-Based Molecular Histology Using Graphical Processing Units

    NASA Astrophysics Data System (ADS)

    Jones, Emrys A.; van Zeijl, René J. M.; Andrén, Per E.; Deelder, André M.; Wolters, Lex; McDonnell, Liam A.

    2012-04-01

    Imaging MS enables the distributions of hundreds of biomolecular ions to be determined directly from tissue samples. The application of multivariate methods, to identify pixels possessing correlated MS profiles, is referred to as molecular histology as tissues can be annotated on the basis of the MS profiles. The application of imaging MS-based molecular histology to larger tissue series, for clinical applications, requires significantly increased computational capacity in order to efficiently analyze the very large, highly dimensional datasets. Such datasets are highly suited to processing using graphical processor units, a very cost-effective solution for high speed processing. Here we demonstrate up to 13× speed improvements for imaging MS-based molecular histology using off-the-shelf components, and demonstrate equivalence with CPU based calculations. It is then discussed how imaging MS investigations may be designed to fully exploit the high speed of graphical processor units.

  12. Finding Novel Molecular Connections between Developmental Processes and Disease

    PubMed Central

    Park, Jisoo; Wick, Heather C.; Kee, Daniel E.; Noto, Keith; Maron, Jill L.; Slonim, Donna K.

    2014-01-01

    Identifying molecular connections between developmental processes and disease can lead to new hypotheses about health risks at all stages of life. Here we introduce a new approach to identifying significant connections between gene sets and disease genes, and apply it to several gene sets related to human development. To overcome the limits of incomplete and imperfect information linking genes to disease, we pool genes within disease subtrees in the MeSH taxonomy, and we demonstrate that such pooling improves the power and accuracy of our approach. Significance is assessed through permutation. We created a web-based visualization tool to facilitate multi-scale exploration of this large collection of significant connections (http://gda.cs.tufts.edu/development). High-level analysis of the results reveals expected connections between tissue-specific developmental processes and diseases linked to those tissues, and widespread connections to developmental disorders and cancers. Yet interesting new hypotheses may be derived from examining the unexpected connections. We highlight and discuss the implications of three such connections, linking dementia with bone development, polycystic ovary syndrome with cardiovascular development, and retinopathy of prematurity with lung development. Our results provide additional evidence that plays a key role in the early pathogenesis of polycystic ovary syndrome. Our evidence also suggests that the VEGF pathway and downstream NFKB signaling may explain the complex relationship between bronchopulmonary dysplasia and retinopathy of prematurity, and may form a bridge between two currently-competing hypotheses about the molecular origins of bronchopulmonary dysplasia. Further data exploration and similar queries about other gene sets may generate a variety of new information about the molecular relationships between additional diseases. PMID:24874013

  13. Charge transfer processes: the role of optimized molecular orbitals.

    PubMed

    Meyer, Benjamin; Domingo, Alex; Krah, Tim; Robert, Vincent

    2014-08-01

    The influence of the molecular orbitals on charge transfer (CT) reactions is analyzed through wave function-based calculations. Characteristic CT processes in the organic radical 2,5-di-tert-butyl-6-oxophenalenoxyl linked with tetrathiafulvalene and the inorganic crystalline material LaMnO3 show that changes in the inner shells must be explicitly taken into account. Such electronic reorganization can lead to a reduction of the CT vertical transition energy up to 66%. A state-specific approach accessible through an adapted CASSCF (complete active space self-consistent field) methodology is capable of reaching good agreement with the experimental spectroscopy of CT processes. A partitioning of the relaxation energy in terms of valence- and inner-shells is offered and sheds light on their relative importance. This work paves the way to the intimate description of redox reactions using quantum chemistry methods. PMID:24781811

  14. Four-body charge transfer processes in proton-helium collisions

    NASA Astrophysics Data System (ADS)

    Chowdhury, U.; Harris, A. L.; Peacher, J. L.; Madison, D. H.

    2012-02-01

    Recent advancements in experimental techniques now allow for the study of fully differential cross sections (FDCS) for four-body collisions. The simplest four-body problem is a charged particle collision with a helium atom, in which both atomic electrons change state. This type of collision can result in many different outcomes, such as double excitation, excitation ionization, double ionization, transfer excitation, transfer ionization and double charge transfer. In this paper, we compare absolute experimental proton-helium FDCS for transfer excitation with the fully quantum mechanical 4BTTE (four-body transfer with target excitation) model. This model was previously used to study TTE for proton energies between 25 and 75 keV and reasonable agreement was found with the experimental data for large scattering angles, but not small angles. Since this is a first-order model, which contains contributions from all higher order terms, one would expect improved agreement with increasing energy and the purpose of this work was to look at higher energies. We found that the agreement with the magnitude of the experimental data became worse with increasing energy while the agreement with the shape of the data was reasonably good. Consequently, we conclude that the model contains the physical effects that determine the shape but not the magnitude of the cross section.

  15. Molecular processes of transgenerational acclimation to a warming ocean

    NASA Astrophysics Data System (ADS)

    Veilleux, Heather D.; Ryu, Taewoo; Donelson, Jennifer M.; van Herwerden, Lynne; Seridi, Loqmane; Ghosheh, Yanal; Berumen, Michael L.; Leggat, William; Ravasi, Timothy; Munday, Philip L.

    2015-12-01

    Some animals have the remarkable capacity to acclimate across generations to projected future climate change; however, the underlying molecular processes are unknown. We sequenced and assembled de novo transcriptomes of adult tropical reef fish exposed developmentally or transgenerationally to projected future ocean temperatures and correlated the resulting expression profiles with acclimated metabolic traits from the same fish. We identified 69 contigs representing 53 key genes involved in thermal acclimation of aerobic capacity. Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity. Our results are the first to reveal the molecular processes that may enable marine fishes to adjust to a future warmer environment over multiple generations.

  16. Measurement of the weak mixing angle with the Drell-Yan process in proton-proton collisions at the LHC

    SciTech Connect

    Chatrchyan, S.; et al.,

    2011-12-01

    A multivariate likelihood method to measure electroweak couplings with the Drell-Yan process at the LHC is presented. The process is described by the dilepton rapidity, invariant mass, and decay angle distributions. The decay angle ambiguity due to the unknown assignment of the scattered constituent quark and antiquark to the two protons in a collision is resolved statistically using correlations between the observables. The method is applied to a sample of dimuon events from proton-proton collisions at sqrt(s) = 7 TeV collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 1.1 inverse femtobarns. From the dominant u-ubar, d-dbar to gamma*/Z to opposite sign dimuons process, the effective weak mixing angle parameter is measured to be sin^2(theta[eff]) = 0.2287 +/- 0.0020 (stat.) +/- 0.0025 (syst.). This result is consistent with measurements from other processes, as expected within the standard model.

  17. Molecular Tracking, through Processing, of Campylobacter Strains Colonizing Broiler Flocks▿

    PubMed Central

    Elvers, Karen T.; Morris, Victoria K.; Newell, Diane G.; Allen, Vivien M.

    2011-01-01

    Many of the poultry flocks produced in the United Kingdom are colonized with Campylobacter, and the intensive nature of poultry processing usually results in contaminated carcasses. In this study, a previously reported molecular oligonucleotide probe method was used to track a specific flock-colonizing strain(s) on broiler carcasses during processing in two United Kingdom commercial poultry processing plants. Five Campylobacter-positive flocks were sampled at four points along the processing line, postbleed, postpluck, prechill, and postchill, and two Campylobacter-negative flocks processed immediately after positive flocks were sampled prechill. flaA was sequenced from Campylobacter strains isolated from these flocks, and strain-specific probes were synthesized. Skin and cecal samples were plated onto selective agar to give individual colonies, which were transferred onto membranes. These were then hybridized with the strain- and genus-specific probes. For all the 5 positive flocks, there was a significant reduction in campylobacters postbleed compared to postpluck but no subsequent fall on sampling pre- and postchill, and the strain(s) predominating on the carcasses throughout processing came from the flock being processed. This indicates that strains from the abattoir environment were not a significant cause of carcass contamination in flocks with well-established campylobacter colonization. However, negative flocks that were preceded by positive flocks were contaminated by strains that did not generally originate from the predominating strains recovered from the ceca of the previous positive flocks. This suggests that the abattoir environment has a significant role in the contamination of carcasses from negative but not fully colonized flocks. PMID:21705532

  18. Collision-induced dissociation of aminophospholipids (PE, MMPE, DMPE, PS): an apparently known fragmentation process revisited.

    PubMed

    Pittenauer, Ernst; Rehulka, Pavel; Winkler, Wolfgang; Allmaier, Günter

    2015-07-01

    A new type of low-mass substituted 4-oxazolin product ions of [M + H](+) precursor ions of aminophospholipids (glycerophosphatidylethanolamine, glycerophosphatidyl-N-methylethanolamine, glycerophosphatidyl-N,N-dimethylethanolamine, glycerophosphatidylserine) resulting from high-energy collision-induced dissociation (matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry) and low-energy collision-induced dissociation (e.g., electrospray ionization quadrupole reflectron time-of-flight mass spectrometry) with accurate mass determination is described; these were previously misidentified as CHO-containing radical cationic product ions. The mechanism for the formation of these ions is proposed to be via rapid loss of water followed by cyclization to an 11-membered-ring transition state for the sn-1 fatty acid substituent and to a ten-membered-ring transition state for the sn-2 fatty acid substituent, and via final loss of monoacylglycerol phosphate, leading to substituted 4-oxazolin product ions. The minimum structural requirement for this interesting skeletal rearrangement fragmentation is an amino group linked to at least one hydrogen atom (i.e., ethanolamine, N-methylethanolamine, serine). Therefore, N,N-dimethylethanolamine derivates do not exhibit this type of fragmentation. The analytical value of these product ions is given by the fact that by post source decay and particularly high-energy collision-induced dissociation achieved via matrix-assisted laser desorption/ionization time-of-flight/reflectron time-of-flight mass spectrometry, the sn-2-related substituted 4-oxazolin product ion is always significantly more abundant than the sn-1-related one, which is quite helpful for detailed structural analysis of complex lipids. All other important product ions found are described in detail (following our previously published glycerophospholipid product ion nomenclature; Pittenauer and Allmaier, Int. J. Mass. Spectrom. 301:90-1012, 2011). PMID:25633216

  19. Reply to Comment on Four-body charge transfer processes in proton helium collisions

    NASA Astrophysics Data System (ADS)

    Chowdhury, U.; Harris, A. L.; Peacher, J. L.; Madison, D. H.

    2013-01-01

    Houamer and Popov have performed a first Born approximation calculation (FBA) for TTE (charge transfer with target excitation) for 300 keV proton-helium collisions. Their results are in reasonable agreement with the absolute measurements of Schffler (2006 PhD thesis, University of Frankfurt am Main) whereas our FBA results yielded the shape of the experimental data reasonably well (except for small scattering angles) but with a magnitude that was a factor of 144 larger than experiment. Consequently, Houamer and Popov conclude that our results must have huge numerical errors. We have extensively tested our codes and we do not find any evidence to support this claim.

  20. Two-photon process and anomalous electron-pair production in /pi/p collisions

    SciTech Connect

    Ernst, D.J.; Albert, C.J.; Bottcher, C.; Strayer, M.R.

    1989-01-01

    The two-photon mechanism for lepton-pair production is calculated in a nonconventional way by treating the relative pion-nucleon motion in the classical limit. The results are compared with existing data for anomalous e/sup +/e/sup /minus// pairs produced in the collision of 16 GeV/c pions with protons. The results for differential cross sections as a function of the invariant pair mass, Feynman x, and transverse momentum are found to be in reasonable agreement with the data. The dominant piece of the cross section arises from the magnetic, spin-flip part of the nucleon current. 14 refs., 4 figs.

  1. Molecular specificity of multiple hippocampal processes governing fear extinction.

    PubMed

    Radulovic, Jelena; Tronson, Natalie C

    2010-01-01

    Over many years, fear extinction has been conceptualized as one dominant process, new inhibitory learning, which serves to dampen previously acquired fear. Here we present an alternative view, that brain region-specific processing of representations, expectations and emotional attributes of the fear-provoking event, recruits unique mechanisms that interdependently contribute to the conditioning and extinction of fear. The co-occurrence of these mechanisms within the fear circuit can thus be tracked and differentiated at a molecular and cellular level. Among others, the transcriptional regulators cFos, cAMP-dependent response element binding protein (CREB), Zif268, and extracellular signal-regulated kinases (Erk) stand out as hippocampal nuclear markers signaling novelty, arousal, retrieval, and prediction error, respectively. Consistent with evidence from human studies, these findings indicate that, beyond inhibitory learning, fear extinction requires modification of the emotional attributes and expectations that define the threatening context. Given the likely dysregulation of one or more of these processes in anxiety disorders, a key research challenge for the future is the identification and enhancement of individual extinction mechanisms to target the specific components of fear. Environmental stimuli lacking affective properties (conditioned stimuli, CS) rapidly become threatening if presented with stressful events (unconditioned stimuli, US). Consequently, based on a CS-US association, the presentation of the CS triggers species-specific fear responses until the US consistently stops occurring. At that point, new learning takes place and the fear response declines, a phenomenon termed extinction. The view that extinction occurs because a new, inhibitory CS-noUS association gains control over behavior, has remained dominant in the field. The implications of impaired fear regulation in the development of anxiety disorders have stimulated intense research in this area. Rodent studies identified the circuits involved in the conditioning and extinction of fear of salient cues, generating data that were confirmed in humans with brain imaging approaches. Nevertheless, research with experimental animals has not fully taken advantage of human data in order to better interpret extinction mechanisms in the framework of learning, expectation and emotion governing fear-motivated behavior. The present article aims to summarize recent molecular evidence on fear extinction, focusing on hippocampal mechanisms and experimental models of contextual fear, and compare the results with other relevant fear paradigms and human imaging studies. Instead of conceptualizing extinction learning as one process, such as CS-noUS association or inhibitory learning, we propose that fear extinction reflects the behavioral output of several region-specific learning processes that modify different components of the conditioning memory. The significance of these findings is discussed in the framework of fear regulation and anxiety disorders. PMID:20458884

  2. Solution processed molecular floating gate for flexible flash memories.

    PubMed

    Zhou, Ye; Han, Su-Ting; Yan, Yan; Huang, Long-Biao; Zhou, Li; Huang, Jing; Roy, V A L

    2013-01-01

    Solution processed fullerene (C60) molecular floating gate layer has been employed in low voltage nonvolatile memory device on flexible substrates. We systematically studied the charge trapping mechanism of the fullerene floating gate for both p-type pentacene and n-type copper hexadecafluorophthalocyanine (F16CuPc) semiconductor in a transistor based flash memory architecture. The devices based on pentacene as semiconductor exhibited both hole and electron trapping ability, whereas devices with F16CuPc trapped electrons alone due to abundant electron density. All the devices exhibited large memory window, long charge retention time, good endurance property and excellent flexibility. The obtained results have great potential for application in large area flexible electronic devices. PMID:24172758

  3. Solution processed molecular floating gate for flexible flash memories

    PubMed Central

    Zhou, Ye; Han, Su-Ting; Yan, Yan; Huang, Long-Biao; Zhou, Li; Huang, Jing; Roy, V. A. L.

    2013-01-01

    Solution processed fullerene (C60) molecular floating gate layer has been employed in low voltage nonvolatile memory device on flexible substrates. We systematically studied the charge trapping mechanism of the fullerene floating gate for both p-type pentacene and n-type copper hexadecafluorophthalocyanine (F16CuPc) semiconductor in a transistor based flash memory architecture. The devices based on pentacene as semiconductor exhibited both hole and electron trapping ability, whereas devices with F16CuPc trapped electrons alone due to abundant electron density. All the devices exhibited large memory window, long charge retention time, good endurance property and excellent flexibility. The obtained results have great potential for application in large area flexible electronic devices. PMID:24172758

  4. Graphics processing units accelerated semiclassical initial value representation molecular dynamics.

    PubMed

    Tamascelli, Dario; Dambrosio, Francesco Saverio; Conte, Riccardo; Ceotto, Michele

    2014-05-01

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly. PMID:24811627

  5. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tamascelli, Dario; Dambrosio, Francesco Saverio; Conte, Riccardo; Ceotto, Michele

    2014-05-01

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.

  6. Graphics processing units accelerated semiclassical initial value representation molecular dynamics

    SciTech Connect

    Tamascelli, Dario; Dambrosio, Francesco Saverio; Conte, Riccardo; Ceotto, Michele

    2014-05-07

    This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.

  7. Molecular dynamics study of structure and graphitization process of nanodiamonds

    NASA Astrophysics Data System (ADS)

    Bródka, A.; Hawełek, Ł.; Burian, A.; Tomita, S.; Honkimäki, V.

    2008-09-01

    Nanodiamond (nD) particles with the shapes of a truncated octahedron and a sphere of an average size of about 23 Å constituted starting configurations for molecular dynamics (MD) simulations using the reactive empirical bond order potential for carbon-carbon interaction. Calculations performed at 300 K showed rebuilding of the surface structure, where trivalent atoms were localised, and in both cases about 72% of atoms localised in the nD interior had tetravalent coordination. The inter-atomic carbon-carbon distances were slightly larger than those for the ideal diamond structure. The results obtained from simulations match quite well the high-energy X-ray diffraction data for explosive diamond nanoparticles recorded at the European Synchrotron Radiation Facility. To study graphitization process of the nDs we performed MD simulations at elevated temperatures up to 1800 K. Transformation of the truncated octahedron nD into onion-like carbon was observed at 1200 K. In this case, bonds between {1 1 1} planes were broken firstly, and then the planes bent forming the onion structure. Graphitization of the spherical nD appeared at 1500 K. The process started at the surface, where fragments of quasi-spherical shells were formed, and evolved into the nD centre. For both nDs the process became faster and more effective with increasing temperature.

  8. Molecular solution processing of metal chalcogenide thin film solar cells

    NASA Astrophysics Data System (ADS)

    Yang, Wenbing

    The barrier to utilize solar generated electricity mainly comes from their higher cost relative to fossil fuels. However, innovations with new materials and processing techniques can potentially make cost effective photovoltaics. One such strategy is to develop solution processed photovoltaics which avoid the expensive vacuum processing required by traditional solar cells. The dissertation is mainly focused on two absorber material system for thin film solar cells: chalcopyrite CuIn(S,Se)2 (CISS) and kesterite Cu2ZnSn(S,Se) 4 organized in chronological order. Chalcopyrite CISS is a very promising material. It has been demonstrated to achieve the highest efficiency among thin film solar cells. Scaled-up industry production at present has reached the giga-watt per year level. The process however mainly relies on vacuum systems which account for a significant percentage of the manufacturing cost. In the first section of this dissertation, hydrazine based solution processed CISS has been explored. The focus of the research involves the procedures to fabricate devices from solution. The topics covered in Chapter 2 include: precursor solution synthesis with a focus on understanding the solution chemistry, CISS absorber formation from precursor, properties modification toward favorable device performance, and device structure innovation toward tandem device. For photovoltaics to have a significant impact toward meeting energy demands, the annual production capability needs to be on TW-level. On such a level, raw materials supply of rare elements (indium for CIS or tellurium for CdTe) will be the bottleneck limiting the scalability. Replacing indium with zinc and tin, earth abundant kesterite CZTS exhibits great potential to reach the goal of TW-level with no limitations on raw material availability. Chapter 3 shows pioneering work towards solution processing of CZTS film at low temperature. The solution processed devices show performances which rival vacuum-based techniques and is partially attributed to the ease in controlling composition and CZTS phase through this technique. Based on this platform, comprehensive characterization on CZTS devices is carried out including solar cells and transistors. Especially defects properties are exploited in Chapter 4 targeting to identify the limiting factors for further improvement on CZTS solar cells efficiency. Finally, molecular structures and precursor solution stability have been explored, potentially to provide a universal approach to process multinary compounds.

  9. Inelastic processes in Na+-Ne, Na+-Ar, Ne+-Na, and Ar+-Na collisions in the energy range 0.5-14 keV

    NASA Astrophysics Data System (ADS)

    Lomsadze, R. A.; Gochitashvili, M. R.; Kezerashvili, R. Ya.

    2015-12-01

    Absolute cross sections for charge-exchange, ionization, and excitation in Na+-Ne and Na+-Ar collisions were measured in the ion energy range 0.5 -10 keV using a refined version of a capacitor method and collision and optical spectroscopy methods simultaneously in the same experimental setup. Ionization cross sections for Ne+-Na and Ar+-Na collisions are measured at energies of 2 -14 keV using a crossed-beam spectroscopy method. The experimental data and the schematic correlation diagrams are used to analyze and determine the mechanisms for these processes. For the charge-exchange process in Na+-Ar collisions two nonadiabatic regions are revealed and mechanisms responsible for these regions are explained. Structural peculiarity on the excitation function for the resonance lines of argon atoms in Na+-Ar collisions are observed and the possible mechanisms of this phenomenon are explored. The measured ionization cross sections for Na+-Ne and Ne+-Na collisions in conjunction with the Landau-Zener formula are used to determine the coupling matrix element and transition probability in a region of pseudocrossing of the potential curves.

  10. Molecular epidemiology biomarkers-Sample collection and processing considerations

    SciTech Connect

    Holland, Nina T. . E-mail: ninah@berkeley.edu; Pfleger, Laura; Berger, Eileen; Ho, Alan; Bastaki, Maria

    2005-08-07

    Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century.

  11. Extracting dwell time sequences from processive molecular motor data.

    PubMed

    Milescu, Lorin S; Yildiz, Ahmet; Selvin, Paul R; Sachs, Frederick

    2006-11-01

    Processive molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. Single-molecule recordings of motor position along a substrate polymer appear as a stochastic staircase. Recordings of other single molecules, such as F1-ATPase, RNA polymerase, or topoisomerase, have the same appearance. We present a maximum likelihood algorithm that extracts the dwell time sequence from noisy data, and estimates state transition probabilities and the distribution of the motor step size. The algorithm can handle models with uniform or alternating step sizes, and reversible or irreversible kinetics. A periodic Markov model describes the repetitive chemistry of the motor, and a Kalman filter allows one to include models with variable step size and to correct for baseline drift. The data are optimized recursively and globally over single or multiple data sets, making the results objective over the full scale of the data. Local binary algorithms, such as the t-test, do not represent the behavior of the whole data set. Our method is model-based, and allows rapid testing of different models by comparing the likelihood scores. From data obtained with current technology, steps as small as 8 nm can be resolved and analyzed with our method. The kinetic consequences of the extracted dwell sequence can be further analyzed in detail. We show results from analyzing simulated and experimental kinesin and myosin motor data. The algorithm is implemented in the free QuB software. PMID:16905607

  12. Extracting Dwell Time Sequences from Processive Molecular Motor Data

    PubMed Central

    Milescu, Lorin S.; Yildiz, Ahmet; Selvin, Paul R.; Sachs, Frederick

    2006-01-01

    Processive molecular motors, such as kinesin, myosin, or dynein, convert chemical energy into mechanical energy by hydrolyzing ATP. The mechanical energy is used for moving in discrete steps along the cytoskeleton and carrying a molecular load. Single-molecule recordings of motor position along a substrate polymer appear as a stochastic staircase. Recordings of other single molecules, such as F1-ATPase, RNA polymerase, or topoisomerase, have the same appearance. We present a maximum likelihood algorithm that extracts the dwell time sequence from noisy data, and estimates state transition probabilities and the distribution of the motor step size. The algorithm can handle models with uniform or alternating step sizes, and reversible or irreversible kinetics. A periodic Markov model describes the repetitive chemistry of the motor, and a Kalman filter allows one to include models with variable step size and to correct for baseline drift. The data are optimized recursively and globally over single or multiple data sets, making the results objective over the full scale of the data. Local binary algorithms, such as the t-test, do not represent the behavior of the whole data set. Our method is model-based, and allows rapid testing of different models by comparing the likelihood scores. From data obtained with current technology, steps as small as 8 nm can be resolved and analyzed with our method. The kinetic consequences of the extracted dwell sequence can be further analyzed in detail. We show results from analyzing simulated and experimental kinesin and myosin motor data. The algorithm is implemented in the free QuB software. PMID:16905607

  13. Single- and double-electron processes in collisions of Xe{sup 23+} ions with helium

    SciTech Connect

    Ding Baowei; Wan Chengliang; Chen Shangwen; Yu Deyang; Ruan Fangfang; Lu Rongchun; Cai Xiaohong; Shao Caojie

    2010-09-15

    We report the measurements of relative cross sections for single capture (SC), double capture (DC), single ionization (SI), double ionization (DI), and transfer ionization (TI) in collisions of Xe{sup 23+} ions with helium atoms in the velocity range of 0.65-1.32 a.u. The relative cross sections show a weak velocity dependence. The cross-section ratio of double- (DE) to single-electron (SE) removal from He, {sigma}{sub DE}/{sigma}{sub SE}, is about 0.45. Single capture is the dominant reaction channel which is followed by transfer ionization, while only very small probabilities are found for pure ionization and double capture. The present experimental data are in satisfactory agreement with the estimations by the extended classical over-barrier (ECB) model.

  14. Turbulent thermalization process in heavy-ion collisions at ultrarelativistic energies

    NASA Astrophysics Data System (ADS)

    Berges, J.; Boguslavski, K.; Schlichting, S.; Venugopalan, R.

    2014-04-01

    The nonequilibrium evolution of heavy-ion collisions is studied in the limit of weak coupling at very high energy employing lattice simulations of the classical Yang-Mills equations. Performing the largest classical-statistical simulations to date, we find that the dynamics of the longitudinally expanding plasma becomes independent of the details of the initial conditions. After a transient regime dominated by plasma instabilities and free streaming, the subsequent space-time evolution is governed by a nonthermal fixed point, where the system exhibits the self-similar dynamics characteristic of wave turbulence. This allows us to distinguish between different kinetic scenarios in the classical regime. Within the accuracy of our simulations, the scaling behavior found is consistent with the "bottom-up" thermalization scenario [R. Baier, A. H. Mueller, D. Schiff, and D. T. Son, Phys. Lett. B 502, 51 (2001)].

  15. Digital detection and processing of laser beacon signals for aircraft collision hazard warning

    NASA Technical Reports Server (NTRS)

    Sweet, L. M.; Miles, R. B.; Russell, G. F.; Tomeh, M. G.; Webb, S. G.; Wong, E. Y.

    1981-01-01

    A low-cost collision hazard warning system suitable for implementation in both general and commercial aviation is presented. Laser beacon systems are used as sources of accurate relative position information that are not dependent on communication between aircraft or with the ground. The beacon system consists of a rotating low-power laser beacon, detector arrays with special optics for wide angle acceptance and filtering of solar background light, microprocessors for proximity and relative trajectory computation, and pilot displays of potential hazards. The laser beacon system provides direct measurements of relative aircraft positions; using optimal nonlinear estimation theory, the measurements resulting from the current beacon sweep are combined with previous data to provide the best estimate of aircraft proximity, heading, minimium passing distance, and time to closest approach.

  16. Application of finite element and boundary integral methods in molecular collision theory. I - Introduction and model calculations

    NASA Astrophysics Data System (ADS)

    Sethuraman, V.; Hunt, P. M.

    1988-06-01

    The adaptive multigrid technique in the finite element method of the solution of partial differential equations is examined in the context of model problems in atom-atom and collinear atom-diatom collisions. For the problem leading to scattering along an L-shaped region, the technique yields accurate results for regions of energy far from the threshold for excitation of a new channel without inclusion of virtual states. Close to the threshold, the cusplike structure of the transition probability (vs. energy) and the time delay associated with the onset of a resonance are recovered only by inclusion of the new (closed) channel in the finite element solution. For atom-diatom collinear collisions, use of an orthogonal coordinate system facilitates dicretization and adds no extra labor in the finite element method, compared to the usual mass-weighted system.

  17. Molecular beam epitaxy for advanced gate stack materials and processes

    NASA Astrophysics Data System (ADS)

    Locquet, Jean-Pierre

    2005-03-01

    The material requirements for future CMOS generations - as given by the ITRS roadmap - are very challenging. This includes a high K dielectric without a low K interfacial layer, a high mobility channel and the appropriate metal gate. With the help of two projects INVEST and ET4US, we are building up a molecular beam epitaxy (MBE) infrastructure to grow this material set on large area wafers that can be further processed into small scale devices. In the INVEST project, we have developed an MBE system for the growth of complex oxides on semiconductors. The system follows the overall design of a production tool and is equipped with an RF atomic oxygen source, effusion cells, e-beam evaporators and a differential pumping stage. The oxide growth process starts with desorbing the initial surface oxide on the Si wafers in ultra-high vacuum and high temperature to create a clean reconstructed 2x1 surface. Using the atomic oxygen it is possible to oxidize the surface in a well controlled manner at low temperature and to grow very thin and dense SiOx layers, followed by the growth of 2-6 nm amorphous high K dielectrics. The process parameters permit to tune the interface layer from a SiOx rich to a silicide rich interface with a significant impact on the capacitance and the leakage. Initial focus is on developing an optimized growth recipe for high quality amorphous HfO2 and LaHfO3.5 films. This recipe was subsequently used to make wafers for a transistor batch that gave us the first N short channel MBE MOSFET's (100 nm) using an etched gate process flow. Some highlights of the first batch for 3nm HfO2 MOSFET are a high mobility (> 270 cm^2/Vs) with a corresponding low leakage current of 2 mA/cm^2). While there were some process issues for LaHfO3.5, the 3 nm MOSFET showed very low leakage currents below 10-6 A/cm^2. Interestingly all the LaHFO3.5 MOSFETs showed very low threshold voltage instabilities. In collaboration with C. Marchiori, M. Sousa, A.Guiller, H. Siegwart, D. Caimi, J. Fompeyrine, D. J Webb, C. Rossel, R. Germann of IBM Research GmbH Zurich Switzerland; L. Pantisano, M. Claes, T. Conard, M. Demand, W. Deweerd, S. DeGendt, M. Heyns, M. Houssa, M. Aoulaiche, G. Lujan, L. Ragnarsson, E. Rohr, T. Schram of IMEC Leuven Belgium; J. Hooker, Z.M Rittersma, Y. Furukawa of Philips Research Leuven Belgium and J. W. Seo of EPFL Lausanne Switzerland.

  18. Davisson-Germer Prize in Atomic or Surface Physics Talk: Few-body processes in the quantum limit

    NASA Astrophysics Data System (ADS)

    Greene, Chris

    2010-03-01

    Recent theoretical studies of low energy collisions and resonant processes will be reviewed. These include the process of molecular dissociation induced by electron collision, and the role of universal Efimov physics in collisions of three or four atoms in an ultracold gas. The role of experiment in testing and advancing our understanding of these few-body studies will also be discussed.

  19. The Role of Atomic and Molecular Processes in Magnetic Fusion Plasmas

    NASA Astrophysics Data System (ADS)

    Reiter, Detlev; Baeva, Margarita; Marchuk, Oleksandr; Janev, Ratko K.

    2005-05-01

    Plasma edge physics (plasmas with temperatures in the 1 to 100 eV range, near solid surfaces) has become a key issue in controlled nuclear fusion research. As for the physics of the fully ionized hot plasma core, appropriate dimensionless parameters have been identified: present fusion research acts like wind-channel experiments on downsized models, with respect to future fusion reactors. This is not longer possible for the plasma edge region due to dominant effects from atomic and surface processes. Integrated computational models comprising the physics of the plasma flow near boundaries, the atomic and molecular processes and the particle-surface interactions are the only tool to evaluate present experimental results (LHD, JT60, Tore Supra, JET,…) with respect to their relevance for future fusion power experiments (ITER) or a reactor. In particular proton and electron collisions with the hydrogenic molecules H2, O2, T2, DT, and their ions, play a key role in cooling and attenuating the magnetically confined plasma, before it hits exposed target surfaces. The surface released molecules travel in a bath of electrons and hydrogenic ions, with plasma temperatures (in the relevant region) in the 1 to 20 eV range, and typical (plasma) scale lengths are in the 1 to 10 cm range. Sample calculations with current fusion plasma edge codes, as e.g. used by the international design team for the ITER prototypical fusion reactor, applied to the tokamak with the highest divertor collisionality today (Alcator-C-Mod), are used to demonstrate these issues.

  20. The Role of Atomic and Molecular Processes in Magnetic Fusion Plasmas

    SciTech Connect

    Reiter, Detlev; Baeva, Margarita; Marchuk, Oleksandr; Janev, Ratko K.

    2005-05-27

    Plasma edge physics (plasmas with temperatures in the 1 to 100 eV range, near solid surfaces) has become a key issue in controlled nuclear fusion research. As for the physics of the fully ionized hot plasma core, appropriate dimensionless parameters have been identified: present fusion research acts like wind-channel experiments on downsized models, with respect to future fusion reactors. This is not longer possible for the plasma edge region due to dominant effects from atomic and surface processes. Integrated computational models comprising the physics of the plasma flow near boundaries, the atomic and molecular processes and the particle-surface interactions are the only tool to evaluate present experimental results (LHD, JT60, Tore Supra, JET,...) with respect to their relevance for future fusion power experiments (ITER) or a reactor.In particular proton and electron collisions with the hydrogenic molecules H2, O2, T2, DT, and their ions, play a key role in cooling and attenuating the magnetically confined plasma, before it hits exposed target surfaces. The surface released molecules travel in a bath of electrons and hydrogenic ions, with plasma temperatures (in the relevant region) in the 1 to 20 eV range, and typical (plasma) scale lengths are in the 1 to 10 cm range.Sample calculations with current fusion plasma edge codes, as e.g. used by the international design team for the ITER prototypical fusion reactor, applied to the tokamak with the highest divertor collisionality today (Alcator-C-Mod), are used to demonstrate these issues.

  1. Complex physiological and molecular processes underlying root gravitropism

    NASA Technical Reports Server (NTRS)

    Chen, Rujin; Guan, Changhui; Boonsirichai, Kanokporn; Masson, Patrick H.

    2002-01-01

    Gravitropism allows plant organs to guide their growth in relation to the gravity vector. For most roots, this response to gravity allows downward growth into soil where water and nutrients are available for plant growth and development. The primary site for gravity sensing in roots includes the root cap and appears to involve the sedimentation of amyloplasts within the columella cells. This process triggers a signal transduction pathway that promotes both an acidification of the wall around the columella cells, an alkalinization of the columella cytoplasm, and the development of a lateral polarity across the root cap that allows for the establishment of a lateral auxin gradient. This gradient is then transmitted to the elongation zones where it triggers a differential cellular elongation on opposite flanks of the central elongation zone, responsible for part of the gravitropic curvature. Recent findings also suggest the involvement of a secondary site/mechanism of gravity sensing for gravitropism in roots, and the possibility that the early phases of graviresponse, which involve differential elongation on opposite flanks of the distal elongation zone, might be independent of this auxin gradient. This review discusses our current understanding of the molecular and physiological mechanisms underlying these various phases of the gravitropic response in roots.

  2. Evaluation of tocopherol recovery through simulation of molecular distillation process.

    PubMed

    Moraes, E B; Batistella, C B; Alvarez, M E Torres; Filho, Rubens Maciel; Maciel, M R Wolf

    2004-01-01

    DISMOL simulator was used to determine the best possible operating conditions to guide, in future studies, experimental works. This simulator needs several physical-chemical properties and often it is very difficult to determine them because of the complexity of the involved components. Their determinations must be made through correlations and/or predictions, in order to characterize the system and calculate it. The first try is to have simulation results of a system that later can be validated with experimental data. To implement, in the simulator, the necessary parameters of complex systems is a difficult task. In this work, we aimed to determe these properties in order to evaluate the tocopherol (vitamin E) recovery using a DISMOL simulator. The raw material used was the crude deodorizer distillate of soya oil. With this procedure, it is possible to determine the best operating conditions for experimental works and to evaluate the process in the separation of new systems, analyzing the profiles obtained from these simulations for the falling film molecular distillator. PMID:15054286

  3. Effective QCD and transport description of dilepton and photon production in heavy-ion collisions and elementary processes

    NASA Astrophysics Data System (ADS)

    Linnyk, O.; Bratkovskaya, E. L.; Cassing, W.

    2016-03-01

    In this review we address the dynamics of relativistic heavy-ion reactions and in particular the information obtained from electromagnetic probes that stem from the partonic and hadronic phases. The out-of-equilibrium description of strongly interacting relativistic fields is based on the theory of Kadanoff and Baym. For the modeling of the partonic phase we introduce an effective dynamical quasiparticle model (DQPM) for QCD in equilibrium. In the DQPM, the widths and masses of the dynamical quasiparticles are controlled by transport coefficients that can be compared to the corresponding quantities from lattice QCD. The resulting off-shell transport approach is denoted by Parton-Hadron-String Dynamics (PHSD) and includes covariant dynamical transition rates for hadronization and keeps track of the hadronic interactions in the final phase. It is shown that the PHSD captures the bulk dynamics of heavy-ion collisions from lower SPS to LHC energies and thus provides a solid basis for the evaluation of the electromagnetic emissivity, which is calculated on the basis of the same dynamical parton propagators that are employed for the dynamical evolution of the partonic system. The production of direct photons in elementary processes and heavy-ion reactions is discussed and the present status of the photon v2 "puzzle"-a large elliptic flow v2 of the direct photons experimentally observed in heavy-ion collisions-is addressed for nucleus-nucleus reactions at RHIC and LHC energies. The role of hadronic and partonic sources for the photon spectra and the flow coefficients v2 and v3 is considered as well as the possibility to subtract the QGP signal from the experimental observables. Furthermore, the production of e+e- or μ+μ- pairs in elementary processes and A + A reactions is addressed. The calculations within the PHSD from SIS to LHC energies show an increase of the low mass dilepton yield essentially due to the in-medium modification of the ρ-meson and at the lowest energy also due to a multiple regeneration of Δ-resonances. Furthermore, pronounced traces of the partonic degrees-of-freedom are found in the intermediate dilepton mass regime (1.2 GeV < M < 3 GeV) at relativistic energies, which will also shed light on the nature of the very early degrees-of-freedom in nucleus-nucleus collisions.

  4. Energy transfer dynamics and kinetics of elementary processes (promoted) by gas-phase CO2 -N2 collisions: Selectivity control by the anisotropy of the interaction.

    PubMed

    Lombardi, Andrea; Pirani, Fernando; Laganà, Antonio; Bartolomei, Massimiliano

    2016-06-15

    In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2 -N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc. PMID:27031183

  5. The Two Molecular Clouds in RCW 38: Evidence for the Formation of the Youngest Super Star Cluster in the Milky Way Triggered by Cloud-Cloud Collision

    NASA Astrophysics Data System (ADS)

    Fukui, Y.; Torii, K.; Ohama, A.; Hasegawa, K.; Hattori, Y.; Sano, H.; Ohashi, S.; Fujii, K.; Kuwahara, S.; Mizuno, N.; Dawson, J. R.; Yamamoto, H.; Tachihara, K.; Okuda, T.; Onishi, T.; Mizuno, A.

    2016-03-01

    We present distributions of two molecular clouds having velocities of 2 and 14 km s-1 toward RCW 38, the youngest super star cluster in the Milky Way, in the 12CO J = 1-0 and 3-2 and 13CO J = 1-0 transitions. The two clouds are likely physically associated with the cluster as verified by the high intensity ratio of the J = 3-2 emission to the J = 1-0 emission, the bridging feature connecting the two clouds in velocity, and their morphological correspondence with the infrared dust emission. The velocity difference is too large for the clouds to be gravitationally bound. We frame a hypothesis that the two clouds are colliding with each other by chance to trigger formation of the ˜20 O stars that are localized within ˜0.5 pc of the cluster center in the 2 km s-1 cloud. We suggest that the collision is currently continuing toward part of the 2 km s-1 cloud where the bridging feature is localized. This is the third super star cluster alongside Westerlund 2 and NGC 3603 where cloud-cloud collision has triggered the cluster formation. RCW 38 is the youngest super star cluster in the Milky Way, holding a possible sign of on-going O star formation, and is a promising site where we may be able to witness the moment of O star formation.

  6. A new semiclassical decoupling scheme for electronic transitions in molecular collisions - Application to vibrational-to-electronic energy transfer

    NASA Technical Reports Server (NTRS)

    Lee, H.-W.; Lam, K. S.; Devries, P. L.; George, T. F.

    1980-01-01

    A new semiclassical decoupling scheme (the trajectory-based decoupling scheme) is introduced in a computational study of vibrational-to-electronic energy transfer for a simple model system that simulates collinear atom-diatom collisions. The probability of energy transfer (P) is calculated quasiclassically using the new scheme as well as quantum mechanically as a function of the atomic electronic-energy separation (lambda), with overall good agreement between the two sets of results. Classical mechanics with the new decoupling scheme is found to be capable of predicting resonance behavior whereas an earlier decoupling scheme (the coordinate-based decoupling scheme) failed. Interference effects are not exhibited in P vs lambda results.

  7. Detailed seismic attenuation structure beneath Hokkaido, northeastern Japan: Arc-arc collision process, arc magmatism, and seismotectonics

    NASA Astrophysics Data System (ADS)

    Kita, Saeko; Nakajima, Junichi; Hasegawa, Akira; Okada, Tomomi; Katsumata, Kei; Asano, Youichi; Kimura, Takeshi

    2014-08-01

    In this study, we imaged a detailed seismic attenuation structure (frequency-independent Q-1) beneath Hokkaido, Japan, by merging waveform data from a dense permanent seismic network with those from a very dense temporary network. Corner frequency of each event used for t* estimation was determined by the S coda wave spectral ratio method. The seismic attenuation (Qp-1) structure is clearly imaged at depths down to about 120 km. For the fore-arc side of Hokkaido, high-Qp zones are imaged at depths of 10 to 80 km in the crust and mantle wedge above the Pacific slab. Low-Qp zones are clearly imaged in the mantle wedge beneath the back-arc areas of eastern and southern Hokkaido. These low-Qp zones, extending from deeper regions, extend to the Moho beneath volcanoes, the locations of which are consistent with those of seismic low-velocity regions. These results suggest that the mantle wedge upwelling flow occurs beneath Hokkaido, except in the area where there is a gap in the volcano chain. In contrast, an inhomogeneous seismic attenuation structure is clearly imaged beneath the Hokkaido corner. A broad low-Qp zone is located at depths of 0-60 km to the west of the Hidaka main thrust. The location almost corresponds to that of the seismic low-velocity zone in the collision zone. The fault planes of the 1970 M6.7 and 1982 M7.1 earthquakes are located at the edges of this broad low-Qp zone. Observations in this study indicate that our findings contribute to understanding the detailed arc-arc collision process, magmatism, and seismotectonics beneath Hokkaido.

  8. Binary Raindrop Collisions

    NASA Astrophysics Data System (ADS)

    Testik, Firat; Rahman, Kalimur

    2015-11-01

    In this talk, we will present first-time observations of binary raindrop collisions in natural rainfall and discuss the observed raindrop collision outcomes (i.e. breakup, coalescence, and bounce). Binary raindrop collisions have long been hypothesized as a key process in shaping of the raindrop size distribution, an important quantity for a number of meteorological and hydrological applications. Testik (2009) developed a regime diagram to determine the outcomes of a raindrop collision based upon the collision kinetic energies and surface energies of the colliding raindrops. This regime diagram has been validated previously using two different laboratory datasets for the collision of simulated raindrops. A new instrument that we have developed for precipitation microphysical observations, called High-speed Optical Disdrometer (HOD), made raindrop collision observations possible in natural rainfall and provided a valuable small dataset. In the light of these first time field observations of raindrop collisions, we will discuss Testik's diagram in this talk. Testik, F. Y., 2009. Outcome regimes of binary raindrop collisions. Atmos. Res., 94, 389-399. This material is based upon work supported by the National Science Foundation under Grant No. AGS-1144846.

  9. Tectonic processes during oblique collision: Insights from the St. Elias orogen, northern North American Cordillera

    USGS Publications Warehouse

    Pavlis, T.L.; Picornell, C.; Serpa, L.; Bruhn, R.L.; Plafker, G.

    2004-01-01

    Oblique convergence in the St. Elias orogen of southern Alaska and northwestern Canada has constructed the world's highest coastal mountain range and is the principal driver constructing all of the high topography in northern North America. The orogen originated when the Yakutat terrane was excised from the Cordilleran margin and was transported along margin-parallel strike-slip faults into the subduction-transform transition at the eastern end of the Aleutian trench. We examine the last 3 m.y. of this collision through an analysis of Euler poles for motion of the Yakutat microplate with respect to North America and the Pacific. This analysis indicates a Yakutat-Pacific pole near the present southern triple junction of the microplate and' predicts convergence to dextral-oblique convergence across the offshore Transition fault, onland structures adjacent to the Yakutat foreland, or both, with plate speeds increasing from 10 to 30 mm/yr from southeast to northwest. Reconstructions based on these poles show that NNW transport of the collided block into the NE trending subduction zone forced contraction of EW line elements as the collided block was driven into the subduction-transform transition. This suggests the collided block was constricted as it was driven into the transition. Constriction provides an explanation for observed vertical axis refolding of both earlier formed fold-thrust systems and the collisional suture at the top of the fold-thrust stack. We also suggest that this motion was partially accommodated by lateral extrusion of the western portion of the orogen toward the Aleutian trench. Important questions remain regarding which structures accommodated parts of this motion. The Transition fault may have accommodated much of the Yakutat-Pacific convergence on the basis of our analysis and previous interpretations of GPS-based geodetic data. Nonetheless, it is locally overlapped by up to 800 m of undeformed sediment, yet elsewhere shows evidence of young deformation. This contradiction could be produced if the overlapping sediments are too young to have accumulated significant deformation, or GPS motions may be deflected by transient strains or strains from poorly understood fault interactions. In either case, more data are needed to resolve the paradox. Copyright 2004 by the American Geophysical Union.

  10. Photonic, Electronic and Atomic Collisions

    NASA Astrophysics Data System (ADS)

    Fainstein, Pablo D.; Lima, Marco Aurelio P.; Miraglia, Jorge E.; Montenegro, Eduardo C.; Rivarola, Roberto D.

    2006-11-01

    Plenary. Electron collisions - past, present and future / J. W. McConkey. Collisions of slow highly charged ions with surfaces / J. Burgdörfer ... [et al.]. Atomic collisions studied with "reaction-microscopes" / R. Moshammer ... [et al.]. Rydberg atoms: a microscale laboratory for studying electron-molecule tnteractions / F. B. Dunning -- Collisions involvintg photons. Quantum control of photochemical reaction dynamics and molecular functions / M. Yamaki ... [et al.]. Manipulating and viewing Rydberg wavepackets / R. R. Jones. Angle-resolved photoelectrons as a probe of strong-field interactions / M. Vrakking. Ultracold Rydberg atoms in a structured environment / I. C. H. Liu and J. M. Rost. Synchrotron-radiation-based recoil ion momentum spectroscopy of laser cooled and trapped cesium atoms / L. H. Coutinho. Reconstruction of attosecond pulse trains / Y. Mairesse ... [et al.]. Selective excitation of metastable atomic states by Femto- and attosecond laser pulses / A. D. Kondorskiy. Accurate calculations of triple differential cross sections for double photoionization of the hygrogen molecule / W. Vanroose ... [et al.]. Double and triple photoionization of Li and Be / J. Colgan, M. S. Pindzola and F. Robicheaux. Few/many body dynamics in strong laser fields / J. Zanghellini and T. Brabec. Rescattering-induced effects in electron-atom scattering in the presence of a circularly polarized laser field / A. V. Flegel ... [et al.]. Multidimensional photoelectron spectroscopy / P. Lablanquie ... [et al.]. Few photon and strongly driven transitions in the XUV and beyond / P. Lambropoulos, L. A. A. Nikolopoulos and S. I. Themelis. Ionization dynamics of atomic clusters in intense laser pulses / U. Saalmann and J. M. Rost. On the second order autocorrelation of an XUV attosecond pulse train / E. P. Benis ... [et al.]. Evidence for rescattering in molecular dissociation / I. D. Williams ... [et al.]. Photoionizing ions using synchrotron radiation / R. Phaneuf. Photo double ionization of fixed in space deuterium molecules / T. Weber ... [et al.]. Coherence and intramolecular scattering in molecular photoionization / U. Becker. Experimental observation of interatomic coulombic decay in neon dimers / T. Jahnke ... [et al.]. Ionization by short UV laser pulses: secondary ATI peaks of the electron spectrum / V. D. Rodríguez, E. Cormier and R. Gayet. Molecular frame photoemission in photoionization of H[symbol] and D[symbol]: the role of dissociation on autoionization of the Q[symbol] and Q[symbol] doubly excited states / D. Dowek, M. Lebech and J. C. Houver. 3p photoemission of 3d transition metals - atoms, molecules and clusters / M. Martins -- Collisions involving electrons. Spin-resolved collisions of electrons with atoms and molecules / G. F. Hanne. Calculation of ionization and excitation processes using the convergent close-coupling method / D. V. Fursa, I. Bray and A. T. Stelbovics. The B-spline R-matrix method for electron and photon collisions with atoms and ions / O. Zatsarinny and K. Bartschat. Absolute angle-differential cross sections for excitation of neon atoms electrons of energy 16.6-19.2 eV / M. Allan ... [et al.]. Studies of QED and nuclear size effects with highly charged ions in an EBIT / J. R. Crespo López-Urrutia ... [et al.]. Recombination of astrophysically relevant ions: Be-like C, N, and O / M. Fogle ... [et al.]. Dissociation and excitation of molecules and molecular ions by electron impact / A. E. Orel and J. Royal state-selective X-ray study of the radiative recombination of U[symbol] ions with cooling electrons / M. Pajek ... [et al.]. Electron collisions with trapped, metastable helium / L. J. Uhlmann ... [et al.]. Non-dipole effects in electron and photon impact ionization / N. L. S. Martin. Electron driven processes in atmospheric behaviour / L. Campbell, M. J. Brunger and P. J. 0. Teubner. Calculation of excitation and ionization for electron-molecule collisions at intermediate energies / J. D. Gorfinkiel. Absolute total cross sections for electron-CH[symbol] scattering at intermediate energies / M. C. A. Lopes ... [et al.]. Electron-CO[symbol] scattering in a cluster environment / I. I. Fabrikant. Isomer effect in electron collisions with small hydrocarbons / M. H. F. Bettega ... [et al.]. Low energy electron interactions with bio-molecules / B. P. Marinković ... [et al.]. Narrow resonances in dissociative electron attachment and vibrational excitation in H[symbol] / M. Číček. (e, 2e) experiments with randomly oriented and fixed-in-space hydrogen molecules / M. Takahashi. Initial and final state correlation effects in (e, 3e) processes / G. Gasaneo, S. Otranto and K. V. Rodríguez. An (e, 2˙e) experiment for simultaneous ionization-excitation of helium to the He[symbol](2p)[symbol]P states by electron impact / A. Dorn ... [et al.] -- Collisions involving exotic particles. Antihydrogen in the laboratory / M. Charlton. Atomic collisions involving positrons / H. R. J. Walters and C. Starret. Ionization and positronium formation in noble gases / J. P. Marler, J. P. Sullivan and C. M. Surko. Study of inner-shell ionization by low-energy positron impact / Y. Nagashima ... [et al.]. Positron-atom bound states and interactions / M. W. J. Bromley. Extraction of ultra-slow antiproton beams for single collision experiments / H. A. Torii ... [et al.]. Positronium formation from valence and inner shells in noble gases / L. J. M. Dunlop and G. F. Gribakin. Molecular effects in neutrino mass measurements / N. Doss ... [et al.] -- Collisions involving heavy projectiles. Probing the solar wind with cometary X-ray and far-ultraviolet emission / R. Hoekstra ... [et al.]. Production of O[symbol] + neutrals from the collision of C[symbol] with water / H. Luna ... [et al.]. Vector correlation of fragment ions produced by collision of Ar[symbol] with dimethyldisulfide / T. Matsuoka ... [et al.]. Slow multiply charged ion-molecule collision dynamics studied through a multi-coincidence technique / T. Kaneyasu, T. Azuma and K. Okuno. Recent developments in proton-transfer-reaction mass spectrometry / A. Wisthaler ... [et al.]. Interferences in electron emission from H[symbol] induced by fast ions / N. Stolterfoht. Atomic realization of the young single electron interference process in individual autoionization collisions / R. O. Barrachina and M. Šitnik. Multiple ionization processes related to irradiation of biological tissue / M. E. Galassi ... [et al.]. Atom-diatom collisions at cold and ultra-cold temperatures / F. D. Colavecchia, G. A. Parker and R. T. Pack. Interactions of ions with hydrogen atoms / A. Luca, G. Borodi and D. Gerlich. Analysis of all structures in the elastic and charge transfer cross sections for proton-hydrogen collisions in the range of 10[symbol]-10øeV / P. S. Krstić ... [et al.]. Ab-initio ion-atom collision calculations for many-electron systems / J. Anton and B. Fricke. Fully differential studies on single ionization of helium by slow proton impact / A. Hasan ... [et al.]. Dipole polarization effects on highly-charged-ion-atom electron capture / C. C. Havener ... [et al.]. Proton-, antiproton-, and photon-he collisions in the context of ultra fast processes / T. Morishita ... [et al.]. Impact parameter dependent charge exchange studies with channeled heavy ions / D. Dauvergne ... [et al.]. Crystal assisted atomic physics experiments using heavy ions / K. Komaki -- Collisions involving clusters and surfaces. Structure and dynamics of Van der Waal complexes: from triatomic to medium size clusters / G. Delgado Barrio ... [et al.]. Evaporation, fission and multifragmentation processes of multicharged C[symbol] ions versus excitation energies / S. Martin ... [et al.]. Fragmentation of collisionally excited fullerenes / M. Alcami, S. Diaz-Tendero and F. Martín. Lifetimes of C[symbol] and C[symbol] dianions in a storage ring / S. Tomita ... [et al.]. Clusters and clusters of clusters in collisions / B. Manil ... [et al.]. Fragmentation of small carbon clusters / M. Chabot ... [et al.]. Collective excitations in collisions of photons and electrons with metal clusters and fullerenes / A. V. Solov'yov. Dynamics of H[symbol] chemisorption on metal surfaces / H. F. Busnengo ... [et al.]. Interaction of slow multiply charged ions with insulator surfaces / W. Meissl ... [et al.]. Electron emission during grazing impact of atoms on metals surfaces / H. Winter. Inner-shell collective effects for protons sackscattered from the Al(110) surface / P. L. Grande, A. Hentz and G. Schiwietz. Guiding of highly charged ions by SiO[symbol] nano-capillaries / M. B. Sahana ... [et al.]. Low-energy electron impact on hydrogenated polycrystalline diamond and condensed molecules / A. Lafosse ... [et al.]. Low energy spin-polarized electron-pair (e, 2e)-in-reflection from various surfaces / J. F. Williams ... [et al.] -- List of contributors.

  11. Collision-Induced Absorption Spectra of Binary Mixtures of Molecular Hydrogen with Molecular Deuterium and Argon and of Pure Hydrogen, D

    NASA Astrophysics Data System (ADS)

    Hsieh, Chang-Tsang William

    In the present research project a systematic study of the collision-induced infrared absorption (CIA) spectra of the binary mixtures of H_2 - D_2 in the region of the double fundamental vibrations of H_2 and D_2, and H_2 - Ar in the fundamental band of H_2, and of pure HD in its fundamental and first overtone regions was undertaken. The experiments were carried out with a 2.0 m high-pressure low-temperature transmission-type absorption cell at 77, 201 and 296 K at total gas densities up to 550 amagat. Infrared prism and grating spectrometers equipped with a microprocessor -controlled stepping motor were used to record the spectra. All the experimental results obtained represent first-time observations in collision-induced absorption. Collision-induced infrared absorption spectra of the double transitions of H_2(v=1>=ts 0) and D_2(v=1>=ts 0) have been observed at 77 and 201 K in the spectral region 7000-8000 cm^{-1} for total gas densities up to 550 amagat with a partial gas density ratio of 1:1 of H_2 and D_2. The observed spectra are interpreted in terms of the transitions, Q_1(J) of H_2+Q_1(J) of D _2, Q_1(J) of H_2+S _1(J) of D_2, S_1(J) of H_2 + Q_1(J) of D_2, and S_1(J) of H_2 + S_1(J) of D_2 for J = 0 and 1 for H _2 and J = 0, 1, and 2 for D_2. Analysis of the experimental absorption profiles was carried out using appropriate lineshape functions. The absorption coefficients, lineshape parameters, etc., are obtained from the analysis. Collision-induced enhancement absorption spectra of the fundamental band of H_2 in H_2 - Ar mixtures were recorded at room temperature for a base density of 72 amagat of H_2 for several partial densities of Ar up to 440 amagat. Hexadecapole-induced U transitions, U_1(1), U_1(2), Q_1(0)+U _0(1), and Q_1(1) + U_0(1) have been identified in the spectral region 5400 -6200 cm^{-1}. A "cage" model has been proposed to account for the double transitions of H_2 - H_2 in the H _2 - Ar enhancement spectra. From the analysis of the absorption profiles, the lineshape parameters and the absorption coefficients have been determined. The collision-induced absorption spectrum of the first overtone band of HD in the pure gas was observed at 77 K for gas densities up to 320 amagat. In addition to the allowed transitions P_2(1), R_2(0), and R_2(1), the CIA transitions Q_2(J)+Q_0(J), Q_1(J)+Q_1(J), Q_2(J)+S _0(J), S_2(J)+Q_0(J), Q _1(J)+S_1(J), S_2(J)+S_0(J), and S_1(J)+S_1(J) have been observed. An analysis of the observed absorption profiles has been completed. It is found that the isotropic overlap induction mechanism does not contribute to the intensity of the band and that negative contribution to the intensity of the band comes from the mixed term (2 sqrt{3}lambda_{32}exp [-(R - sigma)/rho_{32 }]times < vJmid Qmid v^' J^'>(R/a _0)^{-4}. The fundamental band of HD has been investigated at 77 K for gas densities in the range 40-310 amagat. For the first time the collision -induced transitions of the type T_1(1) + Q_0(J), Q_1(J) + T_0(1), U_1(0) + Q_0(J), Q_1(J) + U_0(0), V_1(0) + Q_0(J), and Q _1(J) + V_0(0) for HD have been identified. Here T, U, and V transitions correspond to DeltaJ = 3, 4, and 5, respectively.

  12. Molecular processes that handle — and mishandle — dietary lipids

    PubMed Central

    Williams, Kevin Jon

    2008-01-01

    Overconsumption of lipid-rich diets, in conjunction with physical inactivity, disables and kills staggering numbers of people worldwide. Recent advances in our molecular understanding of cholesterol and triglyceride transport from the small intestine to the rest of the body provide a detailed picture of the fed/fasted and active/sedentary states. Key surprises include the unexpected nature of many pivotal molecular mediators, as well as their dysregulation — but possible reversibility — in obesity, diabetes, inactivity, and related conditions. These mechanistic insights provide new opportunities to correct dyslipoproteinemia, accelerated atherosclerosis, insulin resistance, and other deadly sequelae of overnutrition and underexertion. PMID:18830418

  13. Driving ordering processes in molecular-dynamics simulations.

    PubMed

    Dittmar, Harro; Kusalik, Peter G

    2014-05-16

    Self-organized criticality describes the emergence of complexity in dynamical nonequilibrium systems. In this paper we introduce a unique approach whereby a driven energy conversion is utilized as a sampling bias for ordered arrangements in molecular dynamics simulations of atomic and molecular fluids. This approach gives rise to dramatically accelerated nucleation rates, by as much as 30 orders of magnitude, without the need of predefined order parameters, which commonly employed rare-event sampling methods rely on. The measured heat fluxes suggest how the approach can be generalized. PMID:24877946

  14. Molecular clouds toward the super star cluster NGC 3603; possible evidence for a cloud-cloud collision in triggering the cluster formation

    SciTech Connect

    Fukui, Y.; Ohama, A.; Hanaoka, N.; Furukawa, N.; Torii, K.; Hasegawa, K.; Fukuda, T.; Soga, S.; Moribe, N.; Kuroda, Y.; Hayakawa, T.; Kuwahara, T.; Yamamoto, H.; Okuda, T.; Dawson, J. R.; Mizuno, N.; Kawamura, A.; Onishi, T.; Maezawa, H.; Mizuno, A.

    2014-01-01

    We present new large field observations of molecular clouds with NANTEN2 toward the super star cluster NGC 3603 in the transitions {sup 12}CO(J = 2-1, J = 1-0) and {sup 13}CO(J = 2-1, J = 1-0). We suggest that two molecular clouds at 13 km s{sup –1} and 28 km s{sup –1} are associated with NGC 3603 as evidenced by higher temperatures toward the H II region, as well as morphological correspondence. The mass of the clouds is too small to gravitationally bind them, given their relative motion of ∼20 km s{sup –1}. We suggest that the two clouds collided with each other 1 Myr ago to trigger the formation of the super star cluster. This scenario is able to explain the origin of the highest mass stellar population in the cluster, which is as young as 1 Myr and is segregated within the central sub-pc of the cluster. This is the second super star cluster along with Westerlund 2 where formation may have been triggered by a cloud-cloud collision.

  15. Interparticle collision mechanism in turbulence

    NASA Astrophysics Data System (ADS)

    Choi, Jung-Il; Park, Yongnam; Kwon, Ohjoon; Lee, Changhoon

    2016-01-01

    Direct numerical simulations of particle-laden homogeneous isotropic turbulence are performed to investigate interparticle collisions in a wide range of Stokes numbers. Dynamics of the particles are described by Stokes drag including particle-particle interactions via hard-sphere collisions, while fluid turbulence is solved using a pseudospectral method. Particular emphasis is placed on interparticle-collision-based conditional statistics of rotation and dissipation rates of the fluid experienced by heavy particles, which provide essential information on the collision process. We also investigate the collision statistics of collision time interval and angle. Based on a Lamb vortex model for a vortex structure, we claim that collision events occur in the edge region for vortical structures in the intermediate-Stokes-number regime, suggesting that the sling effect enhances collision as well as clustering.

  16. Interparticle collision mechanism in turbulence.

    PubMed

    Choi, Jung-Il; Park, Yongnam; Kwon, Ohjoon; Lee, Changhoon

    2016-01-01

    Direct numerical simulations of particle-laden homogeneous isotropic turbulence are performed to investigate interparticle collisions in a wide range of Stokes numbers. Dynamics of the particles are described by Stokes drag including particle-particle interactions via hard-sphere collisions, while fluid turbulence is solved using a pseudospectral method. Particular emphasis is placed on interparticle-collision-based conditional statistics of rotation and dissipation rates of the fluid experienced by heavy particles, which provide essential information on the collision process. We also investigate the collision statistics of collision time interval and angle. Based on a Lamb vortex model for a vortex structure, we claim that collision events occur in the edge region for vortical structures in the intermediate-Stokes-number regime, suggesting that the sling effect enhances collision as well as clustering. PMID:26871160

  17. New Insights Into the Fission Process by the Study of Relativistic Nuclear Collisions

    SciTech Connect

    Kelic, Aleksandra; Schmidt, Karl-Heinz

    2007-05-22

    An experimental and theoretical campaign dedicated to a better understanding of the fission process has been started at GSI several years ago. The waste amount of data measured at GSI gave new information on different aspects of the nuclear-fission process, such as nuclear viscosity at small deformation, transient effects, influence of shell effects on mass- and charge-division in fission, pairing correlations. All this lead to a development of a model, which proved successful in describing fragment formation in spallation and fragmentation reactions.

  18. Long Timestep Molecular Dynamics on the Graphical Processing Unit

    PubMed Central

    Sweet, James C.; Nowling, Ronald J.; Cickovski, Trevor; Sweet, Christopher R.; Pande, Vijay S.; Izaguirre, Jess A.

    2013-01-01

    Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 ?s/day using implicit solvent models. PMID:24436689

  19. Entropy and chemical change. 1: Characterization of product (and reactant) energy distributions in reactive molecular collisions: Information and enthropy deficiency

    NASA Technical Reports Server (NTRS)

    Bernstein, R. B.; Levine, R. D.

    1972-01-01

    Optimal means of characterizing the distribution of product energy states resulting from reactive collisions of molecules with restricted distributions of initial states are considered, along with those for characterizing the particular reactant state distribution which yields a given set of product states at a specified total energy. It is suggested to represent the energy-dependence of global-type results in the form of square-faced bar plots, and of data for specific-type experiments as triangular-faced prismatic plots. The essential parameters defining the internal state distribution are isolated, and the information content of such a distribution is put on a quantitative basis. The relationship between the information content, the surprisal, and the entropy of the continuous distribution is established. The concept of an entropy deficiency, which characterizes the specificity of product state formation, is suggested as a useful measure of the deviance from statistical behavior. The degradation of information by experimental averaging is considered, leading to bounds on the entropy deficiency.

  20. Molecular and genetic diversity in the metastatic process of melanoma.

    PubMed

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran

    2014-05-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. PMID:24399611

  1. Accurate calculations of the ground state and low-lying excited states of the (RbBa)+ molecular ion: a proposed system for ultracold reactive collisions

    NASA Astrophysics Data System (ADS)

    Knecht, S.; Sørensen, L. K.; Jensen, H. J. Aa; Fleig, T.; Marian, C. M.

    2010-03-01

    Collisions of ultracold Ba+ ions on a Rb Bose-Einstein condensate have been suggested as a possible benchmark system for ultracold ion-neutral collision experiments. However, a priori knowledge of the possible processes is desirable. For this purpose, we here present high-level four-component coupled cluster and multi-reference configuration interaction calculations of potential energy curves, dipole moments and spectroscopic constants of the experimentally interesting low-lying electronic states of the (RbBa)+ molecule. Our results show significant avoided crossings between the ^3 \\Sigma ^+_{1,0^-} Rb + Ba+ entrance channels and low-lying charge transfer ^3 \\Pi _{1,0^-} states of the Rb+ and Ba_{6\\rm{s}^1 5\\rm{d}^1}(3D) atomic channels, indicating that a fast non-radiative charge transfer is possible. Population analysis shows that a partially covalent polar bond is formed in the ground state, which thus deviates significantly from a pure Rb+ + Ba interaction. This finding is corroborated by the electric dipole moment which is found only to be 4.5 D at the equilibrium bond distance, compared with the 14 D for a pure Rb+ + Ba interaction, thereby supporting the view of a partial charge transfer between the two atoms.

  2. The role of orbital dynamics and cloud-cloud collisions in the formation of giant molecular clouds in global spiral structures

    NASA Technical Reports Server (NTRS)

    Roberts, William W., Jr.; Stewart, Glen R.

    1987-01-01

    The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.

  3. Experimental impact cratering provides ground truth data for understanding planetary-scale collision processes

    NASA Astrophysics Data System (ADS)

    Poelchau, Michael H.; Deutsch, Alex; Kenkmann, Thomas

    2013-04-01

    Impact cratering is generally accepted as one of the primary processes that shape planetary surfaces in the solar system. While post-impact analysis of craters by remote sensing or field work gives many insights into this process, impact cratering experiments have several advantages for impact research: 1) excavation and ejection processes can be directly observed, 2) physical parameters of the experiment are defined and can be varied, and 3) cratered target material can be analyzed post-impact in an unaltered, uneroded state. The main goal of the MEMIN project is to comprehensively quantify impact processes by conducting a stringently controlled experimental impact cratering campaign on the meso-scale with a multidisciplinary analytical approach. As a unique feature we use two-stage light gas guns capable of producing impact craters in the decimeter size-range in solid rocks that, in turn, allow detailed spatial analysis of petrophysical, structural, and geochemical changes in target rocks and ejecta. In total, we have carried out 24 experiments at the facilities of the Fraunhofer EMI, Freiburg - Germany. Steel, aluminum, and iron meteorite projectiles ranging in diameter from 2.5 to 12 mm were accelerated to velocities ranging from 2.5 to 7.8 km/s. Targets were solid rocks, namely sandstone, quartzite and tuff that were either dry or saturated with water. In the experimental setup, high speed framing cameras monitored the impact process, ultrasound sensors were attached to the target to record the passage of the shock wave, and special particle catchers were positioned opposite of the target surface to capture the ejected target and projectile material. In addition to the cratering experiments, planar shock recovery experiments were performed on the target material, and numerical models of the cratering process were developed. The experiments resulted in craters with diameters up to 40 cm, which is unique in laboratory cratering research. Target porosity exponentially reduces crater volumes and cratering efficiency relative to non-porous rocks, and also yields less steep ejecta angles. Microstructural analysis of the subsurface shows a zone of pervasive grain crushing and pore space reduction. This is in good agreement with new mesoscale numerical models, which are able to quantify localized shock pressure behavior in the target's pore space. Planar shock recovery experiments confirm these local pressure excursions, based on microanalysis of shock metamorphic features in quartz. Saturation of porous target rocks with water counteracts many of the effects of porosity. Post-impact analysis of projectile remnants shows that during mixing of projectile and target melts, the Fe of the projectile is preferentially partitioned into target melt to a greater degree than Ni and Co. We plan to continue evaluating the experimental results in combination with numerical models. These models help to quantify and evaluate cratering processes, while experimental data serve as benchmarks to validate the improved numerical models, thus helping to "bridge the gap" between experiments and nature. The results confirm and expand current crater scaling laws, and make an application to craters on planetary surfaces possible.

  4. Inelastic processes in K+-He collisions in energy range 0.7-10 keV

    NASA Astrophysics Data System (ADS)

    Lomsadze, R. A.; Gochitashvili, M. R.; Kezerashvili, R. Ya.; Mosulishvili, N. O.; Phaneuf, R.

    2013-04-01

    Absolute cross sections for charge exchange, ionization, stripping, and excitation in K+-He collisions were measured in the ion energy range 0.7-10 keV. The experimental data and the schematic correlation diagrams are used to analyze and determine the mechanisms for these processes. The increase of the excitation probability of inelastic channels with the angle of scattering is revealed. An exceptionally highly excited state of He is observed and a peculiarity for the excitation function of the resonance line is explained. The intensity ratio for the excitation of the K II λ=60.1 nm and λ=61.2 nm lines is 5:1, which indicates the high probability for excitation of the singlet resonance level 1P1 compared to the triplet level 3P1. The similarity of the population of the 4p state of the potassium ion and atom as well as the anomalously small values of the excitation cross sections are explained.

  5. Systematic study of the K X-ray spectra for hollow krypton and xenon atoms in collision process

    NASA Astrophysics Data System (ADS)

    Chen, X.; Ma, K.; Dong, C. Z.; Zhang, D. H.; Shao, C. J.; Yu, D. Y.; Cai, X. H.

    2015-11-01

    The satellite and hypersatellite of K X-rays resulted from additional vacancies in L-shell and M-shell for Kr and Xe atoms have been calculated systematically by using the multiconfiguration-Dirac-Fock (MCDF) method, in which the Breit interaction, QED corrections are also considered. The present calculations for diagram lines are in good agreement with available previous results. It is found that the number of spectator vacancies in L shell varies nearly linearly with the energy shifts of both K X-ray satellites and hypersatellites for Kr and Xe atoms. While an additional M shell hole has nearly no effect on the Kα energy shifts in comparison with the small but evident energy shifts of Kβ lines. The simulated spectra based on our results show a good agreement with the current experimental spectra at Heavy-ion Research Facility (HIRFL) in Lanzhou. The results of this paper will be helpful in further interpretation of various K X-ray spectra and better understanding of the collision processes.

  6. Molecular and genetic diversity in the metastatic process of melanoma

    PubMed Central

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran

    2014-01-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk PMID:24399611

  7. Analysis of In-Flight Collision Process During V-Type Firing Pattern in Surface Blasting Using Simple Physics

    NASA Astrophysics Data System (ADS)

    Chouhan, Lalit Singh; Raina, Avtar K.

    2015-10-01

    Blasting is a unit operation in Mine-Mill Fragmentation System (MMFS) and plays a vital role in mining cost. One of the goals of MMFS is to achieve optimum fragment size at minimal cost. Blast fragmentation optimization is known to result in better explosive energy utilization. Fragmentation depends on the rock, explosive and blast design variables. If burden, spacing and type of explosive used in a mine are kept constant, the firing sequence of blast-holes plays a vital role in rock fragmentation. To obtain smaller fragmentation size, mining professionals and relevant publications recommend V- or extended V-pattern of firing sequence. In doing so, it is assumed that the in-flight air collision breaks larger rock fragments into smaller ones, thus aiding further fragmentation. There is very little support to the phenomenon of breakage during in-flight collision of fragments during blasting in published literature. In order to assess the breakage of in-flight fragments due to collision, a mathematical simulation was carried over using basic principles of physics. The calculations revealed that the collision breakage is dependent on velocity of fragments, mass of fragments, the strength of the rock and the area of fragments over which collision takes place. For higher strength rocks, the in-flight collision breakage is very difficult to achieve. This leads to the conclusion that the concept demands an in-depth investigation and validation.

  8. Molecular connections between nuclear and ciliary import processes

    PubMed Central

    2013-01-01

    As an organelle, the cilium contains a unique complement of protein and lipid. Recent work has begun to shed light on the mechanisms that regulate entry of ciliary proteins into the compartment. Here, we focus on the mechanisms that regulate ciliary entry of cytosolic molecules. Studies have revealed a size exclusion mechanism for ciliary entry that is similar to the barrier to nuclear entry. Active import into the ciliary compartment involves nuclear trafficking components including importins, a Ran-guanosine triphosphate gradient, and nucleoporins. Together, this work indicates that nuclei and cilia share molecular, structural and mechanistic components that regulate import into the compartments. PMID:23985042

  9. Applying CLIPS to control of molecular beam epitaxy processing

    NASA Technical Reports Server (NTRS)

    Rabeau, Arthur A.; Bensaoula, Abdelhak; Jamison, Keith D.; Horton, Charles; Ignatiev, Alex; Glover, John R.

    1990-01-01

    A key element of U.S. industrial competitiveness in the 1990's will be the exploitation of advanced technologies which involve low-volume, high-profit manufacturing. The demands of such manufacture limit participation to a few major entities in the U.S. and elsewhere, and offset the lower manufacturing costs of other countries which have, for example, captured much of the consumer electronics market. One such technology is thin-film epitaxy, a technology which encompasses several techniques such as Molecular Beam Epitaxy (MBE), Chemical Beam Epitaxy (CBE), and Vapor-Phase Epitaxy (VPE). Molecular Beam Epitaxy (MBE) is a technology for creating a variety of electronic and electro-optical materials. Compared to standard microelectronic production techniques (including gaseous diffusion, ion implantation, and chemical vapor deposition), MBE is much more exact, though much slower. Although newer than the standard technologies, MBE is the technology of choice for fabrication of ultraprecise materials for cutting-edge microelectronic devices and for research into the properties of new materials.

  10. Transfer-excitation processes in collisions of N{sup 3+} ions with H{sub 2}, He, Ne, and Ar targets

    SciTech Connect

    Kamber, E.Y.; Akguengoer, K.; Leather, C.; Brenton, A.G.

    1996-08-01

    High-resolution translational energy-gain spectra for single-electron capture by N{sup 3+} ions from H{sub 2}, He, Ne, and Ar have been measured experimentally at laboratory impact energies of 6, 9, 12, and 15 keV. For N{sup 3+}-He and Ne collisions, transfer excitation into the 2{ital s}2{ital p}{sup 2} state of N{sup 2+} is significantly populated, while in N{sup 3+}-H{sub 2} collisions, transfer excitation into the 2{ital s}2{ital p}{sup 2}{sup 2}{ital P} state dominates at low energies. In N{sup 3+}-Ar collisions, pure single-electron capture into 3{ital s} is selectively populated. In all the collision systems studied here, contributions from processes commencing with a long-lived metastable state of N{sup 3+}{bold (}2{ital s}({sup 2}{ital S})2{ital p}{sup 3}{ital P}{bold )} are detected. The translational energy-gain spectra are interpreted qualitatively in terms of the reaction windows, which are calculated using the single-crossing Landau-Zener model and the extended version of the classical over-the-barrier model. Total cross sections for single-electron capture for N{sup 3+} ions colliding with He and H{sub 2} are also measured and compared with available measurements and theoretical calculations. {copyright} {ital 1996 The American Physical Society.}

  11. Inelastic vibrational processes in charge transfers between H/D and molecular ions

    NASA Astrophysics Data System (ADS)

    Heczko, Sarah L.; Bacani, Kieffer G.; Strom, Richard A.; Andrianarijaona, Vola M.; Seely, David G.; Havener, Charles C.

    2014-03-01

    Charge transfer on molecule proceeds through dynamically coupled electronic, vibrational, and rotational degrees of freedom. The inelastic vibrational processes, which go along with the reaction, can be experimentally investigated by using H/D systems, which do not allow multi-electron capture. Using the upgraded ion-atom merged-beams apparatus at Oak Ridge National Laboratory, absolute direct charge transfer cross sections for H2+, D2+, CO+, O2+, and H3+ are measured from keV/u collision energies where the collision is considered ``ro-vibrationally frozen'' to few eV/u energies where collision times are long enough to sample vibrational modes. The measurements presented here benchmark high energy theory and vibrationally specific adiabatic theory (V. M. Andrianarijaona et al., Phys. Rev. A 84, 062716, 2011). Research supported by the NASA Solar & Heliospheric Physics Program NNH07ZDA001N, the Office of Fusion Energy Sciences and Division of Chemical Sciences, Geosciences, and Biosciences, the Office of Basic Energy Sciences of the US Department of Energy. VA et al. is supported by the National Science Foundation through Grant No. PHY-106887.

  12. Deformation processes in polycrystalline Zr by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lu, Zizhe; Noordhoek, Mark J.; Chernatynskiy, Aleksandr; Sinnott, Susan B.; Phillpot, Simon R.

    2015-07-01

    Molecular dynamics simulation is used to characterize the deformation behavior of polycrystalline Zr. The predictions of two different potentials, an embedded atom method potential and a charge optimized many body potential are compared. The experimentally observed prismatic dislocations, pyramidal dislocations and twinning behaviors are produced in the simulations of [ 1 1 2 bar 0 ] and [0 0 0 1] textured structures and in fully 3D structure simulations. The relationship between the generalized stacking fault energy and the mechanical properties is discussed. In particular we find that the different shapes of the generalized stacking-fault energy curve for the two different interatomic descriptions of Zr have a significant effect on the deformation mechanisms. The deformation behavior of Zr is compared with analogous simulations of deformation of polycrystalline Mg.

  13. Atmospheric processes on ice nanoparticles in molecular beams

    PubMed Central

    Fárník, Michal; Poterya, Viktoriya

    2014-01-01

    This review summarizes some recent experiments with ice nanoparticles (large water clusters) in molecular beams and outlines their atmospheric relevance: (1) Investigation of mixed water–nitric acid particles by means of the electron ionization and sodium doping combined with photoionization revealed the prominent role of HNO3 molecule as the condensation nuclei. (2) The uptake of atmospheric molecules by water ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. (3) Photodissociation of hydrogen halides on water ice particles has been shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecules in clusters is also mentioned. Possible atmospheric consequences of all these results are briefly discussed. PMID:24790973

  14. Nonperturbative treatment of multielectron processes in ion-molecule scattering: Application to He{sup 2+}-H{sub 2} collisions

    SciTech Connect

    Sisourat, Nicolas; Dubois, Alain; Pilskog, Ingjald

    2011-11-15

    We present a nonperturbative theory to describe multielectronic processes occurring in the course of collisions between an ion and a molecule. The approach is based on the expansion of the electronic scattering wave function onto asymptotic mono- or multicenter states with proper translational conditions and includes both static and dynamical electronic correlations. Therefore, it has a wide application range around intermediate impact velocities v{approx_equal}v{sub e}, where v{sub e} is the averaged electron velocity in the initial state. As a first application, we report results on single- and double-electron capture processes in He{sup 2+}-H{sub 2} collisions for impact energies ranging from 0.01 to 25 keV/u. Special emphasis on the prediction of cross sections for double-electron capture into doubly excited states of helium is addressed.

  15. Molecular Modeling of Environmentally Important Processes: Reduction Potentials

    ERIC Educational Resources Information Center

    Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

    2004-01-01

    The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.

  16. Molecular formula analysis of fragment ions by isotope-selective collision-induced dissociation tandem mass spectrometry of pharmacologically active compounds.

    PubMed

    Bianco, Giuliana; Buchicchio, Alessandro; Lelario, Filomena; Cataldi, Tommaso R I

    2014-12-01

    The purpose of this work is to explore the mass fragment characterization of commonly used drugs through a novel approach, which involves isotope-selective tandem mass spectrometry (MS/MS). Collision-induced dissociation (CID) was performed with a low-resolution linear ion trap mass spectrometer in positive electrospray ionization. Three pharmacologically active ingredients, i.e. omeprazole, meloxicam and brinzolamide, selected as model compounds in their own formulation, were investigated as a sodiated adduct [C17 H19 N3 O3 S + Na](+) (omeprazole) and as protonated adducts, [C14 H13 N3 O4 S2  + H](+) and [C12 H21 N3 O5 S3  + H](+) , meloxicam and brinzolamide, respectively. Selecting a narrow window of ±0.5 m/z units, precursor ion fragmentation by CID-MS/MS of isotopologues A + 0, A + 1 and A + 2 was found very useful to confirm the chemical formula of product ions, thus aiding the establishment of characteristic fragmentation pathways of all three examined compounds. The correctness of putative molecular formula of product ions was easily demonstrated by exploiting the isotope peak abundance ratios (i.e. IF+0 /IF+1 and IF+0 /IF+2 ) as simple constraints in low-resolution MS instrumentations. PMID:25476951

  17. Conformation and diffusion behavior of ring polymers in solution: A comparison between molecular dynamics, multiparticle collision dynamics, and lattice Boltzmann simulations

    NASA Astrophysics Data System (ADS)

    Hegde, Govind A.; Chang, Jen-fang; Chen, Yeng-long; Khare, Rajesh

    2011-11-01

    We have studied the effect of chain topology on the structural properties and diffusion of polymers in a dilute solution in a good solvent. Specifically, we have used three different simulation techniques to compare the chain size and diffusion coefficient of linear and ring polymers in solution. The polymer chain is modeled using a bead-spring representation. The solvent is modeled using three different techniques: molecular dynamics (MD) simulations with a particulate solvent in which hydrodynamic interactions are accounted through the intermolecular interactions, multiparticle collision dynamics (MPCD) with a point particle solvent which has stochastic interactions with the polymer, and the lattice Boltzmann method in which the polymer chains are coupled to the lattice fluid through friction. Our results show that the three methods give quantitatively similar results for the effect of chain topology on the conformation and diffusion behavior of the polymer chain in a good solvent. The ratio of diffusivities of ring and linear polymers is observed to be close to that predicted by perturbation calculations based on the Kirkwood hydrodynamic theory.

  18. Collision-Dependent Line Areas in the a1Δ_g← X^3σ^-_g Band of Molecular Oxygen

    NASA Astrophysics Data System (ADS)

    Sironneau, Vincent; Fleisher, Adam J.; Hodges, Joseph

    2015-06-01

    We report precise line areas for individual rotationally resolved transitions within the a^1Δ_g← X^3σ^-_g electronic band of molecular oxygen recorded as a function of pressure for both neat samples of O_2 as well as samples of O_2 dilute with a variety of collisional partners. Using optical frequency comb referenced frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) near 1.27 μm we measure line areas with a quality-of-fit QF ≤ 50,000 using a partially correlated quadratic-speed-dependent Nelkin-Ghatak profile. This spectrometer has achieved this high QF by both suppressing coupled cavity effects and by preserving a high-fidelity frequency axis with absolute frequency accuracy approaching 1 part in 10^9. With this instrument we are also currently exploring collision-induced absorption (CIA) and perturbative line mixing effects in O_2 over the entire 7800-7940 wn spectral range.

  19. Gas-Phase Synthesis of Boronylallene (H2CCCH(BO)) under Single Collision Conditions: A Crossed Molecular Beams and Computational Study.

    PubMed

    Maity, Surajit; Parker, Dorian S N; Kaiser, Ralf I; Ganoe, Brad; Fau, Stefan; Perera, Ajith; Bartlett, Rodney J

    2014-05-15

    The gas phase reaction between the boron monoxide radical ((11)BO; X(2)Σ(+)) and allene (H2CCCH2; X(1)A1) was investigated experimentally under single collision conditions using the crossed molecular beam technique and theoretically exploiting ab initio electronic structure and statistical (RRKM) calculations. The reaction was found to follow indirect (complex forming) scattering dynamics and proceeded via the formation of a van der Waals complex ((11)BOC3H4). This complex isomerized via addition of the boron monoxide radical ((11)BO; X(2)Σ(+)) with the radical center located at the boron atom to the terminal carbon atom of the allene molecule forming a H2CCCH2(11)BO intermediate on the doublet surface. The chemically activated H2CCCH2(11)BO intermediate underwent unimolecular decomposition via atomic hydrogen elimination from the terminal carbon atom holding the boronyl group through a tight exit transition state to synthesize the boronylallene product (H2CCCH(11)BO) in a slightly exoergic reaction (55 ± 11 kJ mol(-1)). Statistical (RRKM) calculations suggest that minor reaction channels lead to the products 3-propynyloxoborane (CH2((11)BO)CCH) and 1-propynyloxoborane (CH3CC(11)BO) with fractions of 1.5% and 0.2%, respectively. The title reaction was also compared with the cyano (CN; X(2)Σ(+))-allene and boronyl-methylacetylene reactions to probe similarities, but also differences of these isoelectronic systems. Our investigation presents a novel gas phase synthesis and characterization of a hitherto elusive organyloxoborane (RBO) monomer-boronylallene-which is inherently tricky to isolate in the condensed phase except in matrix studies; our work further demonstrates that the crossed molecular beams approach presents a useful tool in investigating the chemistry and synthesis of highly reactive organyloxoboranes. PMID:24806514

  20. Heavy particle atomic collisions in astrophysics: Beyond H and He targets

    SciTech Connect

    Stancil, P.C.; Krstic, P.S.; Schultz, D.R.

    1998-06-01

    The physical conditions relating to the emission of x-rays from Jovian and cometary atmospheres and to supernova ejecta are briefly described. Emphasis is placed on elucidating the relevance and importance of atomic collision processes, the availability of data, and the outstanding data needs for modeling these environments. Some preliminary theoretical studies of electron capture for important collisions systems, involving molecular and atomic metal targets, are presented.

  1. Young stellar disks formed by the collision of a molecular cloud with a circumnuclear disk at the Galactic center

    NASA Astrophysics Data System (ADS)

    Alig, C.; Schartmann, M.; Burkert, A.; Dolag, K.

    2014-05-01

    We suggest a new formation mechanism for the inclined, sub-parsec scale and counterrotating stellar disks observed around the central black hole in the Milky Way Galactic center. The simulation of a single molecular cloud crashing into a circumnuclear ring of gas leads to the inflow of multiple streams of gas towards the central parsec region. The time delayed arrival of those streams forms multiple, sub-parsec scale accretion disks, with angular momentum depending on the ratio of cloud and circumnuclear ring material. These accretion disks could then be the progenitors which fragmented into the observed stellar disks. A similar event might have also led to the creation of the so-called minispiral in the Galactic center.

  2. Procesos cuasi-moleculares en enanas blancas frías

    NASA Astrophysics Data System (ADS)

    Rohrmann, R. D.; Althaus, L. G.; Kepler, S. O.

    We show that the radiation emitted by very cool white dwarf stars (Teff ~< 3000 K) with pure hydrogen atmospheres, is fully formed by radiative processes induced by atomic and molecular collisions. FULL TEXT IN SPANISH

  3. Molecular processes in a high temperature shock layer

    NASA Technical Reports Server (NTRS)

    Guberman, S. L.

    1985-01-01

    The development of techniques for the calculation of electron capture widths, electronic wave functions, cross sections and rates needed for the description of the dissociative recombination (DR) of molecular ions with electrons were described. The cross sections and rates were calculated by using harmonic oscillator wave functions for the ion and a delta function approximation for the continuum vibrational wave function in the repulsive dissociative channel. In order to obtain DR cross sections of quantitative accuracy, a computer program which solves the one dimensional nuclear motion wave equation was revised to calculate the cross sections and rates. The program and the new results are described. Included is a discussion of large windows found in the dissociative recombination cross sections from excited ion vibrational levels. These windows have not been previously reported in the literature. The magnitude of the DR cross sections for several dissociative routes are sensitive to the location of the crossing of the neutral and ion potential curves. Studies of the effects of basis set and CI wave function size on vertical excitation energies are described. Preliminary studies on N2 and O2 using large scale wave functions are also reported.

  4. Post-processing interstitialcy diffusion from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Bhardwaj, U.; Bukkuru, S.; Warrier, M.

    2016-01-01

    An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms.

  5. Electron-Driven Molecular Processes Induced in Biological Systems by Electromagnetic and Other Ionizing Sources

    NASA Astrophysics Data System (ADS)

    Baccarelli, I.; Gianturco, F. A.; Grandi, A.; Lucchese, R. R.; Sanna, N.

    We describe, and analyse in some detail, a selection of the most recent theoretical and computational models which attempt to explain, at the molecular level, the dynamics of metastable negative ion formation from biological molecules in the gas-phase. Such Transient Negative Ions (TNIs) are related to the nanoscopic nuclear dynamics presiding over the occurrence of irreversible damage in the biosystems through the many possible pathways leading to dissociative attachment decay of the initial TNI. We will review the theoretical approach we adopted to study electron-molecule collision as applied to systems of biological interest. The connection between the spatial symmetry of the metastable anion and its role during the dissociative electron attachment event is also discussed and analysed through several examples.

  6. Molecular processes in astrophysics: Calculations of hydrogen + hydrogen gas excitation, de-excitation, and cooling

    NASA Astrophysics Data System (ADS)

    Kelley, Matthew Thomas

    The implications of H+H2 cooling in astrophysics is important to several applications. One of the most significant and pure applications is its role in cooling in the early universe. Other applications would include molecular dynamics in nebulae and their collapse into stars and astrophysical shocks. Shortly after the big bang, the universe was a hot primordial gas of photons, electrons, and nuclei among other ingredients. By far the most dominant nuclei in the early universe was hydrogen. In fact, in the early universe the matter density was 90 percent hydrogen and only 10 percent helium with small amounts of lithium and deuterium. In order for structure to form in the universe, this primordial gas must form atoms and cool. One of the significant cooling mechanisms is the collision of neutral atomic hydrogen with a neutral diatomic hydrogen molecule. This work performs calculations to determine collisional cooling rates of hydrogen using two potential surfaces.

  7. Determination of the collisional energy transfer distribution responsible for the collision-induced dissociation of NO2 with Ar

    NASA Astrophysics Data System (ADS)

    Steill, Jeffrey D.; Jasper, Ahren W.; Chandler, David W.

    2015-09-01

    Collisional energy transfer is an essential aspect of chemical reactivity and maintenance of thermal equilibrium. Here we report the shape (energy-dependence) of the collisional energy transfer probability function for collisions of vibrationally excited NO2 entrained in a molecular beam and photoexcited to within 40 cm-1 of its dissociation threshold. The internally excited molecules undergo collisions with Ar atoms in a crossed beam apparatus. Dissociative collisions rapidly produce the NO(J) fragment, which is observed by velocity-mapped ion imaging and REMPI techniques. The measured collisional energy transfer function is obtained via energy conservation and is compared with the results of classical trajectory calculations. Good agreement between the theory and experiment is found for collisions that transfer small amounts of energy, but the theory predicts a higher likelihood of energetic collisions than is observed experimentally. We explore possible explanations for this discrepancy in the dynamics of the collision excitation process.

  8. Crossed Molecular Beams and Quasiclassical Trajectory Surface Hopping Studies of the Multichannel Nonadiabatic O((3)P) + Ethylene Reaction at High Collision Energy.

    PubMed

    Balucani, Nadia; Leonori, Francesca; Casavecchia, Piergiorgio; Fu, Bina; Bowman, Joel M

    2015-12-17

    The combustion relevant O((3)P) + C2H4 reaction stands out as a prototypical multichannel nonadiabatic reaction involving both triplet and singlet potential energy surfaces (PESs), which are strongly coupled. Crossed molecular beam (CMB) scattering experiments with universal soft electron ionization mass spectrometric detection have been used to characterize the dynamics of this reaction at the relatively high collision energy Ec of 13.7 kcal/mol, attained by crossing the reactant beams at an angle of 135°. This work is a full report of the data at the highest Ec investigated for this reaction. From laboratory product angular and velocity distribution measurements, angular and translational energy distributions in the center-of-mass system have been obtained for the five observed exothermic competing reaction channels leading to H + CH2CHO, H + CH3CO, CH3 + HCO, CH2 + H2CO, and H2 + CH2CO. The product branching ratios (BRs) have been derived. The elucidation of the reaction dynamics is assisted by synergic full-dimensional quasiclassical trajectory surface-hopping calculations of the reactive differential cross sections on coupled ab initio triplet/singlet PESs. This joint experimental/theoretical study extends and complements our previous combined CMB and theoretical work at the lower collision energy of 8.4 kcal/mol. The theoretically derived BRs and extent of intersystem crossing (ISC) are compared with experimental results. In particular, the predictions of the QCT results for the three main channels (those leading to vinoxy + H, methyl + HCO and methylene + H2CO formation) are compared directly with the experimental data in the laboratory frame. Good overall agreement is noted between theory and experiment, although some small, yet significant shortcomings of the theoretical differential cross section are noted. Both experiment and theory find almost an equal contribution from the triplet and singlet surfaces to the reaction, with a clear tendency of the degree of ISC to decrease with increasing Ec and with theory slightly overestimating the extent of ISC. PMID:26413909

  9. Collinear Collision Chemistry: 1. A Simple Model for Inelastic and Reactive Collision Dynamics

    ERIC Educational Resources Information Center

    Mahan, Bruce H.

    1974-01-01

    Discusses a model for the collinear collision of an atom with a diatomic molecule on a simple potential surface. Indicates that the model can provide a framework for thinking about molecular collisions and reveal many factors which affect the dynamics of reactive and inelastic collisions. (CC)

  10. Molecular basis of processing wheat gluten toward biobased materials.

    PubMed

    Lagrain, Bert; Goderis, Bart; Brijs, Kristof; Delcour, Jan A

    2010-03-01

    The unique properties of the wheat grain reside primarily in the gluten-forming storage proteins of its endosperm. Wheat gluten's structural and functional properties have led to an expanding diversity of applications in food products. However, its viscoelastic properties and low water solubility also are very interesting features for nonfood applications. Moreover, gluten is annually renewable and perfectly biodegradable. In the processing and setting of gluten containing products, temperature plays a very important role. In this review, the structure and reactivity of gluten are discussed and the importance of sulfhydryl (SH) and disulfide (SS) groups is demonstrated. Wheat gluten aggregation upon thermosetting proceeds through direct covalent cross-linking in and between its protein groups, glutenin and gliadin. Predominant reactions include SH oxidation and SH/SS interchange reactions leading to the formation of SS cross-links. Additionally, thermal treatment of gluten can result in the formation of other than SS covalent bonds. We here review two main technological approaches to make gluten-based materials: wet processes resulting in thin films and dry processes, such as extrusion or compression molding, exploiting the thermoplastic properties of proteins under low moisture conditions and potentially resulting in very useful materials. Gluten bioplastics can also be reinforced with natural fibers, resulting in biocomposites. Although a lot of progress has been made the past decade, the current gluten materials are still outperformed by their synthetic polymer counterparts. PMID:20141101

  11. X-Ray Emission from Stellar Jets by Collision against High-density Molecular Clouds: an Application to HH 248

    NASA Astrophysics Data System (ADS)

    Lpez-Santiago, J.; Bonito, R.; Orellana, M.; Miceli, M.; Orlando, S.; Ustamujic, S.; Albacete-Colombo, J. F.; de Castro, E.; Gmez de Castro, A. I.

    2015-06-01

    We investigate the plausibility of detecting X-ray emission from a stellar jet that impacts a dense molecular cloud, a scenario that may be typical for classical T Tauri stars with jets in dense star-forming complexes. We first model the impact of a jet against a dense cloud using two-dimensional axisymmetric hydrodynamic simulations, exploring different configurations of the ambient environment. Then, we compare our results with XMM-Newton observations of the Herbig-Haro object HH 248, where extended X-ray emission aligned with the optical knots is detected at the edge of the nearby IC 434 cloud. Our simulations show that a jet can produce plasma with temperatures up to 107 K, consistent with production of X-ray emission, after impacting a dense cloud. We find that jets denser than the ambient medium but less dense than the cloud produce detectable X-ray emission only at impact with the cloud. From an exploration of the model parameter space, we constrain the physical conditions (jet density and velocity and cloud density) that reproduce the intrinsic luminosity and emission measure of the X-ray source possibly associated with HH 248 well. Thus, we suggest that the extended X-ray source close to HH 248 corresponds to a jet impacting a dense cloud.

  12. Coffee husk composting: an investigation of the process using molecular and non-molecular tools.

    PubMed

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-03-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

  13. Coffee husk composting: An investigation of the process using molecular and non-molecular tools

    PubMed Central

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H.; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-01-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

  14. Singlet molecular oxygen generated in dark biological process.

    PubMed

    Di Mascio, Paolo; Medeiros, Marisa H G

    2014-10-01

    Ultraweak chemiluminescence arising from biomolecules oxidation has been attributed to the radiative deactivation of singlet molecular oxygen [(1)O2] and electronically excited triplet carbonyl products involving dioxetane intermediates. As examples, we will discuss the generation of (1)O2 from lipid hydroperoxides, which involves a cyclic mechanism from a linear tetraoxide intermediate. The generation of (1)O2 in aqueous solution via energy transfer from the excited triplet acetone arising from the thermodecomposition of dioxetane a chemical source, and horseradish peroxidase-catalyzed oxidation of 2-methylpropanal, as an enzymatic source, will also be discussed. The approach used to unequivocally demonstrate the generation of (1)O2 in these reactions is the use of (18)O-labeled hydroperoxide / triplet dioxygen ((18)[(3)O2]), the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O2 light emission. Characteristic light emission at 1,270nm, corresponding to the singlet delta state monomolecular decay was observed. Using(18)[(3)O2], we observed the formation of (18)O-labeled (1)O2 ((18)[(1)O2]) by the chemical trapping of (18)[(1)O2]with the anthracene-9,10-diyldiethane-2,1-diyl disulfate disodium salt (EAS) and detected the corresponding (18)O-labeled EAS endoperoxide usingHPLC-MS/MS. The combined use of the thermolysis of a water-soluble naphthalene endoperoxide as a generator of (18)O labeled (1)O2 and the sensitivity of HPLC-MS/MS allowed the study of (1)O2reactivity toward biomolecules. Photoemission properties and chemical trapping clearly demonstrate that the production of hydroperoxide and excited carbonyls generates (18)[(1)O2], and points to the involvement of (1)O2 in physiological and pathophysiological mechanism. Supported by FAPESP (2012/12663-1), CAPES, INCT Redoxoma (FAPESP/CNPq/CAPES; 573530/2008-4), NAP Redoxoma (PRPUSP; 2011.1.9352.1.8), CEPID Redoxoma (FAPESP; 2013/07937-8). PMID:26461325

  15. Final Report, "Molecular Design of Hydrocarbon Oxidation Catalytic Processes"

    SciTech Connect

    Professor Francisco Zaera

    2007-08-09

    The main goal of this project had been to use model systems to correlate selectivities in partial oxidation catalysis with the presence of specific sites on the surface of the catalyst. Extensive work was performed this year on characterizing oxygen-treated nickel surfaces by chemical means. Specifically, the surface chemistry of ammonia coadsorbed with atomic oxygen on Ni(110) single-crystal surfaces was studied by temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). It was determined that at intermediate oxygen coverages direct ammonia adsorption on nickel sites is suppressed, but a new high-temperature reaction regime is generated at 400 K where NHx surface fragments are rehydrogenated concurrently with the production of water and molecular hydrogen. The extensive isotope scrambling and hydrogen transfer seen from nitrogen- to oxygen-containing surface intermediates, and the optimum yields seen for this 400 K state at intermediate oxygen coverages, strongly suggest the direct interaction of the adsorbed ammonia with oxygen atoms at the end of the –Ni–O- rows that form upon reconstruction of the surface. Hydrogen transfer between ammonia and oxygen appears to take place directly via hydrogen bonding, and to be reversible but biased towards water formation. An equilibrium is reached between the produced water and the reacting surface oxygen and hydrogen. The strong influence of the OH surface groups on the thermal chemistry of the adsorbed ammonia was interpreted in terms of the adsorbing geometry of the OH groups on the surface, and of hydrogen bonding between adsorbed OH and NH3 species. In terms of alcohol reactivity, the adsorption of 2-iodoethanol, a precursor for the preparation of 2-hydroxyethyl and oxametallacycle surface species, was found to lead to two configurations involving either just the iodine atom or both iodine and hydroxyl ends of the molecule. A complex chemical behavior starts around 140 K with the production of small amounts of ethylene and water, most likely via the concerted decomposition or disproportionation of the adsorbed molecular species. The bulk of the 2-iodoethanol decomposes at about 150 K via an initial carbon-iodine scission to form –O(H)CH2CH2– (~80%) and 2-hydroxyethyl (~20%) intermediates. Two competing reactions are involved with the subsequent conversion of the 2-hydroxyethyl species around 160 K, a reductive elimination with surface hydrogen to yield ethanol, and a β-H elimination to surface vinyl alcohol. The –O(H)CH2CH2–, on the other hand, dehydrogenates to a –OCH2CH2– oxametallacycle species about the same temperature. Both 2-hydroxyethyl and oxametallacycle species tautomerize to acetaldehyde, around 210 K and above 250 K, respectively, and some of that acetaldehyde desorbs while the rest decomposes to hydrogen and carbon monoxide. We contend that a better understanding of the surface chemistry of oxygen-containing surfaces can lead to better selectivities in catalysis. This is arguably the most important issue in the field of catalysis in the near future, and one that impacts several technologies of interest to DOE such as the manufacturing of speciality chemicals and the control and removal of pollutants. Additional work was performed on the characterization of the chemistry of methyl and methylene adsorbed species on oxygen-treated nickel surfaces. Complex chemistry was observed involving not only hydrogenation and dehydrogenation steps, but also C-C couplings and methylene insertions to produce heavier hydrocarbons, and oxygen insertion reactions that yield oxygenates. Finally, a dual titration technique employing xenon and a chemically sensitive probe was developed to identify minority catalytic sites on oxide surfaces. In the case of oxygen-treated Ni(110) single crystals, it was found that both hydrogen transfer with adsorbed water or ammonia and certain hydrocarbon hydrogenation reactions take place at the end of the –Ni–O rows that form in this system. Carbon and nitrogen oxides, on the other hand, display no preference for adsorption on those sites.

  16. Control of ultracold atomic collisions with resonant light

    NASA Astrophysics Data System (ADS)

    Bohn, John L.; Julienne, Paul S.

    1997-04-01

    We present a detailed semianalytic theory of cold atom collisions in the presence of one or more laser fields tuned near molecular resonances. This theory expands upon a previous development(J. L. Bohn and P. S. Julienne, Phys. Rev. A 54), R4367 (1996). by accounting explicitly for light-induced shifts and line broadenings apparent at high laser intensities. We use this theory to determine realistic laser settings for guiding the outcome of cold collision processes. One aspect of such control is the production of ensembles of ultracold molecules, which can then be trapped in FORT experiments.

  17. GR@PPA 2.8: Initial-state jet matching for weak-boson production processes at hadron collisions

    NASA Astrophysics Data System (ADS)

    Odaka, Shigeru; Kurihara, Yoshimasa

    2012-04-01

    The initial-state jet matching method introduced in our previous studies has been applied to the event generation of single W and Z production processes and diboson (WW, WZ and ZZ) production processes at hadron collisions in the framework of the GR@PPA event generator. The generated events reproduce the transverse momentum spectra of weak bosons continuously in the entire kinematical region. The matrix elements (ME) for hard interactions are still at the tree level. As in previous versions, the decays of weak bosons are included in the matrix elements. Therefore, spin correlations and phase-space effects in the decay of weak bosons are exact at the tree level. The program package includes custom-made parton shower programs as well as ME-based hard interaction generators in order to achieve self-consistent jet matching. The generated events can be passed to general-purpose event generators to make the simulation proceed down to the hadron level. Catalogue identifier: ADRH_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADRH_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 112 146 No. of bytes in distributed program, including test data, etc.: 596 667 Distribution format: tar.gz Programming language: Fortran; with some included libraries coded in C and C++ Computer: All Operating system: Any UNIX-like system RAM: 1.6 Mega bytes at minimum Classification: 11.2 Catalogue identifier of previous version: ADRH_v2_0 Journal reference of previous version: Comput. Phys. Comm. 175 (2006) 665 External routines: Bash and Perl for the setup, and CERNLIB, ROOT, LHAPDF, PYTHIA according to the user's choice. Does the new version supersede the previous version?: No, this version supports only a part of the processes included in the previous versions. Nature of problem: We need to combine those processes including 0 jet and 1 jet in the matrix elements using an appropriate matching method, in order to simulate weak-boson production processes in the entire kinematical region. Solution method: The leading logarithmic components to be included in parton distribution functions and parton showers are subtracted from 1-jet matrix elements. Custom-made parton shower programs are provided to ensure satisfactory performance of the matching method. Reasons for new version: An initial-state jet matching method has been implemented. Summary of revisions: Weak-boson production processes associated with 0 jet and 1 jet can be consistently merged using the matching method. Restrictions: The built-in parton showers are not compatible with the PYTHIA new PS and the HERWIG PS. Unusual features: A large number of particles may be produced by the parton showers and passed to general-purpose event generators. Running time: About 10 min for initialization plus 25 s for every 1k-event generation for W production in the LHC condition, on a 3.0-GHz Intel Xeon processor with the default setting.

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

    SciTech Connect

    Hebner, G.A.

    1998-10-14

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

  19. Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations

    SciTech Connect

    Giorgi, G.L.; Roncaglia, M.; Raffa, F.A.; Genovese, M.

    2015-10-15

    During the long course of evolution, nature has learnt how to exploit quantum effects. In fact, recent experiments reveal the existence of quantum processes whose coherence extends over unexpectedly long time and space ranges. In particular, photosynthetic processes in light-harvesting complexes display a typical oscillatory dynamics ascribed to quantum coherence. Here, we consider the simple model where a dimer made of two chromophores is strongly coupled with a quasi-resonant vibrational mode. We observe the occurrence of wide oscillations of genuine quantum correlations, between electronic excitations and the environment, represented by vibrational bosonic modes. Such a quantum dynamics has been unveiled through the calculation of the negativity of entanglement and the discord, indicators widely used in quantum information for quantifying the resources needed to realize quantum technologies. We also discuss the possibility of approximating additional weakly-coupled off-resonant vibrational modes, simulating the disturbances induced by the rest of the environment, by a single vibrational mode. Within this approximation, one can show that the off-resonant bath behaves like a classical source of noise.

  20. Bsoft: image and molecular processing in electron microscopy.

    PubMed

    Heymann, J B

    2001-01-01

    Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages. PMID:11472087

  1. Projectile angular-differential cross sections for electron transfer processes in ion-helium collisions: Evidence for the applicability of the independent electron model

    SciTech Connect

    Zapukhlyak, Myroslav; Kirchner, Tom

    2009-12-15

    The electron dynamics in p-He and He{sup 2+}-He collisions have been investigated on the level of the independent electron model by using the two-center basis generator method. Projectile angular-differential cross sections for various one- and two-electron processes involving electron transfer have been calculated with the eikonal approximation. Overall, the calculated cross sections are in good agreement with the most recent experimental cold target recoil ion momentum spectroscopy data taken at impact energies in the range from 40 to 630 keV/amu. This demonstrates, somewhat surprisingly, that electron correlations play but a minor role for the processes and the energies considered.

  2. Molecular Insights into Poly(ADP-ribose) Recognition and Processing

    PubMed Central

    Žaja, Roko; Mikoč, Andreja; Barkauskaite, Eva; Ahel, Ivan

    2012-01-01

    Poly(ADP-ribosyl)ation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosyl)ation (PAR) in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding). The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells. PMID:24970154

  3. The Henry Ford Production System: LEAN Process Redesign Improves Service in the Molecular Diagnostic Laboratory

    PubMed Central

    Cankovic, Milena; Varney, Ruan C.; Whiteley, Lisa; Brown, Ron; D'Angelo, Rita; Chitale, Dhananjay; Zarbo, Richard J.

    2009-01-01

    Accurate and timely molecular test results play an important role in patient management; consequently, there is a customer expectation of short testing turnaround times. Baseline data analysis revealed that the greatest challenge to timely result generation occurred in the preanalytic phase of specimen collection and transport. Here, we describe our efforts to improve molecular testing turnaround times by focusing primarily on redesign of preanalytic processes using the principles of LEAN production. Our goal was to complete greater than 90% of the molecular tests in less than 3 days. The project required cooperation from different laboratory disciplines as well as individuals outside of the laboratory. The redesigned processes involved defining and standardizing the protocols and approaching blood and tissue specimens as analytes for molecular testing. The LEAN process resulted in fewer steps, approaching the ideal of a one-piece flow for specimens through collection/retrieval, transport, and different aspects of the testing process. The outcome of introducing the LEAN process has been a 44% reduction in molecular test turnaround time for tissue specimens, from an average of 2.7 to 1.5 days. In addition, extending LEAN work principles to the clinician suppliers has resulted in a markedly increased number of properly collected and shipped blood specimens (from 50 to 87%). These continuous quality improvements were accomplished by empowered workers in a blame-free environment and are now being sustained with minimal management involvement. PMID:19661386

  4. Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron.

    PubMed

    Keil, Matthias S

    2015-10-01

    Power laws describe brain functions at many levels (from biophysics to psychophysics). It is therefore possible that they are generated by similar underlying mechanisms. Previously, the response properties of a collision-sensitive neuron were reproduced by a model which used a power law for scaling its inhibitory input. A common characteristic of such neurons is that they integrate information across a large part of the visual field. Here we present a biophysically plausible model of collision-sensitive neurons with η-like response properties, in which we assume that each information channel is noisy and has a response threshold. Then, an approximative power law is obtained as a result of pooling these channels. We show that with this mechanism one can successfully predict many response characteristics of the Lobula Giant Movement Detector Neuron (LGMD). Moreover, the results depend critically on noise in the inhibitory pathway, but they are fairly robust against noise in the excitatory pathway. PMID:26513150

  5. Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron

    PubMed Central

    Keil, Matthias S.

    2015-01-01

    Power laws describe brain functions at many levels (from biophysics to psychophysics). It is therefore possible that they are generated by similar underlying mechanisms. Previously, the response properties of a collision-sensitive neuron were reproduced by a model which used a power law for scaling its inhibitory input. A common characteristic of such neurons is that they integrate information across a large part of the visual field. Here we present a biophysically plausible model of collision-sensitive neurons with η-like response properties, in which we assume that each information channel is noisy and has a response threshold. Then, an approximative power law is obtained as a result of pooling these channels. We show that with this mechanism one can successfully predict many response characteristics of the Lobula Giant Movement Detector Neuron (LGMD). Moreover, the results depend critically on noise in the inhibitory pathway, but they are fairly robust against noise in the excitatory pathway. PMID:26513150

  6. Ion Collision, Theory

    SciTech Connect

    Shukla, Anil K.

    2013-09-11

    The outcome of a collision between an ion and neutral species depends on the chemical and physical properties of the two reactants, their relative velocities, and the impact parameter of their trajectories. These include elastic and inelastic scattering of the colliding particles, charge transfer (including dissociative charge transfer), atom abstraction, complex formation and dissociation of the colliding ion. Each of these reactions may be characterized in terms of their energy-dependent rate coefficients, cross sections and reaction kinetics. A theoretical framework that emphasizes simple models and classical mechanics is presented for these processes. Collision processes are addressed in two categories of low-energy and high-energy collisions. Experiments under thermal or quasi-thermal conditions–swarms, drift tubes, chemical ionization and ion cyclotron resonance are strongly influenced by long-range forces and often involve collisions in which atom exchange and extensive energy exchange are common characteristics. High-energy collisions are typically impulsive, involve short-range intermolecular forces and are direct, fast processes.

  7. Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases.

    PubMed

    Beckham, Gregg T; Ståhlberg, Jerry; Knott, Brandon C; Himmel, Michael E; Crowley, Michael F; Sandgren, Mats; Sørlie, Morten; Payne, Christina M

    2014-06-01

    Polysaccharide depolymerization in nature is primarily accomplished by processive glycoside hydrolases (GHs), which abstract single carbohydrate chains from polymer crystals and cleave glycosidic linkages without dissociating after each catalytic event. Understanding the molecular-level features and structural aspects of processivity is of importance due to the prevalence of processive GHs in biomass-degrading enzyme cocktails. Here, we describe recent advances towards the development of a molecular-level theory of processivity for cellulolytic and chitinolytic enzymes, including the development of novel methods for measuring rates of key steps in processive action and insights gained from structural and computational studies. Overall, we present a framework for developing structure-function relationships in processive GHs and outline additional progress towards developing a fundamental understanding of these industrially important enzymes. PMID:24863902

  8. Advances in Coupling of Kinetics and Molecular Scale Tools to Shed Light on Soil Biogeochemical Processes

    SciTech Connect

    Sparks, Donald

    2014-09-02

    Biogeochemical processes in soils such as sorption, precipitation, and redox play critical roles in the cycling and fate of nutrients, metal(loid)s and organic chemicals in soil and water environments. Advanced analytical tools enable soil scientists to track these processes in real-time and at the molecular scale. Our review focuses on recent research that has employed state-of-the-art molecular scale spectroscopy, coupled with kinetics, to elucidate the mechanisms of nutrient and metal(loid) reactivity and speciation in soils. We found that by coupling kinetics with advanced molecular and nano-scale tools major advances have been made in elucidating important soil chemical processes including sorption, precipitation, dissolution, and redox of metal(loids) and nutrients. Such advances will aid in better predicting the fate and mobility of nutrients and contaminants in soils and water and enhance environmental and agricultural sustainability.

  9. Tuning ultracold collisions of excited rotational dipolar molecules

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven

    2015-05-01

    Ultracold molecular dipolar gases often suffer from losses due to chemical reactions (or eventual sticky collisions for non-reactive molecules). Loss suppression for both bosonic and fermionic dipolar species can be obtained in a one-dimensional optical lattice but this requires usually strong confinements to get into a pure two-dimensional collision regime. An alternative way can be found without confinement using rotationally excited molecules. In this talk I will explore the ultracold collisions of rotationally excited dipolar molecules in free space. I will focus on electric dipolar molecules of KRb and electric and magnetic dipolar molecules of RbSr. I will show that we can sharply tune the elastic, inelastic and reactive rate coefficients of lossy molecular collisions when a second rotationally excited colliding channel crosses the threshold of the initial colliding channel, with the help of an applied electric field. We can increase or decrease the loss processes whether the second channel is above or below the initial channel. This could lead to favorable conditions for evaporative cooling. Additionally, we include the electric quadrupole and octopole moment to the dipole moment in the expression of the long-range multipole-multipole interaction. For processes mediated by the incident channel like elastic and loss collisions, the inclusion of quadrupole and octopole moments are not important at ultralow energies. They are important for processes mediated by state-to-state transitions like inelastic collisions. I acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche.

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

    SciTech Connect

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

    1982-10-01

    This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  11. Peripheral processes 2 {yields} 3 and 2 {yields} 4 in QED and QCD in p-p-bar high-energy collisions

    SciTech Connect

    Ahmadov, A. I. Bystritskiy, Yu. M. Kuraev, E. A.

    2011-10-15

    Differential cross sections of processes with high-energy p(-p)p collisions-creation of a scalar, a pseudoscalar and a lepton pair-are considered in the Weizsacker-Williams approximation in QED in the QCD framework, processes with conversion of the initial proton (antiproton) to fermionic jets accompanied with one gluon jet and the state of two gluons and a quark-antiquark pair (without a rapidity gap) are considered in the framework of the effective Regge action of Lipatov's theory. The process of creation of a Higgs boson accompanied with two fermionic jets is considered. The azimuthal correlation in the process of two gluon jets separated by a rapidity gap is investigated. The gluon Reggeization effects are taken into account. Some distributions are illustrated by numerical calculations.

  12. Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands.

    PubMed

    Barboiu, Mihail; Stadler, Adrian-Mihail; Lehn, Jean-Marie

    2016-03-18

    General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories. PMID:26894262

  13. Electron emission in collisions of highly charged ions with atoms and diatomic molecules

    NASA Astrophysics Data System (ADS)

    Rivarola, R. D.; Fainstein, P. D.

    2003-05-01

    A short review of theoretical models previously used to study single and multiple electron ionization in collisions of bare fast highly charged ions with atomic and diatomic molecular targets is given. Electron emission with simultaneous electron capture by the projectile is also considered. The principal mechanisms producing the different reactions are revisited. It is emphasized that two-center descriptions are necessary for an adequate description of the existing experimental data. The role of electron correlation in the initial bound state and during the collision process is analyzed as well as the presence of effects associated with the two-center character of diatomic molecular targets.

  14. Quantum Chemical Molecular Dynamics Studies on the Chemical Mechanical Polishing Process of Cu Surface

    NASA Astrophysics Data System (ADS)

    Yokosuka, Toshiyuki; Sasata, Katsumi; Kurokawa, Hitoshi; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    2003-04-01

    The dynamic behavior of the oxidation reaction of the Cu surface during the Cu chemical-mechanical polishing (CMP) process was investigated by a novel tight-binding quantum chemical molecular dynamics method. We confirmed that our tight-binding quantum chemical molecular dynamics method with first-principles parameterization can calculate the structures, and electronic states of various molecules and solids related to the Cu-CMP process as accurately as the density functional calculations, while the CPU time of the new method is around 5,000 times faster than that of the first-principles molecular dynamics calculations. We employed hydrogen peroxide solution as a slurry and the Cu surface as a substrate to simulate the Cu-CMP process by using our accelerated quantum chemical molecular dynamics method. Three types of models were constructed to analyze the effect of the pH of the slurry and Miller plane of the Cu surface on the dynamic behaviors of the oxidation process of the Cu surface. We indicate that the pH of the slurry strongly affects the oxidation process of Cu surface. Moreover, we clarified that the oxidation mechanism depends on the Miller plane of the Cu surfaces.

  15. Interference asymmetry of molecular frame photoelectron angular istributions in bichromatic UV ionization processes

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2016-03-01

    We investigate molecular photoionization by ultrafast bichromatic linearly polarized UV laser pulses at frequencies 2{ω }1={ω }2 perpendicular to the internuclear axis R involving π orbital excitation. Results from numerical solutions of time dependent Schrödinger equations for aligned {{{H}}}2+ show that molecular frame photoelectron angular distributions (MFPADs) exhibit signatures of asymmetry perpendicular to the molecular symmetry axis, arising from interference of coherent electron wave packets created by respectively one {ω }2 and two-photon 2{ω }1 absorption. A resonant excitation process between the ground 1s{σ }{{g}} state and the excited 2p{π }{{u}} state is triggered by the {ω }1 pulse. The asymmetry of MFPADs varies periodically with pulse intensity I 0 and duration T, which we attribute to coherent resonant Rabi oscillations in electronic state population. A perturbative model is adopted to qualitatively describe and analyze these effects in both resonant and nonresonant photoionization processes.

  16. Magnitude of long-term non-lithostatic pressure variations in lithospheric processes: insight from thermo-mechanical subduction/collision models

    NASA Astrophysics Data System (ADS)

    Gerya, Taras

    2014-05-01

    On the one hand, the principle of lithostatic pressure is habitually used in metamorphic geology to calculate paleo-depths of metamorphism from mineralogical pressure estimates given by geobarometry. On the other hand, it is obvious that this lithostatic (hydrostatic) pressure principle should only be valid for an ideal case of negligible deviatoric stresses during the long-term development of the entire tectono-metamorphic system - the situation, which newer comes to existence in natural lithospheric processes. The question is therefore not "Do non-lithostatic pressure variations exist?" but " What is the magnitude of long-term non-lithostatic pressure variations in various lithospheric processes, which can be recorded by mineral equilibria of respective metamorphic rocks?". The later question is, in particular, relevant for various types of high-pressure (HP) and ultrahigh-pressure (UHP) rocks, which are often produced in convergent plate boundary settings (e.g., Hacker and Gerya, 2013). This question, can, in particular, be answered with the use of thermo-mechanical models of subduction/collision processes employing realistic P-T-stress-dependent visco-elasto-brittle/plastic rheology of rocks. These models suggest that magnitudes of pressure deviations from lithostatic values can range >50% underpressure to >100% overpressure, mainly in the regions of bending of rheologically strong mantle lithosphere (Burg and Gerya, 2005; Li et al., 2010). In particular, strong undepresures along normal faults forming within outer rise regions of subducting plates can be responsible for downward water suction and deep hydration of oceanic slabs (Faccenda et al., 2009). Weaker HP and UHP rocks of subduction/collision channels are typically subjected to lesser non-lithostatic pressure variations with characteristic magnitudes ranging within 10-20% from the lithostatic values (Burg and Gerya, 2005; Li et al., 2010). The strength of subducted crustal rocks and the degree of confinement of the subduction/collision channel are the key factors controlling this magnitude (Burg and Gerya, 2005; Li et al., 2010). High-temperature (>700 C) UHP rocks formed by continental crust subduction typically demonstrate negligible non-lithostatic pressure variations at peak metamorphic conditions, although these variations can be larger at the prograde stage (Gerya et al., 2008; Li et al., 2010). However, the variability of tectonic mechanisms by which UHP rocks can form (e.g., Sizova et al., 2012; Hacker and Gerya, 2013) precludes generalization of this result for all types of UHP-complexes. References Burg, J.-P., Gerya, T.V. (2005) Viscous heating and thermal doming in orogenic metamorphism: numerical modeling and geological implications. J. Metamorph. Geol., 23, 75-95. Faccenda, M., Gerya, T.V., Burlini, L. (2009) Deep slab hydration induced by bending related variations in tectonic pressure. Nature Geoscience, 2, 790-793. Gerya T.V., Perchuk, L.L., Burg J.-P. (2008) Transient hot channels: perpetrating and regurgitating ultrahigh-pressure, high temperature crust-mantle associations in collision belts. Lithos, 103, 236-256. Hacker, B., Gerya, T.V. (2013) Paradigms, new and old, for ultrahigh-pressure tectonism. Tectonophysics, 603, 79-88. Li, Z., Gerya, T.V., Burg, J.P. (2010) Influence of tectonic overpressure on P-T paths of HP-UHP rocks in continental collision zones: Thermomechanical modelling. J. Metamorphic Geol., 28, 227-247. Sizova, E., Gerya, T., Brown M. (2012) Exhumation mechanisms of melt-bearing ultrahigh pressure crustal rocks during collision of spontaneously moving plates. Journal of Metamorphic Geology, 30, 927-955.

  17. Belowground Carbon Cycling Processes at the Molecular Scale: An EMSL Science Theme Advisory Panel Workshop

    SciTech Connect

    Hess, Nancy J.; Brown, Gordon E.; Plata, Charity

    2014-02-21

    As part of the Belowground Carbon Cycling Processes at the Molecular Scale workshop, an EMSL Science Theme Advisory Panel meeting held in February 2013, attendees discussed critical biogeochemical processes that regulate carbon cycling in soil. The meeting attendees determined that as a national scientific user facility, EMSL can provide the tools and expertise needed to elucidate the molecular foundation that underlies mechanistic descriptions of biogeochemical processes that control carbon allocation and fluxes at the terrestrial/atmospheric interface in landscape and regional climate models. Consequently, the workshop's goal was to identify the science gaps that hinder either development of mechanistic description of critical processes or their accurate representation in climate models. In part, this report offers recommendations for future EMSL activities in this research area. The workshop was co-chaired by Dr. Nancy Hess (EMSL) and Dr. Gordon Brown (Stanford University).

  18. MOLECULAR-LEVEL PROCESS GOVERNING THE INTERACTION OF CONTAMINANTS WITH IRON AND MANGANESE OXIDES

    EPA Science Inventory

    Many of the inorganic and organic contaminants present in sediments at DOE sites can bealtered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on stru...

  19. Reversible Simulations of Elastic Collisions

    SciTech Connect

    Perumalla, Kalyan S; Protopopescu, Vladimir A

    2013-01-01

    Consider a system of N identical hard spherical particles moving in a d-dimensional box and undergoing elastic, possibly multi-particle, collisions. We develop a new algorithm that recovers the pre-collision state from the post-collision state of the system, across a series of consecutive collisions, \\textit{with essentially no memory overhead}. The challenge in achieving reversibility for an n-particle collision (where, in general, n<< N) arises from the presence of nd-d-1 degrees of freedom (arbitrary angles) during each collision, as well as from the complex geometrical constraints placed on the colliding particles. To reverse the collisions in a traditional simulation setting, all of the particular realizations of these degrees of freedom (angles) during the forward simulation must be tracked. This requires memory proportional to the number of collisions, which grows very fast with N and d, thereby severely limiting the \\textit{de facto} applicability of the scheme. This limitation is addressed here by first performing a pseudo-randomization of angles, which ensures determinism in the reverse path for any values of n and d. To address the more difficult problem of geometrical and dynamic constraints, a new approach is developed which correctly samples the constrained phase space. Upon combining the pseudo-randomization with correct phase space sampling, perfect reversibility of collisions is achieved, as illustrated for n<=3, d=2, and n=2, d=3. This result enables, for the first time, reversible simulations of elastic collisions with essentially zero memory accumulation. In principle, the approach presented here could be generalized to larger values of n, which would be of definite interest for molecular dynamics simulations at high densities.

  20. A study of quark energy loss via Drell-Yan process in p+A collisions at Fermilab

    NASA Astrophysics Data System (ADS)

    Liu, Kun; E906/SeaQuest Collaboration

    2013-10-01

    E906/SeaQuest is a new fixed-target experiment being operated at Fermi National Accelerator Laboratory. Using the 120 GeV proton beam from the main injector, E906/SeaQuest measures the Drell-Yan productions in the dimuon mass range 4-8 GeV in p+p and p+A collisions over a wide xF range, with A = D, C, Fe, W. These new measurements will help us to clarify the nature of parton energy loss mechanisms in nuclear medium. Parton energy loss in QGP is considered the dominant contributor to the observed jet quenching phenomena at RHIC and LHC. Since the center of mass energy of p+A collisions at E906/SeaQuest is low and out of the nuclear shadowing region, the measurements will provide the clean determination of parton energy loss effect in cold nuclear medium. E906/SeaQuest conducted a short commissioning run in 2012 and will resume data taking in September 2013. I will present the current status and the prospect of the parton energy loss measurements with the E906/SeaQuest experiment at Fermilab.

  1. Late Paleozoic subduction and collision processes during the amalgamation of the Central Asian Orogenic Belt along the South Tianshan suture zone

    NASA Astrophysics Data System (ADS)

    Han, Yigui; Zhao, Guochun; Sun, Min; Eizenhöfer, Paul R.; Hou, Wenzhu; Zhang, Xiaoran; Liu, Qian; Wang, Bo; Liu, Dongxing; Xu, Bing

    2016-03-01

    The provenance of late Paleozoic siliciclastic sedimentary strata on the northern margin of the Tarim Craton and the South Tianshan Orogenic Belt provides important insights into subduction and collision processes during the formation of the southern Central Asian Orogenic Belt. Detrital zircons from Carboniferous and Permian sedimentary rocks in the South Tianshan belt show two predominant age populations of 500-400 and 305-270 Ma, and three subordinate clusters around ~ 2.5 Ga, 2.0-1.7 Ga, and 1.2-0.6 Ma. Such age patterns are similar to major magmatic episodes in the Tarim Craton but are distinct from those in the Central Tianshan-Yili Block, implying that the Carboniferous-Permian strata in the South Tianshan belt were deposited on the northern margin of the Tarim Craton. These data, in combination with Carboniferous passive margin deposition along the South Tianshan and northern Tarim regions and intense arc magmatism in the Central Tianshan area, support the northward subduction of the South Tianshan oceanic crust. The abrupt decrease of zircon εHf(t) values at ~ 310 Ma indicates the tectonic transformation from oceanic subduction to continental collision. However, syn- and post-collisional sediments in the South Tianshan and northern Tarim regions did not contain detritus from the Central Tianshan-Yili Block, as evidenced by the absence/paucity of 380-310 Ma detrital zircons in the late Paleozoic strata and by the stratigraphic record in the regions. Insignificant surface erosion and uplifting during the collision and (ultra-)high-pressure rock exhumation require divergence in the frontal wedge. We propose that the switch from a convergent to a divergent regime was triggered by the arrival of the Tarim mantle plume in the latest Carboniferous, which possibly had profound effects on regional sedimentation and exhumation of (ultra-)high-pressure rocks in the orogenic belt.

  2. Smallest artificial molecular neural-net for collective and emergent information processing

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Anirban; Sahu, Satyajit; Fujita, Daisuke

    2009-09-01

    While exploring the random diffusion of 2 bit molecular switches (we define as molecular neuron) on an atomic flat Au (111) substrate, we have found that at least four molecules are required to construct a functional neural net. Surface electron density wave enables communication of one to many molecules at a time—a prerequisite for the parallel processing. Here we have shown that in a neural net of several molecules, some of them could dynamically store information as memory and consistently replicate the fundamental relationship that is found only in a collective and emergent computing system like our brain.

  3. Molecular motors that digest their track to rectify Brownian motion: processive movement of exonuclease enzymes

    NASA Astrophysics Data System (ADS)

    Xie, Ping

    2009-09-01

    A general model is presented for the processive movement of molecular motors such as λ-exonuclease, RecJ and exonuclease I that use digestion of a DNA track to rectify Brownian motion along this track. Using this model, the translocation dynamics of these molecular motors is studied. The sequence-dependent pausing of λ-exonuclease, which results from a site-specific high affinity DNA interaction, is also studied. The theoretical results are consistent with available experimental data. Moreover, the model is used to predict the lifetime distribution and force dependence of these paused states.

  4. In-silico design of computational nucleic acids for molecular information processing.

    PubMed

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  5. In-silico design of computational nucleic acids for molecular information processing

    PubMed Central

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  6. Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations.

    PubMed

    Rode, Michał F; Jankowska, Joanna; Sobolewski, Andrzej L

    2016-04-01

    In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other. PMID:27059566

  7. Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

    NASA Astrophysics Data System (ADS)

    Rode, Michał F.; Jankowska, Joanna; Sobolewski, Andrzej L.

    2016-04-01

    In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

  8. Process evaluation of an open architecture real-time molecular laboratory platform.

    PubMed

    Felder, Robin A; Jackson, Keith D; Walter, Adam M

    2014-10-01

    The needs of molecular diagnostic laboratories that perform both Food and Drug Administration-cleared as well as laboratory-developed tests are usually not met on a single analytical platform. Furthermore, little information is available about the direct impact of molecular automation on labor costs and efficiency in clinical laboratories. We performed a process impact analysis from time and motion studies of a novel molecular diagnostic robotic system designed to automate sample preparation, extraction, and analysis. All 27 preanalytical tasks were quantified for the amount of time spent preparing 24 specimens for analysis. These steps were completed in 899 s (14 min, 59 s) followed by 7887 s (131 min, 27 s) of instrument operation independent of operator control (walk-away time). Postanalytical results evaluation required 1 min per specimen. The instrument automatically extracted the nucleic acid from the specimen, added the eluted DNA to the amplification reagents, and performed the analysis. Only 12% of the total instrument operations required relatively unskilled human labor. Thus, the availability of automated molecular diagnostic instruments will facilitate the expansion of molecular testing in the clinical laboratory because they reduce operator costs with respect to time and complexity of the tasks they are asked to perform. PMID:24811476

  9. Molecular control of electron and hole transfer processes: Theory and applications

    SciTech Connect

    Newton, M.D.; Cave, R.J.

    1996-02-01

    Recent decades have seen remarkable advances in microscopic understanding of electron transfer (ET) processes in widely ranging contexts, including solid-state, liquid solution, and complex biological assemblies. The primary goal of this chapter is to report recent advances in the modeling, calculation, and analysis of electronic coupling in complex molecular aggregates, thereby allowing an assessment of current progress toward the goal of molecular-level control and design. The control of electron transfer kinetics (i.e., enhancing desired processes, while inhibiting others) involves, of course, system energetics (especially activation and reorganization energies) as well as electronic coupling, which is most directly relevant only after the system has reached the appropriate point (or region) along the reaction coordinate. Nevertheless, to focus the discussion in this chapter, the authors will consider such energetics, and the associated molecular and solvent coordinates which control then, only to the extent that they bear on the analysis of the electronic coupling. In the following sections they first discuss the formulation of basic ET models, including the definition of initial and final states, the role of orbitals and 1-particle models in a many-electron context, the utility of various effective Hamiltonians, and the role of vibronic as well as purely electronic effects. With these theoretical tools in hand, they then examine very recent applications to complex molecular systems using the techniques of computational quantum chemistry, followed by detailed analysis of the numerical results. They then conclude with some comments regarding the current ``state of the art`` and remaining challenges.

  10. Molecular Basis of a Million-Fold Affinity Maturation Process in a Protein-Protein Interaction

    SciTech Connect

    D Bonsor; S Postel; B Pierce; N Wang; P Zhu; R Buonpane; Z Weng; D Kranz; E Sundberg

    2011-12-31

    Protein engineering is becoming increasingly important for pharmaceutical applications where controlling the specificity and affinity of engineered proteins is required to create targeted protein therapeutics. Affinity increases of several thousand-fold are now routine for a variety of protein engineering approaches, and the structural and energetic bases of affinity maturation have been investigated in a number of such cases. Previously, a 3-million-fold affinity maturation process was achieved in a protein-protein interaction composed of a variant T-cell receptor fragment and a bacterial superantigen. Here, we present the molecular basis of this affinity increase. Using X-ray crystallography, shotgun reversion/replacement scanning mutagenesis, and computational analysis, we describe, in molecular detail, a process by which extrainterfacial regions of a protein complex can be rationally manipulated to significantly improve protein engineering outcomes.

  11. Effect of vacuum processing on outgassing within an orbiting molecular shield

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.

    1982-01-01

    The limiting hydrogen number density in an orbiting molecular shield is highly dependent on the outgassing rates from the materials of construction for the shield, experimental apparatus, and other hardware contained within the shield. Ordinary degassing temperatures used for ultrahigh vacuum studies (less than 450 C) are not sufficient to process metals so that the contribution to the number density within the shield due to outgassing is less than the theoretically attainable level (approximately 200 per cu. cm). Pure aluminum and type 347 stainless steel were studied as candidate shield materials. Measurements of their hydrogen concentration and diffusion coefficients were made, and the effects of high temperature vacuum processing (greater than 600 C) on their resulting outgassing rates was determined. The densities in a molecular shield due to the outgassing from either metal were substantially less ( 0.003) than the density due to the ambient atomic hydrogen flux at an orbital altitude of 500 km.

  12. Direct pulse technique for spontaneous polarization dynamics and molecular reorientation processes in ferroelectric liquid crystals

    NASA Astrophysics Data System (ADS)

    Bawa, S. S.; Biradar, A. M.; Saxena, K.; Chandra, Subhas

    1988-09-01

    A method has been devised for studying the spontaneous polarization, dynamics of polarization reversal, and the molecular reorientation processes that occur in the bulk and surfaces of ferroelectric liquid crystals. These studies have been carried out by analyzing the current response to triangular- and square-wave forms. The current response to a triangular wave yields the spontaneous polarization by conveniently subtracting the background contribution due to the conductive and capacitive currents. Molecular reorientation processes which take place within the bulk and the boundary surface layer can be studied by the appearance of polarization current peaks on the triangular-wave response. The dynamics of polarization reversal between bistable states and of the polarization change between the zero-field relaxed state and either of the saturation remanent polarization states have been studied by applying ``symmetric'' and ``asymmetric'' square waves. The technique can also be successfully applied to solid ferroelectrics for studying the spontaneous polarization and the domain dynamics during switching.

  13. Ultrasmall volume molecular isothermal amplification in microfluidic chip with advanced surface processing

    NASA Astrophysics Data System (ADS)

    Huang, Guoliang; Ma, Li; Yang, Xiaoyong; Yang, Xu

    2011-01-01

    In this paper, we developed a metal micro-fluidic chip with advanced surface processing for ultra-small volume molecular isothermal amplification. This method takes advantages of the nucleic acid amplification with good stability and consistency, high sensitivity about 31 genomic DNA copies and bacteria specific gene identification. Based on the advanced surface processing, the bioreaction assays of nucleic acid amplification was dropped about 392nl in volume. A high numerical aperture confocal optical detection system was advanced to sensitively monitor the DNA amplification with low noise and high power collecting fluorescence near to the optical diffraction limit. A speedy nucleic acid isothermal amplification was performed in the ultra-small volume microfluidic chip, where the time at the inflexions of second derivative to DNA exponential amplified curves was brought forward and the sensitivity was improved about 65 folds to that of in current 25?l Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  14. Formation, molecular structure, and morphology of humins in biomass conversion: influence of feedstock and processing conditions.

    PubMed

    van Zandvoort, Ilona; Wang, Yuehu; Rasrendra, Carolus B; van Eck, Ernst R H; Bruijnincx, Pieter C A; Heeres, Hero J; Weckhuysen, Bert M

    2013-09-01

    Neither the routes through which humin byproducts are formed, nor their molecular structure have yet been unequivocally established. A better understanding of the formation and physicochemical properties of humins, however, would aid in making biomass conversion processes more efficient. Here, an extensive multiple-technique-based study of the formation, molecular structure, and morphology of humins is presented as a function of sugar feed, the presence of additives (e.g., 1,2,4-trihydroxybenzene), and the applied processing conditions. Elemental analyses indicate that humins are formed through a dehydration pathway, with humin formation and levulinic acid yields strongly depending on the processing parameters. The addition of implied intermediates to the feedstocks showed that furan and phenol compounds formed during the acid-catalyzed dehydration of sugars are indeed included in the humin structure. IR spectra, sheared sum projections of solid-state 2DPASS (13) C NMR spectra, and pyrolysis GC-MS data indicate that humins consist of a furan-rich polymer network containing different oxygen functional groups. The structure is furthermore found to strongly depend on the type of feedstock. A model for the molecular structure of humins is proposed based on the data presented. PMID:23836679

  15. Molecular disassembly of rice and lotus starches during thermal processing and its effect on starch digestibility.

    PubMed

    Wang, Shujun; Sun, Yue; Wang, Jinrong; Wang, Shuo; Copeland, Les

    2016-02-17

    The molecular disassembly of starch during thermal processing is a major determinant for the susceptibility of starch to enzymatic digestion. In the present study, the effects of thermal processing on the disassembly of the granular structure and the in vitro enzymatic digestibility of rice and lotus starches were investigated. After heating at 50 °C, rice and lotus starches did not show significant changes in granular morphology, long-range crystallinity and short-range molecular order. As the temperature increased to 60 °C, rice starch underwent a partial gelatinization followed by an incomplete disruption of granular morphology, crystallites and molecular order. In contrast, lotus starch was almost completely gelatinized at 60 °C. At 70 °C or higher, both starches were fully gelatinized with complete disruption of the micro and macro structures. Our results show that gelatinization greatly increased the in vitro enzymatic digestibility of both starches, but that the degree of disassembly of the starch structure during thermal processing was not a major determinant of the digestibility of gelatinized starch. PMID:26829664

  16. Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report

    SciTech Connect

    Brown Jr., G. E.; Chambers, S. A.

    1999-10-31

    Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals.

  17. Utilization of efficient gradient and Hessian computations in the force field optimization process of molecular simulations

    NASA Astrophysics Data System (ADS)

    Hülsmann, Marco; Kopp, Sonja; Huber, Markus; Reith, Dirk

    2013-01-01

    Computer simulations of chemical systems, especially systems of condensed matter, are highly important for both scientific and industrial applications. Thereby, molecular interactions are modeled on a microscopic level in order to study their impact on macroscopic phenomena. To be capable of predicting physical properties quantitatively, accurate molecular models are indispensable. Molecular interactions are described mathematically by force fields, which have to be parameterized. Recently, an automated gradient-based optimization procedure was published by the authors based on the minimization of a loss function between simulated and experimental physical properties. The applicability of gradient-based procedures is not trivial at all because of two reasons: firstly, simulation data are affected by statistical noise, and secondly, the molecular simulations required for the loss function evaluations are extremely time-consuming. Within the optimization process, gradients and Hessians were approximated by finite differences so that additional simulations for the respective modified parameter sets were required. Hence, a more efficient approach to computing gradients and Hessians is presented in this work. The method developed here is based on directional instead of partial derivatives. It is compared with the classical computations with respect to computation time. Firstly, molecular simulations are replaced by fit functions that define a functional dependence between specific physical observables and force field parameters. The goal of these simulated simulations is to assess the new methodology without much computational effort. Secondly, it is applied to real molecular simulations of the three chemical substances phosgene, methanol and ethylene oxide. It is shown that up to 75% of the simulations can be avoided using the new algorithm.

  18. Inelastic processes in ion/surface collisions: Direct recoil ion fractions as a function of kinetic energy

    NASA Astrophysics Data System (ADS)

    Rabalais, J. Wayne; Chen, Jie-Nan

    1986-09-01

    Time-of-flight (TOF) spectra of the scattered and recoiled particles resulting from 1-10 keV Ar+ ions impingent on surfaces of MgO, Mg(OH)2, graphite, Si, and SiO2 have been obtained. Measurements of directly recoiled (DR) neutrals plus ions and neutrals only are used to calculate positive and negative ion fractions Y+,- from DR events. These positive and negative ion yields observed for DR of H, C, O, and Si have distinctly different behavior as a function of ion kinetic energy. The Y+ values exhibit a ``threshold-type'' behavior with a steep rise followed by a slowly rising or plateau region at higher energy. The Y- values exhibit a maximum in the low energy region followed by a decreasing yield as energy increases. The Y-/Y+ ratio for C and O is very sensitive to the amount of hydrogen present, with the Y+ yields dropping as hydrogen concentration increases. The recently developed model for electronic transitions in keV ion/surface collisions which considers Auger and resonant transitions along the ion trajectory and electron promotions in the quasidiatomic molecule of the close atomic encounter is extended to include DR events. Analytical expressions for Y+,- are derived for the case of surface atoms in positive, neutral, and negative bonding environments. These model expressions are fitted to the experimental data, allowing determination of the probabilities of ionization in the close atomic encounter and of electron capture along the outgoing trajectory.

  19. Stochastic processes, galactic star formation, and chemical evolution. Effects of accretion, stripping, and collisions in multiphase multi-zone models

    NASA Astrophysics Data System (ADS)

    Valle, G.; Shore, S. N.; Galli, D.

    2005-05-01

    This paper reports simulations allowing for stochastic accretion and mass loss within closed and open systems modeled using a previously developed multi-population, multi-zone (halo, thick disk, thin disk) treatment. The star formation rate is computed as a function of time directly from the model equations and all chemical evolution is followed without instantaneous recycling. Several types of simulations are presented here: (1) a closed system with bursty mass loss from the halo to the thick disk, and from the thick to the thin disk, in separate events to the thin disk; (2) open systems with random environmental (extragalactic) accretion, e.g. by infall of high velocity clouds directly to the thin disk; (3) schematic open system single and multiple collision events and intracluster stripping. For the open models, the mass of the Galaxy has been explicitly tracked with time. We present the evolution of the star formation rate, metallicity histories, and concentrate on the light elements. We find a wide range of possible outcomes, including an explanation for variations in the Galactic D/H ratio, and highlight the problems for uniquely reconstructing star forming histories from contemporary abundance measurements.

  20. Magnetic field-dependent molecular and chemical processes in biochemistry, genetics and medicine

    NASA Astrophysics Data System (ADS)

    Buchachenko, A. L.

    2014-01-01

    The molecular concept (paradigm) in magnetobiology seems to be most substantiated and significant for explaining the biomedical effects of electromagnetic fields, for the new medical technology of transcranial magnetic stimulation of cognitive activity, for the nuclear magnetic control of biochemical processes and for the search of new magnetic effects in biology and medicine. The key structural element of the concept is a radical ion pair as the receiver of magnetic fields and the source of magnetic effects. The existence of such pairs was recently detected in the two life-supporting processes of paramount importance — in enzymatic ATP and DNA syntheses. The bibliography includes 80 references.

  1. Atomic-orbital expansion model for describing ion-atom collisions at intermediate and low energies

    SciTech Connect

    Lin, C.D.; Fritsch, W.

    1983-01-01

    In the description of inelastic processes in ion-atom collisions at moderate energies, the semiclassical close-coupling method is well established as the standard method. Ever since the pioneering work on H/sup +/ + H in the early 60's, the standard procedure is to expand the electronic wavefunction in terms of molecular orbitals (MO) or atomic orbitals (AO) for describing collisions at, respectively, low or intermediate velocities. It has been recognized since early days that traveling orbitals are needed in the expansions in order to represent the asymptotic states in the collisions correctly. While the adoption of such traveling orbitals presents no conceptual difficulties for expansions using atomic orbitals, the situation for molecular orbitals is less clear. In recent years, various forms of traveling MO's have been proposed, but conflicting results for several well-studied systems have been reported.

  2. Molecularly mediated processing and assembly of nanoparticles: exploring the interparticle interactions and structures.

    PubMed

    Lim, Stephanie I; Zhong, Chuan-Jian

    2009-06-16

    The harnessing of the nanoscale properties of nanoparticles in most technological applications requires the abilities of controlled processing and assembly, which has been an important challenge because of the difficulty in manipulating interparticle properties. Molecularly mediated processing and assembly of nanoparticles have emerged as an important strategy for addressing this challenge. The capability of this strategy in manipulating size, shape, composition, and interparticle properties has significant implications for designing sensing, biosensing, nanoprobing, and many other functional nanostructures. This Account highlights some of the important findings in investigating both interparticle and collective properties as a forum for discussing new opportunities in exploiting nanoparticle-based designs and applications. The concept of mediator-template assembly of nanoparticles explores the combination of the forces from a mediator and a templating molecule for designing and controlling the interparticle interactions. The manipulation of the interparticle interaction properties and the detection of the molecular signatures are two of the key elements in this concept. A series of well-defined molecular mediators ranging from inorganic, organic, supramolecular, to biological molecules have been explored to ascertain how these two elements can be achieved in nanoparticle assemblies. The emphasis is the fundamental understanding of interparticle molecular interactions, such as covalent, electrostatic, hydrogen bonding, multidentate coordination, pi-pi interactions, etc. Each of these molecular interactions has been examined using specific molecules, such as multifunctional ligands, tunable sizes, shapes, or charges, well-defined molecular rigidity and chirality, or spectroscopic signatures, such as fluorescence and Raman scattering. Examples included thiols, thioethers, carboxylic acids, fullerenes, dyes, homocysteines, cysteines, glutathiones, proteins, and DNAs as molecular mediators for the assembly of gold, alloy, and magnetic nanoparticles. The understanding of these systems provided insights into how the unique electrical, optical, magnetic, and spectroscopic properties of the nanoparticle assemblies can be exploited for potential applications. This Account also highlights a few examples in chemical sensing and bioprobing to illustrate the importance of interparticle interactions and structures in exploiting these properties. One example involves thin-film assemblies of metal nanoparticles as biomimetic ion channels or chemiresistor sensing arrays by exploiting the nanostructured ligand framework interactions. Other examples explore the surface-enhanced Raman scattering signature as nanoprobes for the detection of protein binding or the enzyme-based cutting of interparticle DNAs. The detailed understanding of the design and control parameters in these and other systems should have a profound impact on the exploration of nanoparticles in a wide range of technological applications. PMID:19378982

  3. Studies on Deformation Mechanism and Punch Taper Effects on Nanoimprint Processes by Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Hsu, Quang-Cherng; Wu, Chen-Da; Fang, Te-Hua

    2004-06-01

    A molecular dynamics analysis model is proposed to study the effects of parameters on nanoimprint process, for example: taper angle, imprint depth and spring back. The nanoimprint process comprises one punch and one specimen at an isothermal state of 400K, while the deformed material is a copper FCC single crystal and the punch material is a nickel FCC single crystal. There were a total of 10,080 atoms in copper measuring 12.02 nm × 5.72 nm in length and height, respectively. There were a total of 4,200 atoms in nickel where the typical length and depth in punch tooth are 6.24 nm × 3.52 nm, respectively. Computer simulation codes based on Hamiltonian dynamics, periodical boundary conditions and Morse potential function were used to simulate the nanoimprint processes. By varying the punch taper angle and the imprinting depth, useful information for nanoimprint process has been obtained.

  4. Deformation Mechanism and Punch Taper Effects on Nanoimprint Process by Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Hsu, Quang-Cherng; Wu, Chen-Da; Fang, Te-Hua

    2004-11-01

    A molecular dynamics analysis model is proposed to study the effects of parameters on the nanoimprint process, for example, taper angle, imprint depth and spring back. The nanoimprint process comprises one punch and one specimen at an isothermal state of 400 K, while the deformed material is a copper fcc single crystal and the punch material is a nickel fcc single crystal. There were a total of 10,080 atoms in copper measuring 12.02 nm and 5.72 nm in length and height, respectively. There were a total of 4,200 atoms in nickel with a typical length and depth in a punch tooth of 6.24 nm and 3.52 nm, respectively. Computer simulation codes based on Hamiltonian dynamics, periodical boundary conditions and the Morse potential function were used to simulate the nanoimprint process. By varying the punch taper angle and the imprint depth, useful information about the nanoimprint process was obtained.

  5. Continental collisions and seismic signature

    NASA Astrophysics Data System (ADS)

    Meissner, R.; Wever, Th.; Sadowiak, P.

    1991-04-01

    Reflection seismics in compressional belts has revealed the structure of crustal shortening and thickening processes, showing complex patterns of indentation and interfingering of colliding crusts and subcrustal lithospheres. Generally, in the upper crust large zones of detachments develop, often showing duplexes and 'crocodile' structures. The lower crust from zones of active collision (e.g. Alps, Pyrenees) is characterized by strongly dipping reflections. The base of the crust with the Moho must be continuously equilibrating after orogenic collapse as areas of former continental collision exhibit flat Mohos and subhorizontal reflections. The depth to the Moho increases during collision and decreases after the onset of post-orogenic extension, until finally the crustal root disappears completely together with the erosion of the mountains. Processes, active during continental collisions and orogenic collapse, create distinct structures which are imaged by reflection seismic profiling. Examples are shown and discussed.

  6. Comparative studies of ion-pair formation and resonant quenching processes in collisions of Rydberg atoms with the alkaline-earth atoms

    NASA Astrophysics Data System (ADS)

    Narits, A. A.; Mironchuk, E. S.; Lebedev, V. S.

    2014-01-01

    We report the results of comparative studies of ion-pair formation and quenching processes in collisions of Rydberg Li(nl) and Cs(nl) atoms with Ca(4s2), Sr(5s2) and Ba(6s2) atoms possessing small electron affinities. Our consideration includes both the cases of selectively excited Rydberg nl-states with small orbital angular momentum (l ≪ n) and nearly circular states with l ˜ n - 1. Calculations of the electron-transfer processes are based on the semiclassical theory of nonadiabatic transitions and exact expression for the Rydberg-covalent-ionic coupling terms. Calculations of nonresonant quenching processes are carried out within the framework of the available theory of inelastic and quasielastic transitions between Rydberg-covalent states. The ion-pair formation and resonant quenching cross sections are shown to be significantly dependent not only on the principal quantum number n but also on the orbital angular momentum l and the binding energy of the alkaline-earth anion. For each system under study we find the regions of n in which either the resonant quenching or the ion-pair formation processes are predominant. The relative role of the resonant and nonresonant mechanisms of depopulation of Rydberg states is investigated.

  7. Molecular and neural mechanisms of sex pheromone reception and processing in the silkmoth Bombyx mori.

    PubMed

    Sakurai, Takeshi; Namiki, Shigehiro; Kanzaki, Ryohei

    2014-01-01

    Male moths locate their mates using species-specific sex pheromones emitted by conspecific females. One striking feature of sex pheromone recognition in males is the high degree of specificity and sensitivity at all levels, from the primary sensory processes to behavior. The silkmoth Bombyx mori is an excellent model insect in which to decipher the underlying mechanisms of sex pheromone recognition due to its simple sex pheromone communication system, where a single pheromone component, bombykol, elicits the full sexual behavior of male moths. Various technical advancements that cover all levels of analysis from molecular to behavioral also allow the systematic analysis of pheromone recognition mechanisms. Sex pheromone signals are detected by pheromone receptors expressed in olfactory receptor neurons in the pheromone-sensitive sensilla trichodea on male antennae. The signals are transmitted to the first olfactory processing center, the antennal lobe (AL), and then are processed further in the higher centers (mushroom body and lateral protocerebrum) to elicit orientation behavior toward females. In recent years, significant progress has been made elucidating the molecular mechanisms underlying the detection of sex pheromones. In addition, extensive studies of the AL and higher centers have provided insights into the neural basis of pheromone processing in the silkmoth brain. This review describes these latest advances, and discusses what these advances have revealed about the mechanisms underlying the specific and sensitive recognition of sex pheromones in the silkmoth. PMID:24744736

  8. Molecular and neural mechanisms of sex pheromone reception and processing in the silkmoth Bombyx mori

    PubMed Central

    Sakurai, Takeshi; Namiki, Shigehiro; Kanzaki, Ryohei

    2014-01-01

    Male moths locate their mates using species-specific sex pheromones emitted by conspecific females. One striking feature of sex pheromone recognition in males is the high degree of specificity and sensitivity at all levels, from the primary sensory processes to behavior. The silkmoth Bombyx mori is an excellent model insect in which to decipher the underlying mechanisms of sex pheromone recognition due to its simple sex pheromone communication system, where a single pheromone component, bombykol, elicits the full sexual behavior of male moths. Various technical advancements that cover all levels of analysis from molecular to behavioral also allow the systematic analysis of pheromone recognition mechanisms. Sex pheromone signals are detected by pheromone receptors expressed in olfactory receptor neurons in the pheromone-sensitive sensilla trichodea on male antennae. The signals are transmitted to the first olfactory processing center, the antennal lobe (AL), and then are processed further in the higher centers (mushroom body and lateral protocerebrum) to elicit orientation behavior toward females. In recent years, significant progress has been made elucidating the molecular mechanisms underlying the detection of sex pheromones. In addition, extensive studies of the AL and higher centers have provided insights into the neural basis of pheromone processing in the silkmoth brain. This review describes these latest advances, and discusses what these advances have revealed about the mechanisms underlying the specific and sensitive recognition of sex pheromones in the silkmoth. PMID:24744736

  9. Identification of mycobacteria in peat moss processing plants: application of molecular biology approaches.

    PubMed

    Cayer, Marie-Pierre; Veillette, Marc; Pageau, Pascal; Hamelin, Richard; Bergeron, Marie-Josée; Mériaux, Anne; Cormier, Yvon; Duchaine, Caroline

    2007-01-01

    Peat moss processing plant workers are exposed to high concentrations of bioaerosols. Although mycobacteria have been cultured from peat moss, no study has examined the workers' exposure to mycobacterial bioaerosols. We evaluated the presence of mycobacteria in air samples from peat moss processing plants using molecular biology approaches (cloning-sequencing and polymerase chain reaction (PCR)) and the workers exposure using immunoglobulin G (IgG) complexes to mycobacteria. In addition, species detected in air samples and in peat moss were compared. Two peat moss processing plants were chosen among 14 previously studied. A total of 49 clones were sequenced. Real-time PCR was also performed on the same air samples to evaluate the airborne concentration of mycobacteria and estimate exposure levels. Several Mycobacterium species were present in the air samples (M. malmoense, M. smegmatis, M. graceum, M. bohemicum, and M. interjectum). Mycobacterium avium was recovered by culture in peat moss but not in the air using the molecular approach. Total airborne Mycobacterium concentration was estimated at 8.2 x 10(8)/m3. Workers had IgG against the mycobacterial mix and M. avium, suggesting significant exposure. The findings from air samples, supported by IgG measurements, demonstrate that peat moss processing plant workers are exposed to mycobacteria in addition to other biological agents. PMID:17496954

  10. Molecular processes leading to aberrant androgen receptor signaling and castration resistance in prostate cancer

    PubMed Central

    Hu, Rong; Denmeade, Samuel R; Luo, Jun

    2011-01-01

    Hormone therapies targeting androgen receptor signaling are the mainstay of treatment for patients with advanced prostate cancer. The length of clinical remission induced by hormone therapies varies substantially among treated patients. Why some patients progress rapidly after treatment while others benefit with prolonged remission is a question that remains unsolved. The androgen receptor signaling pathway is the key molecular determinant of castration resistance, and a key target for prostate cancer drug design. Recent advances in characterizing molecular processes leading to the development of castration-resistant prostate cancer, including the discovery of multiple androgen receptor splicing variants, offer opportunities for rational development of new clinical tools or approaches to predict, monitor or control/prevent prostate cancer progression in the castrate setting. PMID:21318111

  11. Molecular Studies on the Ecology of Listeria monocytogenes in the Smoked Fish Processing Industry

    PubMed Central

    Norton, Dawn M.; McCamey, Meghan A.; Gall, Kenneth L.; Scarlett, Janet M.; Boor, Kathryn J.; Wiedmann, Martin

    2001-01-01

    We have applied molecular approaches, including PCR-based detection strategies and DNA fingerprinting methods, to study the ecology of Listeria monocytogenes in food processing environments. A total of 531 samples, including raw fish, fish during the cold-smoking process, finished product, and environmental samples, were collected from three smoked fish processing facilities during five visits to each facility. A total of 95 (17.9%) of the samples tested positive for L. monocytogenes using a commercial PCR system (BAX for Screening/Listeria monocytogenes), including 57 (27.7%) environmental samples (n = 206), 8 (7.8%) raw material samples (n = 102), 23 (18.1%) samples from fish in various stages of processing(n = 127), and 7 (7.3%) finished product samples (n = 96). L. monocytogenes was isolated from 85 samples (16.0%) using culture methods. Used in conjunction with a 48-h enrichment in Listeria Enrichment Broth, the PCR system had a sensitivity of 91.8% and a specificity of 96.2%. To track the origin and spread of L. monocytogenes, isolates were fingerprinted by automated ribotyping. Fifteen different ribotypes were identified among 85 isolates tested. Ribotyping data established possible contamination patterns, implicating raw materials and the processing environment as potential sources of finished product contamination. Analysis of the distribution of ribotypes revealed that each processing facility had a unique contamination pattern and that specific ribotypes persisted in the environments of two facilities over time (P ? 0.0006). We conclude that application of molecular approaches can provide critical information on the ecology of different L. monocytogenes strains in food processing environments. This information can be used to develop practical recommendations for improved control of this important food-borne pathogen in the food industry. PMID:11133446

  12. Operational Collision Avoidance

    NASA Technical Reports Server (NTRS)

    Guit, Bill

    2015-01-01

    This presentation will describe the early days of the EOS Aqua and Aura operational collision avoidance process. It will highlight EOS debris avoidance maneuvers, EOS high interest event statistic and A-Train systematic conjunctions and conclude with future challenges. This is related to earlier e-DAA (tracking number 21692) that an abstract was submitted to a different conference. Eric Moyer, ESMO Deputy Project Manager has reviewed and approved this presentation on May 6, 2015

  13. Epigenetics and Shared Molecular Processes in the Regeneration of Complex Structures

    PubMed Central

    Rouhana, Labib; Tasaki, Junichi

    2016-01-01

    The ability to regenerate complex structures is broadly represented in both plant and animal kingdoms. Although regenerative abilities vary significantly amongst metazoans, cumulative studies have identified cellular events that are broadly observed during regenerative events. For example, structural damage is recognized and wound healing initiated upon injury, which is followed by programmed cell death in the vicinity of damaged tissue and a burst in proliferation of progenitor cells. Sustained proliferation and localization of progenitor cells to site of injury give rise to an assembly of differentiating cells known as the regeneration blastema, which fosters the development of new tissue. Finally, preexisting tissue rearranges and integrates with newly differentiated cells to restore proportionality and function. While heterogeneity exists in the basic processes displayed during regenerative events in different species—most notably the cellular source contributing to formation of new tissue—activation of conserved molecular pathways is imperative for proper regulation of cells during regeneration. Perhaps the most fundamental of such molecular processes entails chromatin rearrangements, which prime large changes in gene expression required for differentiation and/or dedifferentiation of progenitor cells. This review provides an overview of known contributions to regenerative processes by noncoding RNAs and chromatin-modifying enzymes involved in epigenetic regulation. PMID:26681954

  14. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    NASA Astrophysics Data System (ADS)

    Wang, Bin-Bin; Han, Yong-Chang; Cong, Shu-Lin

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1Σ+) is associated into the molecule in the bound states of the excited state (A1Σ+) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j> on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse.

  15. Reorganization energy of electron transfer processes in ionic fluids: A molecular Debye-Hueckel approach

    SciTech Connect

    Xiao Tiejun; Song Xueyu

    2013-03-21

    The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hueckel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hueckel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids.

  16. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    SciTech Connect

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  17. Reorganization energy of electron transfer processes in ionic fluids: A molecular Debye-Hückel approach

    NASA Astrophysics Data System (ADS)

    Xiao, Tiejun; Song, Xueyu

    2013-03-01

    The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hückel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hückel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids.

  18. Reorganization energy of electron transfer processes in ionic fluids: a molecular Debye-Hückel approach.

    PubMed

    Xiao, Tiejun; Song, Xueyu

    2013-03-21

    The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hückel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hückel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids. PMID:23534625

  19. MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS

    SciTech Connect

    Andrew W. Wang

    2002-04-01

    Several classes of molecular sieves were investigated as methanol dehydration catalysts for the LPDME{trademark} (liquid-phase dimethyl ether) process. Molecular sieves offer a number of attractive features as potential catalysts for the conversion of methanol to DME. These include (1) a wide range of acid strengths, (2) diverse architectures and channel connectivities that provide latitude for steric control, (3) high active site density, (4) well-investigated syntheses and characterization, and (5) commercial availability in some cases. We directed our work in two areas: (1) a general exploration of the catalytic behavior of various classes of molecular sieves in the LPDME{trademark} system and (2) a focused effort to prepare and test zeolites with predominantly Lewis acidity. In our general exploration, we looked at such diverse materials as chabazites, mordenites, pentasils, SAPOs, and ALPOs. Our work with Lewis acidity sought to exploit the structural advantages of zeolites without the interfering effects of deleterious Broensted sites. We used zeolite Ultrastable Y (USY) as our base material because it possesses a high proportion of Lewis acid sites. This work was extended by modifying the USY through ion exchange to try to neutralize residual Broensted acidity.

  20. PTtD evolution of continental crust during subduction-collision processes : example of the Briançonnais domain (Western Alps, France).

    NASA Astrophysics Data System (ADS)

    Strzerzynski, P.; Guillot, S.; Leloup, P. H.; Arnaud, N.; Vidal, O.; Ledru, P.; Courrioux, G.; Darmendrail, X.

    2009-04-01

    Understanding exhumation processes of high to ultra-high pressure (HP to UHP) terrains during plate convergence is a major challenge for the comprehension of plate convergence processes and mountain building. Contemporaneous contraction and extension coupled with erosion are frequently proposed to drive the exhumation process. In the internal alpine belt, HP and UHP metamorphism are recorded both in the Piemont oceanic unit and in the continental units such as the Internal Crystalline Massifs and the Briançonnais zone. In the western Alps, the consensus is to relate the top to NW then W directed D1 thrusting phase to nappe stacking and exhumation of the HP to UHP units within a subduction channel. Although there is an agreement on the occurrence of a top to the east D2 tectonic phase, its significance in terms of shortening or extensional deformation is controversial. On one hand, top to the east D2 shear zones and associated folds are interpreted as backthrusts or backfolds active during the Oligocene syn-collisional shortening phase, post-dating the exhumation of the HP units. On the other hand, D2 structures are interpreted as top the east normal faults that are active during the exhumation of the HP unit within a subduction channel. To decipher between these two different interpretations, we conducted a combined structural, petrological and geochronological study of the Modane-Aussois area in order to build a PTtD path of the Briançonnais zone. The current construction of a high velocity railway tunnel between the Maurienne and Susa valleys provides the opportunity to gather a large amount of geological data in the internal Western Alps and to extend surface observation at depth. We provide a structural analysis on ductile and brittle domains. New PT estimates are obtained using pseudosection and multiequilibra methods. Ar/Ar step heating on phengite provide time constraint on tectonic phases. Then, in light of our data and available literature, we focus on the significance of the D2 structures in the internal Western Alps. Results indicate that polyphased tectonic occurs during exhumation. The first deformation phase (D1) is characterized by nappe stacking in a context of top to the NW shearing, between 37 and 35 Ma deformation occurs between 1.0 and 0.5 GPa and 360-350°C. Top to the East deformation phase (D2) is associated with decompression up to 0.1 GPa and cooling down to 280°C. D2 deformations end at 31Ma. Following these phases of ductile deformation, two successive brittle deformation phases are evidenced: the first one is characterized by a N-S direction of extension and produce the overall tilting toward the south of the studied zone. The second one is characterized by E-W direction of extension. In the Internal Alps, the transition between Oceanic-continental subduction and continental collision occurred at 32Ma. In this context, D1 deformations that are dated between 37 and 35 Ma are clearly related to continental subduction. In the same way, brittle deformation phases are the expression of continental collision. The D2 tectonic phase took place at the transition between subduction and collision. Its attribution to one of these two processes remains ambiguous and will be discussed at the light of these new results.

  1. Puck collisions

    NASA Astrophysics Data System (ADS)

    Hauge, E. H.

    2012-09-01

    Collisions between two ice hockey pucks sliding on frictionless ice are studied, with both inelasticity and frictional contact between the colliding surfaces of the two pucks taken into account. The latter couples translational and rotational motion. The full solution depends on the sign and magnitude of the initial mismatch between the surface velocities at the point of contact. The initial state defines two physically distinct regimes for the friction coefficient. To illustrate the complexities, we discuss at length the typical situation (well known from curling) when puck number 1 is initially at rest, and is hit by puck number 2 with an arbitrary impact parameter, velocity and angular velocity. We find that the total outgoing angle between the pucks exceeds \\frac{1}{2}\\pi if and only if the collision leads to a net increase in the translational part of the kinetic energy. The conditions for this to happen are scrutinized, and the results are presented both analytically and numerically by a set of representative curves. This paper is written with an ambitious undergraduate, and her teacher, in mind.

  2. Extending pathways and processes using molecular interaction networks to analyse cancer genome data

    PubMed Central

    2010-01-01

    Background Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways. Results We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyse their enrichment in pancreatic mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes. Conclusions The proposed method for extending cellular pathways helps to explain the functions of cancer mutated genes by exploiting the synergies of canonical knowledge and large-scale interaction data. PMID:21144022

  3. Digging process in NGC 6951: the molecular disc bumped by the jet

    NASA Astrophysics Data System (ADS)

    May, D.; Steiner, J. E.; Ricci, T. V.; Menezes, R. B.; Andrade, I. S.

    2016-03-01

    We present a study of the central 200 pc of the galaxy NGC 6951, SAB(rs)bc, an active twin of the Milky Way, at a distance of 24 Mpc. Its nucleus has been observed in the optical with the Integral Field Unit of the Gemini Multi-Object Spectrograph, showing an outflow, and with the HST/ACS, revealing two extended structures with similar orientation, suggesting the presence of a collimating and/or obscuring structure. In order to ascertain this hypothesis, adaptive optics assisted NIR integral field spectroscopic observations were obtained with the Near-Infrared Integral Field Spectrograph in the Gemini North telescope. We detected a compact structure of H2 molecular gas, interpreted as a nearly edge-on disc with diameter of ˜47 pc, PA = 124° and velocity range from -40 to +40 km s-1. This disc is misaligned by 32° with respect to the radio jet and the ionization cones seen in the optical. There are two regions of turbulent gas, with position angles similar to the jet/cones, seen both in molecular and ionized phases; these regions are connected to the edges of the molecular disc and coincide with a high ratio of [N II]/H α = 5, suggesting that these regions are shock excited, partially ionized or both. We explain these structures as a consequence of a `digging process' that the jet inflicts on the disc, ejecting the molecular gas towards the ionization cones. The dynamical mass within 17 pc is estimated as 6.3 × 106 M⊙. This is an interesting case of an object presenting evidence of a connected feeding-feedback structure.

  4. Theory of slow atomic collisions

    NASA Astrophysics Data System (ADS)

    Nikitin, E. E.; Umanskii, S. Ia.

    The theory presented in this book is self-contained. It can be applied to the interpretation of various processes occurring in atomic collisions over a relatively wide energy range, from thermal energies to hundreds of eV. The general formulation of the scattering problem under quasi-classical conditions is discussed, taking into account scattering amplitudes and cross sections, scattering equations, collisions of two many-electron atoms, and integral cross sections for isotropic collisions. Other topics explored are related to diatomic electronic states, approximate calculations of the electronic states of diatoms, elastic scattering, approximate calculations of a multichannel quasi-classical scattering matrix, the two-state scattering problem, the linear two-state Landau-Zener model, nonlinear two-state models of nonadiabatic coupling, multistate models of nonadiabatic coupling, and a case study involving intramultiplet mixing and depolarization of alkalis in collisions with noble gases.

  5. Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes

    PubMed Central

    Bonifaci, Núria; Berenguer, Antoni; Díez, Javier; Reina, Oscar; Medina, Ignacio; Dopazo, Joaquín; Moreno, Víctor; Pujana, Miguel Angel

    2008-01-01

    Background Recent advances in whole-genome association studies (WGASs) for human cancer risk are beginning to provide the part lists of low-penetrance susceptibility genes. However, statistical analysis in these studies is complicated by the vast number of genetic variants examined and the weak effects observed, as a result of which constraints must be incorporated into the study design and analytical approach. In this scenario, biological attributes beyond the adjusted statistics generally receive little attention and, more importantly, the fundamental biological characteristics of low-penetrance susceptibility genes have yet to be determined. Methods We applied an integrative approach for identifying candidate low-penetrance breast cancer susceptibility genes, their characteristics and molecular networks through the analysis of diverse sources of biological evidence. Results First, examination of the distribution of Gene Ontology terms in ordered WGAS results identified asymmetrical distribution of Cell Communication and Cell Death processes linked to risk. Second, analysis of 11 different types of molecular or functional relationships in genomic and proteomic data sets defined the "omic" properties of candidate genes: i/ differential expression in tumors relative to normal tissue; ii/ somatic genomic copy number changes correlating with gene expression levels; iii/ differentially expressed across age at diagnosis; and iv/ expression changes after BRCA1 perturbation. Finally, network modeling of the effects of variants on germline gene expression showed higher connectivity than expected by chance between novel candidates and with known susceptibility genes, which supports functional relationships and provides mechanistic hypotheses of risk. Conclusion This study proposes that cell communication and cell death are major biological processes perturbed in risk of breast cancer conferred by low-penetrance variants, and defines the common omic properties, molecular interactions and possible functional effects of candidate genes and proteins. PMID:19094230

  6. Relaxation processes and glass transition in confined 1,4-polybutadiene films: A Molecular Dynamics study

    NASA Astrophysics Data System (ADS)

    Paul, Wolfgang; Solar, Mathieu

    We will present results from Molecular Dynamics simulations of a chemically realistic model of 1,4-polybutadiene (PB) chains confined by graphite walls. Relaxation processes in this system are heterogeneous and anisotropic. We will present evidence for a slow additional relaxation process related to chain desorption from the walls. We also study the structural relaxation resolved with respect to the distance from the graphite walls and show the influence of structural changes on the relaxation behavior. The temperature dependence of the dielectric relaxation in layers of different thickness near the walls shows no indication of a shift of Tg as a function of thickness when analyzed with a Vogel-Fulcher fit. We explain this by the importance of intramolecular dihedral barriers for the glass transition in PB which dominate over the density changes next to a wall except for a 1 nm thick layer directly at the wall.

  7. Statistical mechanics of neocortical interactions: Large-scale EEG influences on molecular processes.

    PubMed

    Ingber, Lester

    2016-04-21

    Calculations further support the premise that large-scale synchronous firings of neurons may affect molecular processes. The context is scalp electroencephalography (EEG) during short-term memory (STM) tasks. The mechanism considered is Π=p+qA (SI units) coupling, where p is the momenta of free Ca(2+) waves, q the charge of Ca(2+) in units of the electron charge, and A the magnetic vector potential of current I from neuronal minicolumnar firings considered as wires, giving rise to EEG. Data has processed using multiple graphs to identify sections of data to which spline-Laplacian transformations are applied, to fit the statistical mechanics of neocortical interactions (SMNI) model to EEG data, sensitive to synaptic interactions subject to modification by Ca(2+) waves. PMID:26874226

  8. Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes

    SciTech Connect

    Prior, Javier; Castro, Enrique; Chin, Alex W.; Almeida, Javier; Huelga, Susana F.; Plenio, Martin B.

    2013-12-14

    New experimental techniques based on nonlinear ultrafast spectroscopies have been developed over the last few years, and have been demonstrated to provide powerful probes of quantum dynamics in different types of molecular aggregates, including both natural and artificial light harvesting complexes. Fourier transform-based spectroscopies have been particularly successful, yet “complete” spectral information normally necessitates the loss of all information on the temporal sequence of events in a signal. This information though is particularly important in transient or multi-stage processes, in which the spectral decomposition of the data evolves in time. By going through several examples of ultrafast quantum dynamics, we demonstrate that the use of wavelets provide an efficient and accurate way to simultaneously acquire both temporal and frequency information about a signal, and argue that this greatly aids the elucidation and interpretation of physical process responsible for non-stationary spectroscopic features, such as those encountered in coherent excitonic energy transport.

  9. Molecular-dynamics investigation of structural transformations of a Cu 201 cluster in its melting process

    NASA Astrophysics Data System (ADS)

    Zhang, Lin; Zhang, Cai-Bei; Qi, Yang

    2009-02-01

    We perform molecular-dynamics calculations to investigate the structural transformation of a copper cluster containing 201 atoms in its melting process within the framework of the embedded-atom method (EAM). Concerning melting, the obtained results reveal that its structural changes are different from those of larger-size clusters containing several hundreds or more atoms and smaller-size clusters containing tens of atoms. The melting process of this Cu 201 cluster involves three stages, firstly some atoms in inner regions of this cluster move into outer regions accompanying the structural transformation of the local atom packing, followed by the continuous interchange of atomic positions, and finally this cluster is wholly disordered. During the temperature increase, the structural changes of different regions determined by atom density profiles result in apparent increases in internal energy. By decomposing peaks of pair distribution functions (PDFs) according to the pair analysis (PA) technique, the local structural patterns are identified for the melting of this cluster.

  10. Dislocation processes in the deformation of nanocrystalline aluminium by molecular-dynamics simulation.

    PubMed

    Yamakov, Vesselin; Wolf, Dieter; Phillpot, Simon R; Mukherjee, Amiya K; Gleiter, Herbert

    2002-09-01

    The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying--in a degree of detail not possible experimentally--the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size. PMID:12618848

  11. Observation of the amorphous zinc oxide recrystalline process by molecular dynamics simulation

    PubMed Central

    Lin, Ken-Huang; Sun, Shih-Jye; Ju, Shin-Pon; Tsai, Jen-Yu; Chen, Hsin-Tsung; Hsieh, Jin-Yuan

    2013-01-01

    The detailed structural variations of amorphous zinc oxide (ZnO) as well as wurtzite (B4) and zinc blende (B3) crystal structures during the temperature elevation process were observed by molecular dynamics simulation. The amorphous ZnO structure was first predicted through the simulated-annealing basin-hopping algorithm with the criterion to search for the least stable structure. The density and X-ray diffraction profiles of amorphous ZnO of the structure were in agreement with previous reports. The local structural transformation among different local structures and the recrystalline process of amorphous ZnO at higher temperatures are observed and can explain the structural transformation and recrystalline mechanism in a corresponding experiment [Bruncko et al., Thin Solid Films 520, 866-870 (2011)]. PMID:23509413

  12. Signal processing for molecular and cellular biological physics: an emerging field

    PubMed Central

    Little, Max A.; Jones, Nick S.

    2013-01-01

    Recent advances in our ability to watch the molecular and cellular processes of life in action—such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer—raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied. PMID:23277603

  13. Molecular Interdiffusion between Stacked Layers by Solution and Thermal Annealing Processes in Organic Light Emitting Devices.

    PubMed

    Ohisa, Satoru; Pu, Yong-Jin; Yamada, Norifumi L; Matsuba, Go; Kido, Junji

    2015-09-23

    In organic light emitting devices (OLEDs), interfacial structures between multilayers have large impacts on the characteristics of OLEDs. Herein, we succeeded in revealing the interdiffusion in solution processed and thermal annealed OLEDs by neutron reflectometry. We investigated interfaces between a polymer under layer and small molecules upper layer. The small molecules diffused into the swollen polymer layer during the interfacial formation by the solution process, but the polymer did not diffuse into the small molecules layer. At temperatures close to the glass transition temperatures of the materials, asymmetric molecular diffusion was observed. We elucidated the effects of the interdiffusion on the characteristics of OLEDs. Partially mixing the interface improved the current efficiencies due to suppressed triplet-polaron quenching at the interface. Controlling and understanding the interfacial structures of the miultilayers will be more important to improve the OLED characteristics. PMID:26331696

  14. Signal processing for molecular and cellular biological physics: an emerging field.

    PubMed

    Little, Max A; Jones, Nick S

    2013-02-13

    Recent advances in our ability to watch the molecular and cellular processes of life in action--such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer--raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied. PMID:23277603

  15. Molecularly and structurally distinct synapses mediate reliable encoding and processing of auditory information.

    PubMed

    Wichmann, Carolin

    2015-12-01

    Hearing impairment is the most common human sensory deficit. Considering the sophisticated anatomy and physiology of the auditory system, disease-related failures frequently occur. To meet the demands of the neuronal circuits responsible for processing auditory information, the synapses of the lower auditory pathway are anatomically and functionally specialized to process acoustic information indefatigably with utmost temporal precision. Despite sharing some functional properties, the afferent synapses of the cochlea and of auditory brainstem differ greatly in their morphology and employ distinct molecular mechanisms for regulating synaptic vesicle release. Calyceal synapses of the endbulb of Held and the calyx of Held profit from a large number of release sites that project onto one principal cell. Cochlear inner hair cell ribbon synapses exhibit a unique one-to-one relation of the presynaptic active zone to the postsynaptic cell and use hair-cell-specific proteins such as otoferlin for vesicle release. The understanding of the molecular physiology of the hair cell ribbon synapse has been advanced by human genetics studies of sensorineural hearing impairment, revealing human auditory synaptopathy as a new nosological entity. PMID:26188105

  16. Quantum control of a molecular ionization process by using Fourier-synthesized laser fields

    NASA Astrophysics Data System (ADS)

    Ohmura, Hideki; Saito, Naoaki

    2015-11-01

    In photoexcitation processes, if the motion of excited electrons can be precisely steered by the instantaneous electric field of an arbitrary waveform of a Fourier-synthesized laser field, the resultant matter response can be achieved within one optical cycle, usually within the attosecond (1 as =10-18s) regime. Fourier synthesis of laser fields has been achieved in various ways. However, the general use of Fourier-synthesized laser fields for the control of matter is extremely limited. Here, we report the quantum control of a nonlinear response of a molecular ionization process by using Fourier-synthesized laser fields. The directionally asymmetric molecular tunneling ionization induced by intense (5.0 ×1012W /c m2) Fourier-synthesized laser fields consisting of fundamental, second-, third-, and fourth-harmonic light achieves the orientation-selective ionization; we utilized the orientation-selective ionization for measurement of the relative phase differences between the fundamental and each harmonic light. Our findings impact not only light-wave engineering but also the control of matter, possibly triggering the creation and establishment of a new methodology that uses Fourier-synthesized laser fields.

  17. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.

    PubMed

    Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

    2014-01-01

    For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer. PMID:25384534

  18. Study the sensitivity of molecular functional groups to bioethanol processing in lipid biopolymer of co-products using DRIFT molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang

    2011-11-01

    To date, there is no study on bioethanol processing-induced changes in molecular structural profiles mainly related to lipid biopolymer. The objectives of this study were to: (1) determine molecular structural changes of lipid related functional groups in the co-products that occurred during bioethanol processing; (2) relatively quantify the antisymmetric CH 3 and CH 2 (ca. 2959 and 2928 cm -1, respectively), symmetric CH 3 and CH 2 (ca. 2871 and 2954 cm -1, respectively) functional groups, carbonyl C dbnd O ester (ca. 1745 cm -1) and unsaturated groups (CH attached to C dbnd C) (ca. 3007 cm -1) spectral intensities as well as their ratios of antisymmetric CH 3 to antisymmetric CH 2, and (3) illustrate the molecular spectral analyses as a research tool to detect for the sensitivity of individual moleculars to the bioethanol processing in a complex plant-based feed and food system without spectral parameterization. The hypothesis of this study was that bioethanol processing changed the molecular structure profiles in the co-products as opposed to original cereal grains. These changes could be detected by infrared molecular spectroscopy and will be related to nutrient utilization. The results showed that bioethanol processing had effects on the functional groups spectral profiles in the co-products. It was found that the CH 3-antisymmetric to CH 2-antisymmetric stretching intensity ratio was changed. The spectral features of carbonyl C dbnd O ester group and unsaturated group were also different. Since the different types of cereal grains (wheat vs. corn) had different sensitivity to the bioethanol processing, the spectral patterns and band component profiles differed between their co-products (wheat DDGS vs. corn DDGS). The multivariate molecular spectral analyses, cluster analysis and principal component analysis of original spectra (without spectral parameterization), distinguished the structural differences between the wheat and wheat DDGS and between the corn and corn DDGS in the antisymmetric and symmetric CH 3 and CH 2 spectral region (ca. 2994-2800 cm -1) and unsaturated group band region (3025-2996 cm -1). Further study is needed to quantify molecular structural changes in relation to nutrient utilization of lipid biopolymer.

  19. Design and synthesis of molecular donors for solution-processed high-efficiency organic solar cells.

    PubMed

    Coughlin, Jessica E; Henson, Zachary B; Welch, Gregory C; Bazan, Guillermo C

    2014-01-21

    Organic semiconductors incorporated into solar cells using a bulk heterojunction (BHJ) construction show promise as a cleaner answer to increasing energy needs throughout the world. Organic solar cells based on the BHJ architecture have steadily increased in their device performance over the past two decades, with power conversion efficiencies reaching 10%. Much of this success has come with conjugated polymer/fullerene combinations, where optimized polymer design strategies, synthetic protocols, device fabrication procedures, and characterization methods have provided significant advancements in the technology. More recently, chemists have been paying particular attention to well-defined molecular donor systems due to their ease of functionalization, amenability to standard organic purification and characterization methods, and reduced batch-to-batch variability compared to polymer counterparts. There are several critical properties for efficient small molecule donors. First, broad optical absorption needs to extend towards the near-IR region to achieve spectral overlap with the solar spectrum. Second, the low lying highest occupied molecular orbital (HOMO) energy levels need to be between -5.2 and -5.5 eV to ensure acceptable device open circuit voltages. Third, the structures need to be relatively planar to ensure close intermolecular contacts and high charge carrier mobilities. And last, the small molecule donors need to be sufficiently soluble in organic solvents (≥10 mg/mL) to facilitate solution deposition of thin films of appropriate uniformity and thickness. Ideally, these molecules should be constructed from cost-effective, sustainable building blocks using established, high yielding reactions in as few steps as possible. The structures should also be easy to functionalize to maximize tunability for desired properties. In this Account, we present a chronological description of our thought process and design strategies used in the development of highly efficient molecular donors that achieve power conversion efficiencies greater than 7%. The molecules are based on a modular D(1)-A-D(2)-A-D(1) architecture, where A is an asymmetric electron deficient heterocycle, which allowed us to quickly access a library of compounds and develop structure-property-performance relationships. Modifications to the D1 and D2 units enable spectral coverage throughout the entire visible region and control of HOMO energy levels, while adjustments to the pendant alkyl substituents dictate molecular solubility, thermal transition temperatures, and solid-state organizational tendencies. Additionally, we discuss regiochemical considerations that highlight how individual atom placements can significantly influence molecular and subsequently device characteristics. Our results demonstrate the utility of this architecture for generating promising materials to be integrated into organic photovoltaic devices, call attention to areas for improvement, and provide guiding principles to sustain the steady increases necessary to move this technology forward. PMID:23984626

  20. Time-dependent wave-packet method for the complete determination of S-matrix elements for reactive molecular collisions in three dimensions

    NASA Technical Reports Server (NTRS)

    Judson, Richard S.; Kouri, Donald J.; Neuhauser, Daniel; Baer, Michael

    1990-01-01

    An alternative time-dependent wave-packet method for treating three-dimensional gas phase reactive atom-diatom collisions is presented. The method employs a nonreactive body-frame wave packet propagation procedure, made possible by judicious use of absorbing optical potentials, a novel scheme for interpolating the wave function from coordinates in one arrangement to those in another and the fact that the time-dependent Schroedinger equation is an initial-value problem. The last feature makes possible a computationally viable and accurate procedure for changing from one arrangement's coordinates to another. In addition, the method allows the determination of S-matrix elements over a wide range of energies from a single wave-packet propagation. The method is illustrated by carrying out detailed calculations of inelastic and reactive scattering in the H + H2 system using the Liu-Siegbahn-Truhlar-Horowitz potential surface.

  1. Isolating signatures of major cloud-cloud collisions using position-velocity diagrams

    NASA Astrophysics Data System (ADS)

    Haworth, T. J.; Tasker, E. J.; Fukui, Y.; Torii, K.; Dale, J. E.; Shima, K.; Takahira, K.; Habe, A.; Hasegawa, K.

    2015-06-01

    Collisions between giant molecular clouds are a potential mechanism for triggering the formation of massive stars, or even super star clusters. The trouble is identifying this process observationally and distinguishing it from other mechanisms. We produce synthetic position-velocity diagrams from models of cloud-cloud collisions, non-interacting clouds along the line of sight, clouds with internal radiative feedback and a more complex cloud evolving in a galactic disc, to try and identify unique signatures of collision. We find that a broad bridge feature connecting two intensity peaks, spatially correlated but separated in velocity, is a signature of a high-velocity cloud-cloud collision. We show that the broad bridge feature is resilient to the effects of radiative feedback, at least to around 2.5 Myr after the formation of the first massive (ionizing) star. However for a head-on 10 km s-1 collision, we find that this will only be observable from 20 to 30 per cent of viewing angles. Such broad-bridge features have been identified towards M20, a very young region of massive star formation that was concluded to be a site of cloud-cloud collision by Torii et al., and also towards star formation in the outer Milky Way by Izumi et al.

  2. Probing GPDs in ultraperipheral collisions

    SciTech Connect

    Ivanov, D.Yu.; Pire, B.; Szymanowski, L.; Wagner, J.

    2015-04-10

    Ultraperipheral collisions in hadron colliders give new opportunities to investigate the hadron structure through exclusive photoproduction processes. We describe the possibility of measuring the Generalized Parton Distributions in the Timelike Compton Scattering process and in the production of heavy vector meson.

  3. Mechanical properties and biocompatibility of melt processed, self-reinforced ultrahigh molecular weight polyethylene.

    PubMed

    Huang, Yan-Fei; Xu, Jia-Zhuang; Li, Jian-Shu; He, Ben-Xiang; Xu, Ling; Li, Zhong-Ming

    2014-08-01

    The low efficiency of fabrication of ultrahigh molecular weight polyethylene (UHMWPE)-based artificial knee joint implants is a bottleneck problem because of its extremely high melt viscosity. We prepared melt processable UHMWPE (MP-UHMWPE) by addition of 9.8 wt% ultralow molecular weight polyethylene (ULMWPE) as a flow accelerator. More importantly, an intense shear flow was applied during injection molding of MP-UHMWPE, which on one hand, promoted the self-diffusion of UHMWPE chains, thus effectively reducing the structural defects; on the other hand, increased the overall crystallinity and induced the formation of self-reinforcing superstructure, i.e., interlocked shish-kebabs and oriented lamellae. Aside from the good biocompatibility, and the superior fatigue and wear resistance to the compression-molded UHMWPE, the injection-molded MP-UHMWPE exhibits a noteworthy enhancement in tensile properties and impact strength, where the yield strength increases to 46.3 ± 4.4 MPa with an increment of 128.0%, the ultimate tensile strength and Young's modulus rise remarkably up to 65.5 ± 5.0 MPa and 1248.7 ± 45.3 MPa, respectively, and the impact strength reaches 90.6 kJ/m(2). These results suggested such melt processed and self-reinforced UHMWPE parts hold a great application promise for use of knee joint implants, particularly for younger and more active patients. Our work sets up a new method to fabricate high-performance UHMWPE implants by tailoring the superstructure during thermoplastic processing. PMID:24835044

  4. The early molecular processes underlying the neurological manifestations of an animal model of Wilson's disease.

    PubMed

    Lee, Beom Hee; Kim, Joo Hyun; Kim, Jae-Min; Heo, Sun Hee; Kang, Minji; Kim, Gu-Hwan; Choi, Jin-Ho; Yoo, Han-Wook

    2013-05-01

    The Long-Evans Cinnamon (LEC) rat shows age-dependent hepatic manifestations that are similar to those of Wilson's disease (WD). The pathogenic process in the brain has, however, not been evaluated in detail due to the rarity of the neurological symptoms. However, copper accumulation is noted in LEC rat brain tissue from 24 weeks of age, which results in oxidative injuries. The current study investigated the gene expression profiles of LEC rat brains at 24 weeks of age in order to identify the important early molecular changes that underlie the development of neurological symptoms in WD. Biological ontology-based analysis revealed diverse altered expressions of the genes related to copper accumulation. Of particular interest, we found altered expression of genes connected to mitochondrial respiration (Sdhaf2 and Ndufb7), calcineurin-mediated cellular processes (Ppp3ca, Ppp3cb, and Camk2a), amyloid precursor protein (Anks1b and A2m) and alpha-synuclein (Snca). In addition to copper-related changes, compensatory upregulations of Cp and Hamp reflect iron-mediated neurotoxicity. Of note, reciprocal expression of Asmt and Bhmt is an important clue that altered S-adenosylhomocysteine metabolism underlies brain injury in WD, which is directly correlated to the decreased expression of S-adenosylhomocysteine hydrolase in hepatic tissue in LEC rats. In conclusion, our study indicates that diverse molecular changes, both variable and complex, underlie the development of neurological manifestations in WD. Copper-related injuries were found to be the principal pathogenic process, but Fe- or adenosylhomocysteine-related injuries were also implicated. Investigations using other animal models or accessible human samples will be required to confirm our observations. PMID:23519153

  5. Fundamental processes of microcrystalline silicon film growth: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Ohira, Tatusya; Ukai, Osamu; Noda, Matsuhei

    2000-06-01

    The fundamental processes of microcrystalline silicon film growth in plasma enhanced chemical vapor deposition (PECVD) with SiH 4 gas diluted by H 2 have been studied using molecular dynamics (MD) simulations with a realistic many-body semiclassical potential developed to describe interatomic interactions in the Si:H system. In this study the fundamental processes have been investigated from the following three viewpoints: (i) Si crystallization processes from SiH 3 radicals; (ii) hydrogen desorption processes; and (iii) stability of the crystallized Si atoms. As a result of MD simulations related to these three points, it was found that when a substrate temperature is ca. 500 K, a SiH 3 radical migrates to a crystalline Si site and is stabilized by bonding two surface Si atoms after releasing one H atom after ca. 200-300 ps, and that surface H desorption occurs as H 2 molecules, SiH 3 radicals and SiH 4 molecules due to atomic H exposure. In addition it was observed that the stabilized Si atom in a crystalline Si site mentioned above cannot be etched by incident atomic H but unrelaxed Si atoms in surface layers can be etched.

  6. Molecular characterization of proteolytic processing of the Gag proteins of human spumaretrovirus.

    PubMed

    Pfrepper, Klaus-Ingmar; Flügel, Rolf M

    2005-01-01

    Molecular characterization of proteolytic processing of the human spumaretrovirus (HSRV) Gag proteins and the precise determination of cleavage sites was performed. For in vitro processing of recombinant HSRV Gag proteins, a recombinant enzymatically active HSRV protease was employed. Recombinant Gag proteins and protease were cloned and expressed as hexa-histidine-tagged proteins in pET-32b and pET-22b vectors, respectively, in the E. coli BL21 expression strain. The recombinant proteins were purified by affinity chromatography on an immobilized metal ion matrix. To determine the precise processing sites, recombinant Gag proteins or synthetic peptides derived from Gag sequences were cleaved in vitro by the recombinant protease. Proteolytic processing reactions were carried out under optimal reaction conditions of HSRV protease in sodium phosphate buffer, pH 6.0, supplied with 2 M NaCl at 37 degrees C. The cleavage sites were determined by amino-terminal amino acid sequencing as well as by matrix-assisted laser desorption/ionization mass spectrometry analysis of the reaction products. Fluorescence spectrophotometry was used to determine cleavage kinetics of peptides mimicking different cleavage sites within the HSRV Gag proteins. PMID:16061995

  7. Study of Higgs boson production and its b-b(bar) decay in gamma-gamma processes in proton-nucleus collisions at the LHC

    SciTech Connect

    d'Enterria, David; Lansberg, Jean-Philippe; /Ecole Polytechnique, CPHT /SLAC

    2010-08-26

    We explore for the first time the possibilities to measure an intermediate-mass (m{sub H} = 115-140 GeV/c{sup 2}) Standard-Model Higgs boson in electromagnetic proton-lead (p Pb) interactions at the CERN Large Hadron Collider (LHC) via its b{bar b} decay. Using equivalent Weizsacker-Williams photon fluxes and Higgs effective field theory for the coupling {gamma}{gamma} {yields} H, we obtain a leading-order cross section of the order of 0.3 pb for exclusive Higgs production in elastic (p Pb {yields} {gamma}{gamma} p H Pb) and semielastic (p Pb {yields} {gamma}{gamma} X H Pb) processes at {radical}S{sub NN} = 8.8 TeV. After applying various kinematics cuts to remove the main backgrounds ({gamma}{gamma} {yields} b{bar b} and misidentified {gamma}{gamma} {yields} q{bar q} events), we find that a Higgs boson with m{sub H} = 120 GeV/c{sup 2} could be observed in the b{bar b} channel with a 3{sigma}-significance integrating 300 pb{sup -1} with an upgraded pA luminosity of 10{sup 31} cm{sup -2}s{sup -1}. We also provide for the first time semielastic Higgs cross sections, along with elastic t{bar t} cross sections, for electromagnetic pp, pA and AA collisions at the LHC.

  8. Dependence of radiative stabilization on the projectile charge state after double-electron-transfer processes in slow, highly charged ion-molecule collisions

    SciTech Connect

    Krok, F.; Tolstikhina, I.Y.; Sakaue, H.A.; Yamada, I.; Hosaka, K.; Kimura, M.; Nakamura, N.; Ohtani, S.; Tawara, H.

    1997-12-01

    We have measured the radiative stabilization probabilities after double-electron-transfer processes in slow (1.5qkeV) I{sup q+}+CO collisions in the charge-state regime 8{le}q{le}26 by using the charge-selected-projectile{endash}recoil-ion-coincidence method. It was found that the radiative stabilization probabilities P{sub rad}, defined as P{sub rad}=T{sub DC}/(T{sub DC}+A{sub DC}) (T{sub DC} is true double capture, and A{sub DC} autoionizing double capture), increases from about 1{percent} at the lowest charge up to about 10{percent} at the highest charge as the charge state of the projectile increases. A model is proposed which can explain such a feature, by incorporating a slight modification of the initial population of the transferred levels in the projectile predicted in the extended classical over-barrier model. Based upon the present model, theoretical radiative and autoionization decay rates have been calculated, using the Cowan code. Fairly good agreement between the measured and calculated results has been obtained. {copyright} {ital 1997} {ital The American Physical Society}

  9. Single-walled carbon nanotube bucky paper/epoxy composites: Molecular dynamics simulation and process development

    NASA Astrophysics Data System (ADS)

    Gou, Jihua

    The discovery of carbon nanotubes by Iijima in 1991 has initiated a large number of scientific investigations to explore their unique properties and potential applications. One of the major applications is nanocomposites with nanotubes as the reinforcing material. Currently, nanotube composites are fabricated by using the direct mixing technique. However, this technique is limited by low weight fraction of nanotubes and uncontrollable nanostructures in the composite. This dissertation research presents a new nanocomposite processing method in which single-walled nanotubes (SWNTs) are first preformed into nanotube bucky papers (NBPs) and then liquid epoxy resins are infiltrated through the NBPs and cured to fabricate the composite. The major technical challenges for developing the NBP/Epoxy nanocomposite include (1) understanding of the molecular interactions between nanotubes and epoxy resin at the nanometer scale; (2) fabricating NBPs with uniform nano-scaled rope size and pore size; and (3) realizing resin infiltration through the nanoporous structure of NBPs. Molecular dynamics (MD) simulations were used to examine the important molecular interactions, including affinity and interfacial bonding. The affinities of two kinds of epoxy systems were examined. Unlike the DGEBA/DETA epoxy system, both EPON 862 epoxy resin and DETDA molecules had good affinities with SWNT and were chosen as the matrix material in the nanocomposites. Pullout simulations of a SWNT from cured epoxy resins were performed to investigate the stress transfer potential of the SWNT/Epoxy interface. The estimated interfacial shear stress is up to 75 MPa. The MD simulation results were found useful to guide the process development and property prediction of NBP/Epoxy nanocomposites. Experimentally, the fabrication process for NBPs was analyzed and optimized using the design of experiments (DOE) approach. The SEM and AFM image analyses of the resultant nanocomposites indicated observable wetting and bonding between nanotubes and the epoxy resin. The dynamics mechanic analysis (DMA) showed that a 200--250% increase of the storage modulus was achieved in the nanocomposites. This research is the first attempt to make nanocomposites using nanotube bucky papers.

  10. Molecular reordering processes on ice (0001) surfaces from long timescale simulations

    SciTech Connect

    Pedersen, Andreas; Wikfeldt, Kjartan T.; Karssemeijer, Leendertjan; Cuppen, Herma; Jónsson, Hannes

    2014-12-21

    We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 μs at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere.

  11. Integrated Collision Avoidance System for Air Vehicle

    NASA Technical Reports Server (NTRS)

    Lin, Ching-Fang (Inventor)

    2013-01-01

    Collision with ground/water/terrain and midair obstacles is one of the common causes of severe aircraft accidents. The various data from the coremicro AHRS/INS/GPS Integration Unit, terrain data base, and object detection sensors are processed to produce collision warning audio/visual messages and collision detection and avoidance of terrain and obstacles through generation of guidance commands in a closed-loop system. The vision sensors provide more information for the Integrated System, such as, terrain recognition and ranging of terrain and obstacles, which plays an important role to the improvement of the Integrated Collision Avoidance System.

  12. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    PubMed

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

  13. The molecular signature of AML mesenchymal stromal cells reveals candidate genes related to the leukemogenic process.

    PubMed

    Binato, Renata; de Almeida Oliveira, Nathalia Correa; Du Rocher, Barbara; Abdelhay, Eliana

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process. PMID:26279521

  14. Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments

    PubMed Central

    Pizzarello, Sandra; Davidowski, Stephen K.; Holland, Gregory P.; Williams, Lynda B.

    2013-01-01

    The composition of the Sutter’s Mill meteorite insoluble organic material was studied both in toto by solid-state NMR spectroscopy of the powders and by gas chromatography–mass spectrometry analyses of compounds released upon their hydrothermal treatment. Results were compared with those obtained for other meteorites of diverse classifications (Murray, GRA 95229, Murchison, Orgueil, and Tagish Lake) and found to be so far unique in regard to the molecular species released. These include, in addition to O-containing aromatic compounds, complex polyether- and ester-containing alkyl molecules of prebiotic appeal and never detected in meteorites before. The Sutter’s Mill fragments we analyzed had likely been altered by heat, and the hydrothermal conditions of the experiments realistically mimic early Earth settings, such as near volcanic activity or impact craters. On this basis, the data suggest a far larger availability of meteoritic organic materials for planetary environments than previously assumed and that molecular evolution on the early Earth could have benefited from accretion of carbonaceous meteorites both directly with soluble compounds and, for a more protracted time, through alteration, processing, and release from their insoluble organic materials. PMID:24019471

  15. Bidirectional transport by molecular motors: enhanced processivity and response to external forces.

    PubMed

    Müller, Melanie J I; Klumpp, Stefan; Lipowsky, Reinhard

    2010-06-01

    Intracellular transport along cytoskeletal filaments is often mediated by two teams of molecular motors that pull on the same cargo and move in opposite directions along the filaments. We have recently shown theoretically that this bidirectional transport can be understood as a stochastic tug-of-war between the two motor teams. Here, we further develop our theory to investigate the experimentally accessible dynamic behavior of cargos transported by strong motors such as kinesin-1 or cytoplasmic dynein. By studying the run and binding times of such a cargo, we show that the properties of biological motors, such as the large ratio of stall/detachment force and the small ratio of superstall backward/forward velocity, are favorable for bidirectional cargo transport, leading to fast motion and enhanced diffusion. In addition, cargo processivity is shown to be strongly enhanced by transport via several molecular motors even if these motors are engaged in a tug-of-war. Finally, we study the motility of a bidirectional cargo under force. Frictional forces arising, e.g., from the viscous cytoplasm, lead to peaks in the velocity distribution, while external forces as exerted, e.g., by an optical trap, lead to hysteresis effects. Our results, in particular our explicit expressions for the cargo binding time and the distance of the peaks in the velocity relation under friction, are directly accessible to in vitro as well as in vivo experiments. PMID:20513405

  16. Analyzing Collisions in Terms of Newton's Laws

    NASA Astrophysics Data System (ADS)

    Roeder, John L.

    2003-02-01

    Although the principle of momentum conservation is a consequence of Newton's second and third laws of motion, as recognized by Newton himself, this principle is typically applied in analyzing collisions as if it is a separate concept of its own. This year I sought to integrate my treatment of collisions with my coverage of Newton's laws by asking students to calculate the effect on the motion of two particles due to the forces they exerted for a specified time interval on each other. For example, "A 50-kg crate slides across the ice at 3 m/s and collides with a 25-kg crate at rest. During the collision process the 50-kg crate exerts a 500 N time-averaged force on the 25 kg for 0.1 s. What are the accelerations of the crates during the collision, and what are their velocities after the collision? What are the momenta of the crates before and after collision?"

  17. ATOMIC AND MOLECULAR PHYSICS: Interference Angle on Quantum Rotational Energy Transfer in Na + Na2 (A1 Σ+u, v = 8 ~ b3п0u, v = 14) Molecular Collision System

    NASA Astrophysics Data System (ADS)

    Wang, Wei-Li; Miao, Gang; Li, Jian; Ma, Feng-Cai

    2009-12-01

    In order to study the collisional quantum interference (CQI) on rotational energy transfer in atom-diatom system, we have studied the relation of the integral interference angle and differential interference angle in Na + Na2 (A1 σ+u, v = 8 ~ b3п0u, v = 14) collision system. In this paper, based on the first-Born approximation of time-dependent perturbation theory and taking into accounts the anisotropic effect of Lennard-Jones interaction potentials, we present a theoretical model of collisional quantum interference in intramolecular rotational energy transfer, and a relationship between differential and integral interference angles.

  18. Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization

    NASA Astrophysics Data System (ADS)

    Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.

    2008-07-01

    We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5 nm and 5.5 nm during extension/compression, with a free energy difference of 10.5 kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring.

  19. Molecular imaging with radionuclides, a powerful technique for studying biological processes in vivo

    NASA Astrophysics Data System (ADS)

    Cisbani, E.; Cusanno, F.; Garibaldi, F.; Magliozzi, M. L.; Majewski, S.; Torrioli, S.; Tsui, B. M. W.

    2007-02-01

    Our team is carrying on a systematic study devoted to the design of a SPECT detector with submillimeter resolution and adequate sensitivity (1 cps/kBq). Such system will be used for functional imaging of biological processes at molecular level in small animal. The system requirements have been defined by two relevant applications: study of atherosclerotic plaques characterization and stem cells diffusion and homing. In order to minimize costs and implementation time, the gamma detector will be basedas much as possibleon conventional components: scintillator crystal and position sensitive PhotoMultipliers read by individual channel electronics. A coded aperture collimator should be adapted to maximize the efficiency. The optimal selection of the detector components is investigated by systematic use of Monte-Carlo simulations (and laboratory validation tests); and finally preliminary results are presented and discussed here.

  20. Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging

    NASA Astrophysics Data System (ADS)

    Dhas, M. Kumara; Jawahar, A.; Benial, A. Milton Franklin

    2014-04-01

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM 14N labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters such as signal intensity ratio, line width, g-value, hyperfine coupling constant and rotational correlation time were determined. The half life time was estimated for 1mM 14N labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. The ESR study reveals that the TEMPONE has narrowest line width and fast tumbling motion compared with TEMPO and TEMPOL. From the results, TEMPONE has long half life time and high stability compared with TEMPO and TEMPOL radical. Therefore, this study reveals that the TEMPONE radical can act as a good redox sensitive spin probe for molecular imaging.

  1. Fine microstructure of processed chitosan nanofibril networks preserving directional packing and high molecular weight.

    PubMed

    Osorio-Madrazo, Anayancy; David, Laurent; Peniche-Covas, Carlos; Rochas, Cyrille; Putaux, Jean-Luc; Trombotto, Stéphane; Alcouffe, Pierre; Domard, Alain

    2015-10-20

    Crystalline chitosan nanofibril networks were prepared, preserving the native structural packing and the polymer high molecular weight. The fine microstructure of the nanomaterial, obtained by mild hydrolysis of chitosan (CHI), was characterized by using synchrotron small- and wide-angle X-ray scattering (SAXS and WAXS), transmission electron microscopy (TEM) and electron diffraction. Hydrolysis of chitosan yielded a network of crystalline nanofibrils, containing both allomorphs of chitosan: hydrated and anhydrous. The comparison of WAXS data in transmission and reflection mode revealed the preferential orientation of the CHI crystals when subjected to mechanical compression constrains. The results are in agreement with the existence of a network nanostructure containing fiber-like crystals with the principal axis parallel to the polymer chain axis. The evolution of the CHI allomorphic composition with temperature was studied to further elucidate the mechanism of structural transitions occurring during CHI nanofibril network processing. PMID:26256153

  2. On the use of graphics processing units (GPUs) for molecular dynamics simulation of spherical particles

    NASA Astrophysics Data System (ADS)

    Hidalgo, R. C.; Kanzaki, T.; Alonso-Marroquin, F.; Luding, S.

    2013-06-01

    General-purpose computation on Graphics Processing Units (GPU) on personal computers has recently become an attractive alternative to parallel computing on clusters and supercomputers. We present the GPU-implementation of an accurate molecular dynamics algorithm for a system of spheres. The new hybrid CPU-GPU implementation takes into account all the degrees of freedom, including the quaternion representation of 3D rotations. For additional versatility, the contact interaction between particles is defined using a force law of enhanced generality, which accounts for the elastic and dissipative interactions, and the hard-sphere interaction parameters are translated to the soft-sphere parameter set. We prove that the algorithm complies with the statistical mechanical laws by examining the homogeneous cooling of a granular gas with rotation. The results are in excellent agreement with well established mean-field theories for low-density hard sphere systems. This GPU technique dramatically reduces user waiting time, compared with a traditional CPU implementation.

  3. Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging

    SciTech Connect

    Dhas, M. Kumara; Benial, A. Milton Franklin; Jawahar, A.

    2014-04-24

    The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM {sup 14}N labeled nitroxyl radicals in pure water and 1 mM concentration of ascorbic acid as a function of time. The electron spin resonance parameters such as signal intensity ratio, line width, g-value, hyperfine coupling constant and rotational correlation time were determined. The half life time was estimated for 1mM {sup 14}N labeled nitroxyl radicals in 1 mM concentration of ascorbic acid. The ESR study reveals that the TEMPONE has narrowest line width and fast tumbling motion compared with TEMPO and TEMPOL. From the results, TEMPONE has long half life time and high stability compared with TEMPO and TEMPOL radical. Therefore, this study reveals that the TEMPONE radical can act as a good redox sensitive spin probe for molecular imaging.

  4. Molecular dynamics simulations of mixed lubrication with smooth particle post-processing.

    PubMed

    Eder, S; Vernes, A; Vorlaufer, G; Betz, G

    2011-05-01

    A post-processing method for molecular dynamics (MD) simulations of friction based on the smooth particle approach is proposed, allowing--among other features--the introduction and evaluation of a solid-solid contact area arising due to direct asperity interaction. In order to illustrate the feasibility of this scheme, a large number of MD calculations of lubricated nanotribological systems with various asperity geometries and carefully selected numbers of lubricant molecules were carried out and analysed. In this manner, it is shown that the friction force as a function of load agrees very well with a three-parameter friction law which, in addition to the adhesion- and the load-controlled terms, contains a load-independent offset. PMID:21493976

  5. MOLOCH computer code for molecular-dynamics simulation of processes in condensed matter

    NASA Astrophysics Data System (ADS)

    Sapozhnikov, F. A.; Dremov, V. V.; Ionov, G. V.; Derbenev, I. V.; Chizhkova, N. E.

    Theoretical and experimental investigation into properties of condensed matter is one of the mainstreams in RFNC-VNIITF scientific activity. The method of molecular dynamics (MD) is an innovative method of theoretical materials science. Modern supercomputers allow the direct simulation of collective effects in multibillion atom sample, making it possible to model physical processes on the atomistic level, including material response to dynamic load, radiation damage, influence of defects and alloying additions upon material mechanical properties, or aging of actinides. During past ten years, the computer code MOLOCH has been developed at RFNC-VNIITF. It is a parallel code suitable for massive parallel computing. Modern programming techniques were used to make the code almost 100% efficient. Practically all instruments required for modelling were implemented in the code: a potential builder for different materials, simulation of physical processes in arbitrary 3D geometry, and calculated data processing. A set of tests was developed to analyse algorithms efficiency. It can be used to compare codes with different MD implementation between each other.

  6. Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Cao, Haining; Srivastava, Pooja; Choi, Keunsu; Kim, Seungchul; Lee, Kwang-Ryeol

    2016-03-01

    Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

  7. Numerical simulation of binary liquid droplet collision

    NASA Astrophysics Data System (ADS)

    Pan, Yu; Suga, Kazuhiko

    2005-08-01

    A numerical investigation of binary droplet collision has been conducted. The complete process of the collision of two liquid droplets is dynamically simulated by solving the incompressible Navier-Stokes equations coupled with the convective equation of the level set function that captures the interface between the liquid and the gas phases. The simulations cover four major regimes of binary collision: bouncing, coalescence, reflexive separation, and stretching separation. For water droplets in air, the numerical results are compared with the experiments by and Ashgriz and Poo [J. Fluid Mech. 221, 183 (1990)] on collision consequences. For hydrocarbon (C14H30) droplets in nitrogen gas, the simulated results are compared in detail with the time-resolved photographic images of the collision processes obtained by Qian and Law [J. Fluid Mech. 331, 59 (1997)] in every collision regime. The present numerical results suggest that the mechanism of a bouncing collision is governed by the macroscopic dynamics. However, the fact that the present macroscopic numerical model is unable to capture the collision regime of coalescence after minor deformation supports the speculation that its mechanism is related to the microscopic dynamics. Furthermore, the transition from bouncing to coalescence collisions has been predicted and agrees well with the analytical model. The mechanism of satellite droplet formation for head-on collision and stretching separation collision is also studied based on the detailed time-resolved dynamic simulation results. It is then confirmed that end pinching is the main cause of satellite formation in head-on collisions whereas the capillary-wave instability becomes dominant in large impact parameter cases. In the case of an intermediate impact parameter, the effects of twisting and stretching due to the angular momentum and the inertia of the colliding droplets are significant for the satellite formation.

  8. Experimental and ab initio studies of the reactive processes in gas phase i-C3H7Br and i-C3H7OH collisions with potassium ions

    NASA Astrophysics Data System (ADS)

    López, E.; Lucas, J. M.; de Andrés, J.; Albertí, M.; Bofill, J. M.; Bassi, D.; Aguilar, A.

    2014-10-01

    Collisions between potassium ions and neutral i-C3H7Br and i-C3H7OH, all in their electronic ground state, have been studied in the 0.10-10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K+ + i-C3H7Br collisions KHBr+ formation was observed and quantified, while the analogous KH2O+ formation in K+ + i-C3H7OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C3H7+ and either KBr or KOH, respectively, have been observed. For all these processes, absolute cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr+ formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.

  9. Angular distribution of low-energy electron emission in collisions of 6-MeV/u bare carbon ions with molecular hydrogen: Two-center mechanism and interference effect

    SciTech Connect

    Misra, Deepankar; Kelkar, A.; Kadhane, U.; Kumar, Ajay; Singh, Y. P.; Tribedi, Lokesh C.; Fainstein, P. D.

    2007-05-15

    We report the energy and angular distribution of electron double differential cross sections (DDCS) in collision of 6-MeV/u C{sup 6+} ions with molecular hydrogen. We explain the observed distributions in terms of the two-center effect and the Young-type interference effect. The secondary electrons having energies between 1 and 1000 eV are detected at about 10 different emission angles between 30 degree sign and 150 degree sign . The measured data are compared with the state-of-the-art continuum distorted wave-eikonal initial state and the first Born model calculations which use molecular wave function. The single differential cross sections are derived and compared with the theoretical predictions. The oscillations due to the interference effect are derived in the DDCS ratios using theoretical cross sections for the atomic H target. The effect of the atomic parameters on the observed oscillations is discussed. An evidence of interference effect has also been shown in the single differential cross section. The electron energy dependence of the forward-backward asymmetry parameter shows a monotonically increasing behavior for an atomic target, such as He, which could be explained in terms of the two-center effect only. In contrast, for the molecular H{sub 2} the asymmetry parameter reveals an oscillatory behavior due to the Young-type interference effect superimposed with the two-center effect. The asymmetry parameter technique provides a self-normalized method to reveal the interference oscillation which does not require either a theoretical model or complementary measurements on the atomic H target.

  10. A novel "correlated ion and neutral time of flight" method: Event-by-event detection of neutral and charged fragments in collision induced dissociation of mass selected ions

    NASA Astrophysics Data System (ADS)

    Teyssier, C.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Märk, T. D.

    2014-01-01

    A new tandem mass spectrometry (MS/MS) method based on time of flight measurements performed on an event-by-event detection technique is presented. This "correlated ion and neutral time of flight" method allows to explore Collision Induced Dissociation (CID) fragmentation processes by directly identifying not only all ions and neutral fragments produced but also their arrival time correlations within each single fragmentation event from a dissociating molecular ion. This constitutes a new step in the characterization of molecular ions. The method will be illustrated here for a prototypical case involving CID of protonated water clusters H+(H2O)n = 1-5 upon collisions with argon atoms.

  11. Collision Broadening Of Line Spectrum In Sonoluminescence

    SciTech Connect

    Li Chaohui; An Yu

    2008-06-24

    The direct measurement of temperature inside a sonoluminescing bubble as it is at its flashing phase is almost impossible due to the smallness of the bubble and the short duration of the flashing. One may estimate the temperature through fitting the continuum spectrum of sonoluminescence by the black body radiation formula, or fitting the shape of atomic or molecular line spectrum (the different temperature, density and pressure result in the different shape of the line spectrum due to the effect of collision broadening). However, the temperature changes in a huge range at short duration as the bubble flashes, therefore, the observed spectra are some kind of average one, so are those fitted results. To evaluate the instantaneous temperature more accurately, we simulate the processes of the bubble motion and the thermodynamics inside the bubble, in which atomic or molecular line spectra with the collision broadening effect and the continuum spectra contributed from the processes of electron-atom bremsstrahlung, electron-ion bremsstrahlung and recombination radiation and radiative attachment of electrons to atoms and molecules are taken into account in calculating the light emission. If both the calculated continuum spectra and the shape of line spectra can well represent the experimental data, we may deduce that the calculation of the temperature, density and pressure is reliable and we indirectly evaluate those quantities inside the bubble. In the present calculation, the line spectra of OH radical at about 310 nm mixing the electron transition with the vibration and rotational bands are considered. The calculation qualitatively consists with the observation, and we expect that with the more precise bubble dynamics model instead of the uniform model employed in the present calculation we may improve the quantitative result.

  12. Sonofragmentation of molecular crystals.

    PubMed

    Zeiger, Brad W; Suslick, Kenneth S

    2011-09-21

    Possible mechanisms for the breakage of molecular crystals under high-intensity ultrasound were investigated using acetylsalicylic acid (aspirin) crystals as a model compound for active pharmaceutical ingredients. Surprisingly, kinetics experiments ruled out particle-particle collisions as a viable mechanism for sonofragmentation. Two other possible mechanisms (particle-horn and particle-wall collisions) were dismissed on the basis of decoupling experiments. Direct particle-shock wave interactions are therefore indicated as the primary mechanism of sonofragmentation of molecular crystals. PMID:21863903

  13. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    NASA Astrophysics Data System (ADS)

    McGuire, S.; Miles, R.

    2014-12-01

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a1?g ? X 1 ?g + electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a ? 1 ?g + electronic state.

  14. Ternary drop collisions

    NASA Astrophysics Data System (ADS)

    Hinterbichler, Hannes; Planchette, Carole; Brenn, Günter

    2015-10-01

    It has been recently proposed to use drop collisions for producing advanced particles or well-defined capsules, or to perform chemical reactions where the merged drops constitute a micro-reactor. For all these promising applications, it is essential to determine whether the merged drops remain stable after the collision, forming a single entity, or if they break up. This topic, widely investigated for binary drop collisions of miscible and immiscible liquid, is quite unexplored for ternary drop collisions. The current study aims to close this gap by experimentally investigating collisions between three equal-sized drops of the same liquid arranged centri-symmetrically. Three drop generators are simultaneously operated to obtain controlled ternary drop collisions. The collision outcomes are observed via photographs and compared to those of binary collisions. Similar to binary collisions, a regime map is built, showing coalescence and bouncing as well as reflexive and stretching separation. Significant differences are observed in the transitions between these regimes.

  15. Calculation of the Trubnikov and Nanbu Collision Kernels: Implications for Numerical Modeling of Coulomb Collisions

    SciTech Connect

    Dimits, A M; Wang, C; Caflisch, R; Cohen, B I; Huang, Y

    2008-08-06

    We investigate the accuracy of and assumptions underlying the numerical binary Monte-Carlo collision operator due to Nanbu [K. Nanbu, Phys. Rev. E 55 (1997)]. The numerical experiments that resulted in the parameterization of the collision kernel used in Nanbu's operator are argued to be an approximate realization of the Coulomb-Lorentz pitch-angle scattering process, for which an analytical solution for the collision kernel is available. It is demonstrated empirically that Nanbu's collision operator quite accurately recovers the effects of Coulomb-Lorentz pitch-angle collisions, or processes that approximate these (such interspecies Coulomb collisions with very small mass ratio) even for very large values of the collisional time step. An investigation of the analytical solution shows that Nanbu's parameterized kernel is highly accurate for small values of the normalized collision time step, but loses some of its accuracy for larger values of the time step. Careful numerical and analytical investigations are presented, which show that the time dependence of the relaxation of a temperature anisotropy by Coulomb-Lorentz collisions has a richer structure than previously thought, and is not accurately represented by an exponential decay with a single decay rate. Finally, a practical collision algorithm is proposed that for small-mass-ratio interspecies Coulomb collisions improves on the accuracy of Nanbu's algorithm.

  16. The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms

    PubMed Central

    de Storme, Nico; Geelen, Danny

    2014-01-01

    In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

  17. Information processing in parallel through directionally resolved molecular polarization components in coherent multidimensional spectroscopy.

    PubMed

    Yan, Tian-Min; Fresch, Barbara; Levine, R D; Remacle, F

    2015-08-14

    We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, kl, kl=∑iliki where ki is the propagation direction of the ith pulse and {li} is a set of integers that encodes the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, which are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by nonlinear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible. PMID:26277126

  18. Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship

    SciTech Connect

    Giannone, Richard J; Huber, Dr. Harald; Karpinets, Tatiana V; Heimerl, Dr. Thomas; Kueper, Dr. Ulf; Rachel, Dr. Reinhard; Keller, Martin; Hettich, Robert {Bob} L; Podar, Mircea

    2011-01-01

    Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis.

  19. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect

    Welch, Gregory C.; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-07-22

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  20. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico.

    PubMed

    Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Sifuentes-Romero, Itzel; Yepiz-Plascencia, Gloria; Gomez-Gil, Bruno; Noriega-Orozco, Lorena

    2016-01-01

    Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution. PMID:26730584

  1. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

    PubMed Central

    Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

  2. Solution processable small molecular host materials for blue and white phosphorescence OLEDs

    NASA Astrophysics Data System (ADS)

    Lee, Yi-Ting; Chang, Yung-Ting; Chen, Chin-Ti; Chen, Chao-Tsen

    2013-09-01

    Three new solution processable small molecular host materials based on bis-[3,5-di(9H-carbazol-9-yl)phenyl] structural moiety have been developed for blue phosphorescence (FIrpic dopant) organic light-emitting diodes. Whereas N,N-bis-[3,5-di(9H-carbazol-9-yl)phenyl]methylamine (CzPAMe) has the highest solid state triplet energy gap (ET) of 2.73 eV, tetrakis-[3,3',5,5'-(9H-carbazol-9-yl)]triphenylphosphine oxide (CzPPO) and N,N-bis-[3,5-di(9H-carbazol-9-yl)phenyl]pyrimidin-2-amine (CzPAPm) are two host materials potentially being bipolar for charge transport due to the electron deficient unit of phenylphosphine oxide and pyrimidine, respectively. Due to the insufficient ET (2.56 eV) of CzPAPm, CzPPO or CzPAMe devices are significantly better than CzPAPm devices with or without 1,3-bis[(4-tert-butylphenyl)-1,3,4-oxadiazolyl]phenylene (OXD-7) co-host. Particularly, having no OXD-7 co-host and no vacuum-thermal-deposited extra electron transporting layer, single-layer devices of CzPPO surpassing CzPAMe devices reach current efficiency as high as 9.32 cd/A (or power efficiency of 4.97 lm/W), which is one of the highest of the kind. Corresponding single-layer white phosphorescence OLEDs are also fabricated with the small molecular host material demonstrated herein.

  3. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming.

    PubMed

    Levine, Benjamin G; Stone, John E; Kohlmeyer, Axel

    2011-05-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

  4. Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    SciTech Connect

    Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel

    2011-05-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

  5. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico

    PubMed Central

    Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Sifuentes-Romero, Itzel; Yepiz-Plascencia, Gloria; Gomez-Gil, Bruno; Noriega-Orozco, Lorena

    2016-01-01

    Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution. PMID:26730584

  6. Fast analysis of molecular dynamics trajectories with graphics processing units—Radial distribution function histogramming

    NASA Astrophysics Data System (ADS)

    Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel

    2011-05-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

  7. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. PMID:15218250

  8. Introduction to the study of collisions between heavy nuclei

    SciTech Connect

    Bayman, B.F.

    1980-01-01

    Current investigations concerning the collisions of nuclei governed by small de Broglie wavelengths are reviewed. The wave packets localize nuclei in regions small compared to their diameters. Cross sections are examined for potential scattering, elastic scattering, quasi-molecular states, peripheral particle-transfer reactions, fusion, and deep inelastic collisions. Theories of fusion and deep inelastic collisions are summarized. This paper is in the nature of a review-tutorial. 45 references, 51 figures, 2 tables. (RWR)

  9. Conformation and orientation dependence in ion-induced collisions with DNA and RNA building blocks

    NASA Astrophysics Data System (ADS)

    Bacchus-Montabonel, Marie-Christine

    2015-04-01

    Action of radiations on biological tissues is of major concern in cancer therapy development. Understanding the mechanisms involved at the molecular level in such reactions may be of crucial interest. In particular ion-induced ionization processes appear at the early stage of damage and a detailed analysis has been performed on the charge transfer dynamics of carbon ions with the different DNA and RNA building blocks in order to analyze their respective behavior in ion-induced collisions. We have considered the pyrimidine nucleobases uracil and thymine and the 5-halouracil molecules corresponding to the same skeleton, as well as the sugar moiety 2-deoxy-D-ribose. The calculations have been performed by means of ab initio quantum chemistry molecular methods followed by a semi-classical collision treatment in a wide collision energy range. Considerations of the structure of the biological target as well as analysis of the anisotropy of the process have been performed. The comparison with proton collisions has been developed with regard to previous results. Qualitative trends of interest for DNA building blocks damage may be pointed out.

  10. Molecular characterization of activated sludge from a seawater?processing wastewater treatment plant

    PubMed Central

    Snchez, Olga; Garrido, Laura; Forn, Irene; Massana, Ramon; Maldonado, Manuel Ignacio; Mas, Jordi

    2011-01-01

    Summary The prokaryotic community composition of activated sludge from a seawater?processing wastewater treatment plant (Almeria, Spain) was investigated by using the rRNA approach, combining different molecular techniques such as denaturing gradient gel electrophoresis (DGGE), clone libraries and in situ hybridization (FISH and CARD?FISH). Most of the sequences retrieved in the DGGE and the clone libraries were similar to uncultured members of different phyla. The most abundant sequence recovered from Bacteria in the clone library corresponded to a bacterium from the DeinococcusThermus cluster (almost 77% of the clones), and the library included members from other groups such as the Alpha, Gamma and Delta subclasses of Proteobacteria, the Bacteroidetes and Firmicutes. Concerning the archaeal clone library, we basically found sequences related to different orders of methanogenic Archaea, in correspondence with the recovered DGGE bands. Enumeration of DAPI (4?,6?diamidino?2?phenylindole) stained cells from two different activated sludge samples after a mechanical flocculation disruption revealed a mean cell count of 1.6??109?ml?1. Around 94% of DAPI counts (mean value from both samples) hybridized with a Bacteria specific probe. Alphaproteobacteria were the dominant bacterial group (36% of DAPI counts), while Beta?, Delta? and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes contributed to lower proportions (between 0.55.7% of DAPI counts). Archaea accounted only for 6% of DAPI counts. In addition, specific primers for amplification of the amoA (ammonia monooxygenase) gene were used to detect the presence of Beta, Gamma and archaeal nitrifiers, yielding positive amplifications only for Betaproteobacteria. This, together with negative in situ hybridizations with probes for well?known nitrifiying bacteria, suggests that nitrification is performed by still undetected microorganisms. In summary, the combination of the three approaches provided different and complementary pictures of the real assemblage composition and allowed to get closer to the main microorganisms involved in key processes of seawater?processing activated sludge. PMID:21414181

  11. Low Energy Electron Molecule Collisions

    NASA Astrophysics Data System (ADS)

    Buckman, Stephen

    2007-06-01

    Low energy electron molecule collisions are important in many technological, environmental and biological processes. Electrons are known to be the `drivers' of technological processes based around gas discharges, from lights and lamps to surface processing plasmas. In such environments electrons are responsible for much of the vibrational and electronic excitation that results in photon emissions, for the formation of long-lived metastable species, and for the production of highly reactive free radicals through processes such as dissociative attachment. Electron collisions also play an important role in our atmosphere and those of all planets and stars. In recent years low energy electrons have also been shown to play a vital role in cell and tissue damage caused by ionizing radiation. One of the key goals for collision physics, both experiment and theory, is to provide accurate, absolute cross sections for such low energy charged particle collisions - elastic scattering, vibrational excitation, near-threshold electronic excitation. This talk will focus on some recent advances in these areas. This work is done in collaboration with James Sullivan, Violaine Vizcaino, Stan Newman, Julian Lower, Subhendu Mondal, Chris Colyer, Michael Brunger, Todd Maddern and Leigh Hargreaves.

  12. The problems of solar-terrestrial coupling and new processes introduced to the physics of the ionosphere from the physics of atomic collisions

    NASA Astrophysics Data System (ADS)

    Avakyan, Sergei

    2010-05-01

    Further progress in research of solar-terrestrial coupling requires better understanding of solar variability influence on the ionosphere. The most powerful manifestations of solar variability are solar flares and geomagnetic storms. During a flare EUV/X-ray irradiations are completely absorbed in the ionosphere producing SID. During geomagnetic storms precipitations of electrons with energy of several keV (and to a lesser extent protons precipitations) from radiation belts and geomagnetosphere produce additional ionization and low latitude auroras. Considering the physics of ionosphere during the last several decades we have been taking into account three novel processes well known in the physics of atomic collisions. These are Auger effect [S. V. Avakyan, The consideration of Auger processes in the upper atmosphere of Earth. In Abstracts of paper presented at the Tenth scien. and techn. Conf. of young specialists of S.I. Vavilov State Optical Institute, 1974, 29-31.], multiple photoionization of upper, valence shell [S.V. Avakyan, The source of O++ ions in the upper atmosphere, 1979, Cosmic Res, 17, 942 - 943] and Rydberg excitation of all the components of upper atmosphere [S.V. Avakyan, The new factor in the physics of solar - terrestrial relations - Rydberg atomic and molecules states. Conf. on Physics of solar-terrestrial relationships, 1994, Almaty, 3 - 5]. In the present paper the results of bringing these new processes in the ionospheric physics are discussed and also its possible role in the physics of solar-terrestrial coupling is considered. Involving these processes to the model estimations allowed us for the first time to come to the following important conclusions: - Auger electrons play the determinant role at the formation of energy spectrum of photoelectrons and secondary auroral electrons at the range above 150 eV; - double photoionization of the outer shell of the oxygen atom (by a single photon) plays a dominant role in the formation of ionospheric doubly charged positive ions, and Auger effect mainly determines the formation of double- and triple charged ions in the low ionosphere of planets and also comets; - transitions in the Rydberg excited ionospheric atoms and molecules play the main role in generation of new type of upper atmospheric emission - microwave characteristic radiation. The ionospheric O++ ions fill the magnetosphere after geomagnetic storms. These ions scatter the solar radiation in one of the most intense lines with a wavelength of 30.4 nm (He+) and also in the 50.7-, 70.3-, 83.3-83.5-nm lines in geocorona to the nocturnal side, giving rise to additional ionization and optical excitation in the F-region. The first calculations of the excitation rate of Rydberg states by photoelectrons and by auroral electrons (including Auger electrons) were carried out. It was shown that such process can generate the microwave ionospheric radioemission. Such emissions were observed during solar flares and in auroras. We suggest that Rydberg microwave radioemissions which take place during ionospheric disturbances produced by the solar flares and geomagnetic storms can be considered as an agent of influence of solar-geomagnetic activity on the biosphere and also as a factor of Sun-weather-climate links All these results obtained experimental confirmation in space investigations and in some ground-based measurements carried out with radiophysical and optical methods. The new processes which we introduced to the physics of upper atmosphere and ionosphere are now widely used in the ionospheric science for interpretation of spacecraft measurement data (the spacecrafts ISIS, GEOS-1, IMAGE, the satellites DE-1,-B, EXOS-D (AKEBOHO), FAST, Intercosmos-19, -24, -25, the orbital stations "Salut", "Mir"). There is a Russian patent on the method of remote registration of radioactive atmospheric clouds and nuclear weapon tests over the atmosphere by means of optical fluorescence which is based on Auger processes.

  13. Aggregation effects in proton collisions with water dimers

    NASA Astrophysics Data System (ADS)

    Ravazzani, A.; Errea, L. F.; Méndez, L.; Rabadán, I.

    2012-07-01

    Charge transfer cross sections in proton collisions with water dimers are calculated using an ab initio method based on molecular orbitals of the system. Results are compared with their counterpart in proton-water collisions to gauge the importance of intermolecular interactions in the cross sections.

  14. Molecular mechanism of the inhibition effect of Lipoxin A4 on corneal dissolving pathology process

    PubMed Central

    Zhou, Hong-Yan; Hao, Ji-Long; Bi, Miao-Miao; Wang, Shuang; Zhang, Hong; Zhang, Wen-Song

    2013-01-01

    AIM Excessive dissolve of corneal tissue induced by MMPs which were activated by cytokins and chemokines will lead to corneal ulcer. The molecular mechanism of Lipoxin A4 (LXA4) on corneal collagen degradation in three dimensions was investigated. METHODS Rabbit corneal fibroblasts were harvested and suspended in serum-free MEM. Type I collagen, DMEM, collagen reconstitution buffer and corneal fibroblast suspension were mixed on ice. The resultant mixture solidified in an incubator, after which test reagents and plasminogen was overlaid and the cultures were returned to the incubator. The supernatants from collagen gel incubations were collected and the amount of hydroxyproline in the hydrolysate was measured. Immunoblot analysis of MMP-1, -3 and TMMP-1,-2 was performed. MMP-2,-9 was detected by the method of Gelatin zymography. Cytotoxicity assay was measured. RESULTS LXA4 inhibited corneal collagen degradation in a dose and time manner. LXA4 inhibited the IL-1β induced increases in the pro-MMP-1, -2, -3, -9 and active MMP-1, -2, -3, -9 in a concentration dependent manner. LXA4 could also inhibit the IL-1β induced increases in TIMP-1, -2. CONCLUSION As a potent anti-inflammation reagent, LXA4 can inhibit corneal collagen degradation induced by IL-1β in corneal fibroblasts thus inhibiting corneal dissolving pathology process. PMID:23550231

  15. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

    PubMed

    Quesne, Matthew G; Borowski, Tomasz; de Visser, Sam P

    2016-02-01

    Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations. PMID:26696271

  16. Molecular Insights into Plant-Microbial Processes and Carbon Storage in Mangrove Ecosystems

    NASA Astrophysics Data System (ADS)

    Romero, I. C.; Ziegler, S. E.; Fogel, M.; Jacobson, M.; Fuhrman, J. A.; Capone, D. G.

    2009-12-01

    Mangrove forests, in tropical and subtropical coastal zones, are among the most productive ecosystems, representing a significant global carbon sink. We report new molecular insights into the functional relationship among microorganisms, mangrove trees and sediment geochemistry. The interactions among these elements were studied in peat-based mangrove sediments (Twin Cays, Belize) subjected to a long-term fertilization experiment with N and P, providing an analog for eutrophication. The composition and δ13C of bacterial PLFA showed that bacteria and mangrove trees had similar nutrient limitation patterns (N in the fringe mangrove zone, P in the interior zone), and that fertilization with N or P can affect bacterial metabolic processes and bacterial carbon uptake (from diverse mangrove sources including leaf litter, live and dead roots). PCR amplified nifH genes showed a high diversity (26% nifH novel clones) and a remarkable spatial and temporal variability in N-fixing microbial populations in the rhizosphere, varying primarily with the abundance of dead roots, PO4-3 and H2S concentrations in natural and fertilized environments. Our results indicate that eutrophication of mangrove ecosystems has the potential to alter microbial organic matter remineralization and carbon release with important implications for the coastal carbon budget. In addition, we will present preliminary data from a new study exploring the modern calibration of carbon and hydrogen isotopes of plant leaf waxes as a proxy recorder of past environmental change in mangrove ecosystems.

  17. Formation of giant crystalline grain via delayed growth process driven by organic molecular anisotropy

    NASA Astrophysics Data System (ADS)

    Al-Mahboob, A.; Fujikawa, Y.; Sadowski, J. T.; Hashizume, T.; Sakurai, T.

    2010-12-01

    The growth of (001)-oriented pentacene ( C22H14 , Pn) thin films on silicon surfaces has been extensively studied to elucidate the role of molecular anisotropy in nucleation and island evolution in organic film growth. In situ real-time low-energy electron microscopy studies of growth of Pn revealed a delayed, low-density nucleation that could be related to the difference in the orientation of this anisotropic molecule in its diffusing state and in the crystalline film. In contrast to the growth of Pn on self-assembled monolayers or SiO2 , we observed a delayed nucleation and formation of extraordinarily large grains (in submillimeter scale) on semiconducting α3-Bi-Si(111) and on semimetallic Bi(0001)/Si(111) with a continuation in film growth after stopping Pn deposition. The delayed and very low-density nucleation and continuing growth after stopping deposition could be explained by a incorporation-limited growth processes resulted from a large energy barrier for Pn nucleation in standing-up orientation, as the molecule needs to reorient itself from a lying-down, diffusing state in order to build into the crystalline film.

  18. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    SciTech Connect

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-07

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  19. Information processing in parallel through directionally resolved molecular polarization components in coherent multidimensional spectroscopy

    NASA Astrophysics Data System (ADS)

    Yan, Tian-Min; Fresch, Barbara; Levine, R. D.; Remacle, F.

    2015-08-01

    We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, kl, k l = ∑ i l i k i where ki is the propagation direction of the ith pulse and {li} is a set of integers that encodes the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, which are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by nonlinear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible.

  20. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    NASA Astrophysics Data System (ADS)

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  1. Molecular Mechanisms Mediating the Adaptive Regulation of Intestinal Riboflavin Uptake Process

    PubMed Central

    Subramanian, Veedamali S.; Ghosal, Abhisek; Kapadia, Rubina; Nabokina, Svetlana M.; Said, Hamid M.

    2015-01-01

    The intestinal absorption process of vitamin B2 (riboflavin, RF) is carrier-mediated, and all three known human RF transporters, i.e., hRFVT-1, -2, and -3 (products of the SLC52A1, 2 & 3 genes, respectively) are expressed in the gut. We have previously shown that the intestinal RF uptake process is adaptively regulated by substrate level, but little is known about the molecular mechanism(s) involved. Using human intestinal epithelial NCM460 cells maintained under RF deficient and over-supplemented (OS) conditions, we now show that the induction in RF uptake in RF deficiency is associated with an increase in expression of the hRFVT-2 & -3 (but not hRFVT-1) at the protein and mRNA levels. Focusing on hRFVT-3, the predominant transporter in the intestine, we also observed an increase in the level of expression of its hnRNA and activity of its promoter in the RF deficiency state. An increase in the level of expression of the nuclear factor Sp1 (which is important for activity of the SLC52A3 promoter) was observed in RF deficiency, while mutating the Sp1/GC site in the SLC52A3 promoter drastically decreased the level of induction in SLC52A3 promoter activity in RF deficiency. We also observed specific epigenetic changes in the SLC52A3 promoter in RF deficiency. Finally, an increase in hRFVT-3 protein expression at the cell surface was observed in RF deficiency. Results of these investigations show, for the first time, that transcriptional and post-transcriptional mechanisms are involved in the adaptive regulation of intestinal RF uptake by the prevailing substrate level. PMID:26121134

  2. Combined papillary and mucoepidermoid carcinoma of the thyroid gland: a possible collision tumor diagnosed on fine-needle cytology. Report of a case with immunocytochemical and molecular correlations.

    PubMed

    Fulciniti, Franco; Vuttariello, Emilia; Calise, Celeste; Monaco, Mario; Pezzullo, Luciano; Chiofalo, Maria Grazia; Di Gennaro, Francesca; Malzone, Maria Gabriella; Campanile, Anna Cipolletta; Losito, Nunzia Simona; Botti, Gerardo; Chiappetta, Gennaro

    2015-05-01

    Fine-needle cytology (FNC) is frequently used to diagnose thyroid nodules discovered by palpation or imaging studies. Molecular tests on FNC material may increase its diagnostic accuracy. We report a case of a classic papillary thyroid carcinoma combined with a mucoepidermoid carcinoma correctly identified on FNC. The papillary component had a classic immunophenotype (CK19+, TTF1+), while the mucoepidermoid one was only focally CK19+. Point mutations (BRAF and RAS) and rearrangements (RET/PTC) of the papillary component have been also investigated on FNC samples, with resulting concurrent rearrangements of RET/PTC1 and RET/PTC3, but no point mutations. The histogenesis of combined papillary and mucoepidermoid carcinoma of the thyroid still remains partly unsettled, and further genomic studies are needed to shed some more light on this peculiar neoplasm. PMID:25771987

  3. (Relativistic heavy ion collisions)

    SciTech Connect

    Hwa, R.C.

    1992-02-01

    This report discusses the following topics: large transverse momentum hadrons in heavy ion collisions at LHC; ECCO -- event generator for soft production in pp collisions; proton-nucleus and nucleus-nucleus collisions; fractal behavior of multiplicity fluctuations; and quark-hadron phase transition. (LSP)

  4. Ab initio study of charge-transfer dynamics in collisions of C{sup 2+} ions with hydrogen chloride

    SciTech Connect

    Rozsalyi, E.; Vibok, A.; Bene, E.; Halasz, G. J.; Bacchus-Montabonel, M. C.

    2011-05-15

    Ab initio quantum chemistry molecular calculations followed by a semiclassical dynamical treatment in the keV collision energy range have been developed for the study of the charge-transfer process in collisions of C{sup 2+} ions with hydrogen chloride. The mechanism has been investigated in detail in connection with avoided crossings between states involved in the reaction. A simple mechanism driven by a strong nonadiabatic coupling matrix element has been pointed out for this process. A comparative analysis with the halogen fluoride target corresponding to a similar electronic configuration shows a quite different charge-transfer mechanism leading to a very different behavior of the cross sections. Such behavior may be correlated to specific nonadiabatic interactions observed in these collision systems.

  5. Single charge exchange in collision of fast protons with hydrogen molecules

    NASA Astrophysics Data System (ADS)

    Ghanbari-Adivi, Ebrahim; Sattarpour, Seyedeh Hedyeh

    2015-11-01

    Single charge transfer process in collision of energetic protons with molecular hydrogens is theoretically studied using a first-order two-effective-center Born approximation. The correct boundary conditions are incorporated in the formalism and the Hartree-Fock molecular wave function for molecular targets and the residual ions are used to calculate the transition amplitude. The interference patterns in the capture differential cross-sections (DCSs) for a given fixed orientation of the molecule, due to the scattering from the two-atomic centers in the molecular targets, are examined. The dependence of the DCSs upon the angle between the molecular axis and the direction of the incident velocity is theoretically investigated. Both average differential and integral cross-sections are calculated. The obtained results are compared with the available experimental data.

  6. Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise

    ERIC Educational Resources Information Center

    Lents, Nathan H.; Cifuentes, Oscar E.; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from "Homo sapiens" and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these…

  7. Decision Processes During Development of Molecular Biomarkers for Gonadal Phenotypic Sex

    EPA Science Inventory

    Molecular biomarkers for determination of gonadal phenotypic sex in the Japanese medaka (Oryzias latipes), will serve as a case study. The medaka has unique features that aid in the development of appropriate molecular biomarkers of gonad phenotype, a) genetic sex can be determin...

  8. Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise

    ERIC Educational Resources Information Center

    Lents, Nathan H.; Cifuentes, Oscar E.; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from "Homo sapiens" and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these

  9. H theorem for many body collisions

    NASA Astrophysics Data System (ADS)

    Agbormbai, A. A.

    2001-08-01

    Although rarefied gas dynamics has traditionally stood on the dilute gas assumption, which supposes that the densities are so low that only binary collisions and single-body gas surface interactions occur, expressions for many-body collision rates and for many-body gas surface interaction (GSI) rates seem to suggest that at lower heights the dilute gas assumption is not valid. In particular, in the pure rarefied regime, two-body GSIs and some three-body interactions occur whereas, in the transition regime into continuum flow, four body collisions and four-body GSIs occur. In this paper I formulate an H theorem for many-body collisions involving atoms. This exercise constitutes the final stage of constructing reciprocity proofs for many body collisions. The first two stages were pursued during the formulation of the many body collision models. They involved demonstrating that reciprocity models for monatomic many-body collisions satisfy detailed balance at equilibrium as well as symmetry with respect to the forward and inverse processes. I begin by deriving the Boltzmann equation for monatomic gases undergoing many body collisions. This leads to the formulation of an elastic collision integral. All these descriptions are carried out in the single-particle phase space of the gas. I formulate the properties of the elastic collision integral and then I use these to formulate an H theorem for reciprocity-based many body collisions. Equilibrium distributions are derived from the approach. An H theorem proof for reciprocity models demonstrates that these models will drive a gas towards equilibrium when used in DSMC computations.

  10. Molecular dynamics investigation of the adhesion mechanism acting between dopamine and the surface of dopamine-processed aramid fibers.

    PubMed

    Chai, Dongliang; Xie, Zhimin; Wang, Youshan; Liu, Li; Yum, Young-Jin

    2014-10-22

    Dopamine, as a universal material for surface treatment, can effectively improve the surface performance of aramid fibers. However, directly processing the surface of aramid fibers using dopamine currently incurs a high cost. To seek dopamine substitutes, one must first explore the adhesion mechanism responsible for binding the dopamine to the surface of the fiber. In this study, we construct an all-atomic molecular dynamics model of an aramid fiber before and after surface modification using dopamine. A force field based on condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) is used. Using it, we analyze the surface adhesion mechanism of polydopamines aggregated by 21 kinds of molecular structures typically found on the surface of aramid fibers. The results show that a clear and smooth interface is formed between the polydopamine nanofilm layer and the surface of the aramid fiber. The high atomic density of the polydopamine in the small interface region is found to be conducive to noncovalent bonds of polydopamines with the surface of the aramid fiber. In addition, we investigate the works of adhesion of the 21 molecular structures typically found on the surface of aramid fibers. The results suggest that the work of adhesion of 5,6-indolequinone is the highest, followed by annular eumelanin molecules with annular planar structure. Straight-chain shaped dimers proved to be the molecules with the highest adhesion ability of the dihydroxyindole chain oligomers. Therefore, there is reason to suppose that more molecular structures (as above) can be formed by processing the surface of aramid fibers using dopamine by controlling the processing conditions. These molecular structures help improve the adhesion ability of the dopamine on the surface of the aramid fiber. Additionally, if these polydopamine molecules with high adhesion ability can be synthesized on a large scale, then new surface-processing materials are possible. PMID:25275919

  11. Annihilation of nematic point defects: pre-collision and post-collision evolution.

    PubMed

    Svetec, M; Kralj, S; Bradac, Z; Zumer, S

    2006-05-01

    The annihilation of the nematic hedgehog and anti-hedgehog within an infinite cylinder of radius R is studied. The semi-microscopic lattice-type model and Brownian molecular dynamics are used. We distinguish among the i) early pre-collision, ii) late pre-collision, iii) early post-collision, and iv) late post-collision stages. In the pre-collision stage our results agree qualitatively with the existing experimental observations and also continuum-type simulations. The core of each defect exhibits a ring-like structure, where the ring axis is set perpendicular to the cylinder symmetry axis. For xi(0)d/(2R) > 1 the interaction between defects is negligible, where xi(0)d describes the initial separation of defects. Consequently, the defects annihilate within the simulation time window for xi(0)d/(2R) < 1. For close enough defects their separation scales as xi(d) [see text] (t(c)- t)(0.4+/-0.1), where t(c) stands for the collision time. In elastically anisotropic medium the hedgehog is faster than the anti-hedgehog. In the early pre-collision stage the defects can be treated as point-like particles, possessing inherent core structure, that interact via the nematic director field. In the late pre-collision stage the cores reflect the interaction between defects. After the collision a charge-less ring structure is first formed. In the early post-collision stage the ring adopts an essentially untwisted circular structure of the radius xi(r). In the late post-collision stage we observe two qualitatively different scenarios. For mu = xi(r)/R < mu(c) approximately 0.25 the ring collapses leading to the escaped radial equilibrium structure. For mu > mu(c) the chargeless ring triggers the nucleation growth into the planar polar structure with line defects. PMID:16733641

  12. A model for energy transfer in collisions of atoms with highly excited molecules.

    PubMed

    Houston, Paul L; Conte, Riccardo; Bowman, Joel M

    2015-05-21

    A model for energy transfer in the collision between an atom and a highly excited target molecule has been developed on the basis of classical mechanics and turning point analysis. The predictions of the model have been tested against the results of trajectory calculations for collisions of five different target molecules with argon or helium under a variety of temperatures, collision energies, and initial rotational levels. The model predicts selected moments of the joint probability distribution, P(Jf,ΔE) with an R(2) ≈ 0.90. The calculation is efficient, in most cases taking less than one CPU-hour. The model provides several insights into the energy transfer process. The joint probability distribution is strongly dependent on rotational energy transfer and conservation laws and less dependent on vibrational energy transfer. There are two mechanisms for rotational excitation, one due to motion normal to the intermolecular potential and one due to motion tangential to it and perpendicular to the line of centers. Energy transfer is found to depend strongly on the intermolecular potential and only weakly on the intramolecular potential. Highly efficient collisions are a natural consequence of the energy transfer and arise due to collisions at "sweet spots" in the space of impact parameter and molecular orientation. PMID:25907301

  13. Antimicrobial resistance profiling and molecular subtyping of Campylobacter spp. from processed turkey

    PubMed Central

    2009-01-01

    Background Campylobacter is a major cause of human disease worldwide and poultry are identified as a significant source of this pathogen. Most disease in humans is associated with the consumption of contaminated poultry or cross-contamination with other foods. The primary drugs of choice for treatment of human campylobacteriosis include erythromycin and ciprofloxacin. In this study, we investigated the prevalence of resistance to erythromycin and ciprofloxacin in Campylobacter isolates recovered from turkey carcasses at two processing plants in the Upper Midwest US. Further analysis of a subset of isolates was carried out to assess resistance and genotype profiles. Results Campylobacter isolates from plant A (n = 439; including 196 C. coli and 217 C. jejuni) and plant B (n = 362, including 281 C. coli and 62 C. jejuni) were tested for susceptibility to ciprofloxacin and erythromycin using agar dilution. C. coli were more frequently resistant than C. jejuni in both plants, including resistance to ciprofloxacin (28% of C. jejuni and 63% of C. coli, plant B; and 11% of C. coli, plant A). Erythromycin resistance was low among C. jejuni (0% plant A and 0.3% plant B) compared to C. coli (41%, plant A and 17%, plant B). One hundred resistant and susceptible isolates were selected for additional antimicrobial susceptibility testing, restriction fragment length polymorphism analysis of the flaA gene (fla typing), and pulsed-field gel electrophoresis (PFGE). Fla-PFGE types obtained (n = 37) were associated with a specific plant with the exception of one type that was isolated from both plants. C. coli isolates (n = 65) were grouped into 20 types, while C. jejuni isolates (n = 35) were grouped into 17 types. Most isolates with identical fla-PFGE patterns shared identical or very similar antimicrobial resistance profiles. PFGE alone and composite analysis using fla-PFGE with resistance profiles separated C. jejuni and C. coli into distinct groups. Conclusion Ciprofloxacin and erythromycin resistance in Campylobacter recovered from processed turkey occurred more frequently among C. coli than C. jejuni. Fla-PFGE types were associated with a particular species, antimicrobial resistance profiles, and a specific plant. Molecular subtyping in this study provided more information about the relationships among antimicrobial-resistant Campylobacter at the processing level. PMID:19772592

  14. Transport processes at alpha-quartz-water interfaces: insights from first-principles molecular dynamics simulations.

    PubMed

    Adeagbo, Waheed A; Doltsinis, Nikos L; Klevakina, Ksenia; Renner, Jörg

    2008-05-16

    Car-Parrinello molecular dynamics (CP-MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the alpha-quartz-water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H(2)O molecules into H(+) and OH(-) is observed at the Si-terminated surface. The OH(-) fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO(2) present as Si(OH)(4) in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)(4) molecule as would have been indicated by a substantial lowering of the Si(OH)(4) diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP-MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si--O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si--O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si--O bond. The final solute species is Si(OH)(4). PMID:18404743

  15. Odd-even effect in heavy-ion collisions at intermediate energies

    SciTech Connect

    Su Jun; Zhang Fengshou; Bian Baoan

    2011-01-15

    Heavy-ion collisions at intermediate energies are studied by the isospin-dependent quantum molecular dynamics model in the company of the GEMINI model. The isospin-dependent quantum molecular dynamics model is applied to describe the violent stage of the collisions, while the GEMINI model is applied to simulate the decays of the prefragments. The present study mainly focuses on the odd-even effect in the yields of the final fragments. We find that the odd-even effect appears in the deexcitation process of the excited prefragments, and is affected by the excitation energies and the isotope distributions of the prefragments. Both the projectile-isospin-dependent odd-even effect in the region of -4{<=}T{sub Z}{<=}1 and the role of the symmetry energy on the odd-even effect are studied. We find that the odd-even effect depends sensitively on the symmetry energy.

  16. Odd-even effect in heavy-ion collisions at intermediate energies

    NASA Astrophysics Data System (ADS)

    Su, Jun; Zhang, Feng-Shou; Bian, Bao-An

    2011-01-01

    Heavy-ion collisions at intermediate energies are studied by the isospin-dependent quantum molecular dynamics model in the company of the GEMINI model. The isospin-dependent quantum molecular dynamics model is applied to describe the violent stage of the collisions, while the GEMINI model is applied to simulate the decays of the prefragments. The present study mainly focuses on the odd-even effect in the yields of the final fragments. We find that the odd-even effect appears in the deexcitation process of the excited prefragments, and is affected by the excitation energies and the isotope distributions of the prefragments. Both the projectile-isospin-dependent odd-even effect in the region of -4⩽TZ⩽1 and the role of the symmetry energy on the odd-even effect are studied. We find that the odd-even effect depends sensitively on the symmetry energy.

  17. Diffractive processes in antiproton-proton collision at s**(1/2) = 1.96 TeV in the D0 experiment

    SciTech Connect

    Otec, Roman; /Prague, Tech. U.

    2006-09-01

    A first study of single diffractive central high-p{sub T} dijet events in p{bar p} collisions at center-of-mass energy {radical}s = 1.96 TeV is presented, using data recorded by the D0 detector at the Tevatron during RunIIa in 2002-2004. The total integrated luminosity corresponding to the data sample is 398 pb{sup -1}. A diffractive sample is selected using a rapidity gap approach. A precise definition of the rapidity gap constitutes the first part of the thesis. The rapidity gap is defined by means of two parts of the D0 detector--luminosity detectors and calorimeter. Luminosity detectors serve as a basic indicators of diffractive candidates and the calorimeter is used to confirm the low energy activity in the forward region (a rapidity gap). Presented studies of energy deposited in forward part of calorimeter by various types of events yield two rapidity gap definitions. Both of them use a fixed rapidity interval in calorimeter |{eta}| {element_of} [2.6,5.2] and introduce an upper limit on the energy deposited in this region. First definition, which corresponds to the lowest systematical errors, uses a limit of 10 GeV, an energy limit in the second definition is set to 3 GeV. This alternative definition corresponds to the lowest contamination of diffractive sample by non-diffractive events, on the other hand it is accompanied with rejection of high percentage of diffractive candidates. Using the gap definition dijet diffractive data are then selected and compared to inclusive dijet events in various distributions. The main focus is to measure the difference in azimuthal angles between two leading jets in events with at least two high p{sub t} central jets. This variable is sensitive to the dynamics of the process. Indeed, the results show the different behavior of {Delta}{phi} distributions between the inclusive and diffractive samples. It is also shown that this difference is bigger for lower p{sub T} jets. Other distributions presented in the thesis show that most of the properties are the same for inclusive and diffractive events. The only observed difference is in the transversal properties of the jets, which could be explained as that diffractive jets are narrower than inclusive ones. Results are compared to Monte Carlo Pomwig (for diffractive sample) and Herwig (for inclusive sample); both show a good agreement with the data.

  18. The role of angular momentum in collision-induced vibration-rotation relaxation in polyatomics.

    PubMed

    McCaffery, Anthony J; Osborne, Mark A; Marsh, Richard J; Lawrance, Warren D; Waclawik, Eric R

    2004-07-01

    Vibrational relaxation of the 6(1) level of S(1)((1)B(2u)) benzene is analyzed using the angular momentum model of inelastic processes. Momentum-(rotational) angular momentum diagrams illustrate energetic and angular momentum constraints on the disposal of released energy and the effect of collision partner on resultant benzene rotational excitation. A kinematic "equivalent rotor" model is introduced that allows quantitative prediction of rotational distributions from inelastic collisions in polyatomic molecules. The method was tested by predicting K-state distributions in glyoxal-Ne as well as J-state distributions in rotationally inelastic acetylene-He collisions before being used to predict J and K distributions from vibrational relaxation of 6(1) benzene by H(2), D(2), and CH(4). Diagrammatic methods and calculations illustrate changes resulting from simultaneous collision partner excitation, a particularly effective mechanism in p-H(2) where some 70% of the available 6(1)-->0(0) energy may be disposed into 0-->2 rotation. These results support the explanation for branching ratios in 6(1)-->0(0) relaxation given by Waclawik and Lawrance and the absence of this pathway for monatomic partners. Collision-induced vibrational relaxation in molecules represents competition between the magnitude of the energy gap of a potential transition and the ability of the colliding species to generate the angular momentum (rotational and orbital) needed for the transition to proceed. Transition probability falls rapidly as DeltaJ increases and for a given molecule-collision partner pair will provide a limit to the gap that may be bridged. Energy constraints increase as collision partner mass increases, an effect that is amplified when J(i)>0. Large energy gaps are most effectively bridged using light collision partners. For efficient vibrational relaxation in polyatomics an additional requirement is that the molecular motion of the mode must be capable of generating molecular rotation on contact with the collision partner in order to meet the angular momentum requirements. We postulate that this may account for some of the striking propensities that characterize polyatomic energy transfer. PMID:15260535

  19. Coulomb excitation of highly charged projectile ions in relativistic collisions with diatomic molecules

    SciTech Connect

    Artemyev, A. N.; McConnell, S. R.; Surzhykov, A.; Najjari, B.; Voitkiv, A. B.

    2011-10-15

    We investigate the Coulomb excitation of highly charged ions colliding with diatomic molecules. In this process, the coherent interaction between the projectile electron and two molecular centers may cause clear interference patterns in the (collision) energy dependencies of the total cross sections and alignment parameters. We discuss such a Young-type interference for the particular case of the K{yields}L excitation of hydrogen- and helium-like projectile ions. Calculations, performed for the scattering of these ions on nitrogen molecules, indicate that the interference effects are extremely sensitive to the collisional geometry and are pronounced only if the molecular axis is aligned almost parallel to the incident beam trajectory.

  20. Elastic Collisions and Gravity

    NASA Astrophysics Data System (ADS)

    Ball, Steven

    2009-04-01

    Elastic collisions are fascinating demonstrations of conservation principles. The mediating force must be conservative in an elastic collision. Truly elastic collisions take place only when the objects in collision do not touch, e.g. magnetic bumpers on low friction carts. This requires that we define a collision as a momentum transfer. Elastic collisions in 1-D can be solved in general and the implications are quite remarkable. For example, a heavy object moving initially towards a light object followed by an elastic collision results in a final velocity of the light object greater than either initial velocity. This is easily demonstrated with low friction carts. Gravitational elastic collisions involving a light spacecraft and an extremely massive body like a moon or planet can be approximated as 1-D collisions, such as the ``free return'' trajectory of Apollo 13 around the moon. The most fascinating gravitational collisions involve the gravitational slingshot effect used to boost spacecraft velocities. The maximum gravitational slingshot effect occurs when approaching a nearly 1-D collision, revealing that the spacecraft can be boosted to greater than twice the planet velocity, enabling the spacecraft to travel much further away from the Sun.

  1. Mechanism of fragmentation and atomization of molecular ions in gasdynamic transport cell

    NASA Astrophysics Data System (ADS)

    Bazhenov, A. N.; Bulovich, S. V.; Gall, L. N.; Kretinina, A. V.; Lapushkin, M. N.; Gall, N. R.

    2010-04-01

    The fragmentation of molecular ions formed upon the electrospraying of a sample and transported through the gasdynamic system of a mass spectrometer equipped with an IESAP (Ion Extraction from Solution at Atmospheric Pressure) source has been experimentally studied. It is established that ion fragmentation in a Kantorowicz-Gray type cell takes place in the immediate vicinity of a skimmer port, apparently, as a result of collisions between ions (accelerated in an electric field) and stagnant gas. Molecular mechanisms of fragmentation are considered and it is concluded that this process can take place in a single ion-molecule collision event.

  2. COMPLEMENTARY MOLECULAR AND ELEMENTAL DETECTION OF SPECIATED THIOARSENICALS USING ESI-MS IN COMBINATION WITH A XENON-BASED COLLISION-CELL ICP-MS WITH APPLICATION TO FORTIFIED NIST FREEZE-DRIED URINE

    EPA Science Inventory

    The simultaneous detection of arsenic and sulfur in thio-arsenicals was achieved using xenonbased collision cell ICP-MS in combination with HPLC. In an attempt to minimize the 16O16O+ interference at m/z 32, both sample introduction and collision cell experimental parameters were...

  3. Experimental and ab initio studies of the reactive processes in gas phase i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH collisions with potassium ions

    SciTech Connect

    López, E.; Lucas, J. M.; Andrés, J. de; Albertí, M.; Aguilar, A.; Bofill, J. M.; Bassi, D.

    2014-10-28

    Collisions between potassium ions and neutral i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH, all in their electronic ground state, have been studied in the 0.10–10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K{sup +} + i-C{sub 3}H{sub 7}Br collisions KHBr{sup +} formation was observed and quantified, while the analogous KH{sub 2}O{sup +} formation in K{sup +} + i-C{sub 3}H{sub 7}OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C{sub 3}H{sub 7}{sup +} and either KBr or KOH, respectively, have been observed. For all these processes, absolute cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr{sup +} formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.

  4. Molecular Subtyping and Tracking of Listeria monocytogenes in Latin-Style Fresh-Cheese Processing Plants.

    PubMed

    Kabuki, D Y; Kuaye, A Y; Wiedmann, M; Boor, K J

    2004-09-01

    Latin-style fresh cheeses, which have been linked to at least 2 human listeriosis outbreaks in the United States, are considered to be high-risk foods for Listeria monocytogenes contamination. We evaluated L. monocytogenes contamination patterns in 3 Latin-style fresh-cheese processing plants to gain a better understanding of L. monocytogenes contamination sources in the manufacture of these cheeses. Over a 6-mo period, 246 environmental samples were collected and analyzed for L. monocytogenes using both the Food and Drug Administration (FDA) method and the Biosynth L. monocytogenes detection system (LMDS). Finished cheese samples from the same plants (n = 111) were also analyzed by the FDA method, which was modified to include L. monocytogenes plating medium (LMPM) and the L. monocytogenes confirmatory plating medium (LMCM) used in the LMDS method. Listeria monocytogenes was detected in 6.3% of cheese and 11.0% of environmental samples. Crates, drains, and floor samples showed the highest contamination rates, with 55.6, 30.0, and 20.6% L. monocytogenes positive samples, respectively. Finished products and food contact surfaces were positive in only one plant. The FDA method showed a higher sensitivity than the LMDS method for detection of L. monocytogenes from environmental samples. The addition of LMPM and LMCM media did not further enhance the performance of the FDA method for L. monocytogenes detection from finished products. Molecular subtyping (PCR-based allelic analysis of the virulence genes actA and hly and automated ribotyping) was used to track contamination patterns. Ribotype DUP-1044A, which had previously been linked to a 1998 multistate human listeriosis outbreak in the United States, was the most commonly identified subtype (20/36 isolates) and was isolated from 2 plants. This ribotype was persistent and widespread in one factory, where it was also responsible for the contamination of finished products. We hypothesize that this ribotype may represent a clonal group with a specific ability to persist in food processing environments. While previous listeriosis outbreaks were linked to Latin-style fresh cheeses made from unpasteurized milk, the presence of this organism in pasteurized cheese products illustrates that persistent environmental contamination also represents an important source of finished product contamination. PMID:15375038

  5. Molecular basis of processing-induced changes in protein structure in relation to intestinal digestion in yellow and green type pea (Pisum sativum L.): A molecular spectroscopic analysis.

    PubMed

    Yu, Gloria Qingyu; Warkentin, Tom; Niu, Zhiyuan; Khan, Nazir A; Yu, Peiqiang

    2015-12-01

    The objectives of this study were (1) to quantify the protein inherent molecular structural features of green cotyledon (CDC Striker) and yellow cotyledon (CDC Meadow) pea (Pisum sativum L.) seeds using molecular spectroscopic technique (FT/IR-ATR); (2) measure the denaturation of protein molecular makeup in the two types of pea during dry roasting (120°C for 60 min), autoclaving (120°C for 60 min) or microwaving (for 5 min); and (3) correlate the heat-induced changes in protein molecular makeup to the corresponding changes in protein digestibility determined using modified three-step in vitro procedure. Compared with yellow-type, the green-type peas had higher (P<0.05) ratios of amide I to II peak height (1.698 vs. 1.805) and area (1.843 vs. 2.017). A significant correlation was observed between the amide I and II peak height (r=0.48) and peak area (r=-0.42) ratio with protein content. Compared with yellow-type, the green-type peas had lower (P<0.05) α-helix:β-sheet ratio (1.015 vs. 0.926), indicating varietal difference in protein secondary structure makeup. All processing applications increased α-helix:β-sheet ratio, with the largest (P<0.05) increase being observed with roasting and microwaving. The heat-induced changes in α-helix:β-sheet ratio was strongly correlated to intestinal digestibility of protein within the green (r=-0. 86) and yellow (r=0.81) pea-types. However, across the pea types the correlation was not significant. Principal component and hierarchical cluster analyses on the entire spectral data from the amide region (ca. 1727-1480 cm(-1)) were able to visualize and discriminate the structural difference between pea varieties and processing treatments. This study shows that the molecular spectroscopy can be used as a rapid tool to screen the protein value of raw and heat-treated peas. PMID:26188704

  6. Two-potential approach for electron-molecular collisions at intermediate and high energies - Application to e-N2 scatterings

    NASA Technical Reports Server (NTRS)

    Choi, B. H.; Poe, R. T.; Sun, J. C.; Shan, Y.

    1979-01-01

    A general theoretical approach is proposed for the calculation of elastic, vibrational, and rotational transitions for electron-molecule scattering at intermediate and high-electron-impact energies. In this formulation, contributions to the scattering process come from the incoherent sum of two dominant potentials: a short-range shielded nuclear Coulomb potential from individual atomic centers, and a permanent/induced long-range potential. Application to e-N2 scattering from 50-500 eV incident electron energies has yielded good agreement with absolutely calibrated experiments. Comparisons with other theoretical approaches are made. The physical picture as well as the general features of electron-molecule scattering process are discussed within the framework of the two-potential approach.

  7. Enantiopure Functional Molecular Motors Obtained by a Switchable Chiral-Resolution Process.

    PubMed

    van Leeuwen, Thomas; Gan, Jefri; Kistemaker, Jos C M; Pizzolato, Stefano F; Chang, Mu-Chieh; Feringa, Ben L

    2016-05-17

    Molecular switches, rotors, and motors play an important role in the development of nano-machines and devices, as well as responsive and adaptive functional materials. For unidirectional rotors based on chiral overcrowded alkenes, their stereochemical homogeneity is of crucial importance. Herein, a method to obtain new and functionalizable overcrowded alkenes in enantiopure form is presented. The procedure involves a short synthesis of three steps and a solvent-switchable chiral resolution by using a readily available resolving agent. X-ray crystallography revealed the mode of binding of the motor with the resolving agent, as well as the absolute configuration of the motor. (1) H NMR and UV/Vis spectroscopy techniques were used to determine the dynamic behavior of this molecular motor. This method provides rapid access to ample amounts of enantiopure molecular motors, which will greatly facilitate the further development of responsive molecular systems based on chiral overcrowded alkenes. PMID:27072290

  8. Computational study of alkali-metal-noble gas collisions in the presence of nonresonant lasers - Na + Xe + h/2/pi/omega sub 1 + h/2/pi/omega sub 2 system

    NASA Technical Reports Server (NTRS)

    Devries, P. L.; Chang, C.; George, T. F.; Laskowski, B.; Stallcop, J. R.

    1980-01-01

    The collision of Na with Xe in the presence of both the rhodamine-110 dye laser and the Nd-glass laser is investigated within a quantum-mechanical close-coupled formalism, utilizing ab initio potential curves and transition dipole matrix elements. Both one- and two-photon processes are investigated; the Na + Xe system is not asymptotically resonant with the radiation fields, so that these processes can only occur in the molecular collision region. The one-photon processes are found to have measurable cross sections at relatively low intensities; even the two-photon process has a significant section for field intensities as low as 10 MW/sq cm.

  9. The dynamics of electronic to vibrational, rotational, and translational energy transfer in collision of Ba( sup 1 P sub 1 ) with diatomic molecules

    SciTech Connect

    Suits, A.G.; de Pujo, P.; Sublemontier, O.; Visticot, J.; Berlande, J.; Cuvellier, J.; Gustavsson, T.; Mestdagh, J.; Meynadier, P. ); Lee, Y.T. )

    1992-09-15

    Doppler measurements taken over a range of probe-laser angles in a crossed-beam experiment were used, in conjunction with forward convolution analysis, to obtain flux--velocity contour maps for Ba({sup 3}{ital P}{sub 2}) produced in a collision of Ba({sup 1}{ital P}{sub 1}) with H{sub 2}, N{sub 2}, O{sub 2}, and NO. The contour maps suggest a general model for the dynamics of this process in which large impact parameter collisions result in a near-resonant transfer of initial electronic energy into final vibrational energy, while close collisions produce sideways scattering and effectively couple electronic energy to translation. The molecular collision partners fall into two categories: for one group, comprising O{sub 2} and NO, the existence of a well-defined molecular anion with favorable Franck--Condon factors linking excited vibrational levels to the ground vibrational state of the neutral results in greatly enhanced coupling for the near-resonant process. Molecules for which there exist no stable anions, such as N{sub 2} and H{sub 2}, represent a second category. The electronically inelastic collision for this group is instead dominated by the nonresonant process yielding the ground vibrational state and large translational energy release.

  10. Vibrational energy transfer in shocked molecular crystals.

    PubMed

    Hooper, Joe

    2010-01-01

    We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state. PMID:20078172

  11. Exotics from Heavy Ion Collisions

    SciTech Connect

    Ohnishi, Akira; Jido, Daisuke; Cho, Sungtae; Furumoto, Takenori; Yazaki, Koichi; Hyodo, Tetsuo; Ko, Che Ming; Lee, Su Houng; Nielsen, Marina; Sekihara, Takayasu; Yasui, Shigehiro

    2011-10-21

    Discriminating hadronic molecular and multi-quark states is a long standing problem in hadronic physics. We propose here to utilize relativistic heavy ion collisions to resolve this problem, as exotic hadron yields are expected to be strongly affected by their structures. Using the coalescence model, we find that the exotic hadron yield relative to the statistical model result is typically an order of magnitude smaller for a compact multi-quark state, and larger by a factor of two or more for a loosely bound hadronic molecule. We further find that some of the newly proposed heavy exotic states could be produced and realistically measured at RHIC and LHC.

  12. A collision avoidance system for workpiece protection

    SciTech Connect

    Schmitt, D.J.; Weber, T.M.; Novak, J.L.; Maslakowski, J.E.

    1995-04-01

    This paper describes an application of Sandia`s non-contact capacitive sensing technology for collision avoidance during the manufacturing of rocket engine thrust chambers. The collision avoidance system consists of an octagon shaped collar with a capacitive proximity sensor mounted on each face. The sensors produced electric fields which extend several inches from the face of the collar and detect potential collisions between the robot and the workpiece. A signal conditioning system processes the sensor output and provides varying voltage signals to the robot controller for stopping the robot.

  13. Use of molecular typing methods to trace the dissemination of Listeria monocytogenes in a shrimp processing plant.

    PubMed Central

    Destro, M T; Leitão, M F; Farber, J M

    1996-01-01

    Molecular typing of bacteria has been widely used in epidemiological studies but not as extensively for tracing the transmission of pathogenic bacteria in food plants. This study was conducted to examine the potential use of two molecular typing methods, random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE), to trace Listeria monocytogenes contamination in a shrimp processing plant. Ribotyping and phase typing were also performed on a select number of strains. One hundred fifteen strains of L. monocytogenes collected in different areas of a shrimp processing plant were first serotyped and then subtyped by molecular typing. RAPD and PFGE showed great promise for typing L. monocytogenes isolates since distinguishable and reproducible DNA polymorphisms were obtained. When the composite profile from both (RAPD and PFGE) methods was generated, there was an increase in the discriminatory power to discern differences between strains of L. monocytogenes. The results indicated that environmental strains all fell into composite profile groupings unique to the environment, while strains from both water and utensils shared another composite profile group. L. monocytogenes fresh shrimp isolates belonging to one profile group were found in different areas of the processing line. This same profile group was also present in food handlers from the processing and packaging areas of the plant. PMID:8593073

  14. Gravity-induced cellular and molecular processes in plants studied under altered gravity conditions

    NASA Astrophysics Data System (ADS)

    Vagt, Nicole; Braun, Markus

    With the ability to sense gravity plants possess a powerful tool to adapt to a great variety of environmental conditions and to respond to environmental changes in a most beneficial way. Gravity is the only constant factor that provides organisms with reliable information for their orientation since billions of years. Any deviation of the genetically determined set-point angle of the plants organs from the vector of gravity is sensed by specialized cells, the statocytes of roots and shoots in higher plants. Dense particles, so-called statoliths, sediment in the direction of gravity and activate membrane-bound gravireceptors. A physiological signalling-cascade is initiated that eventually results in the gravitropic curvature response, namely, the readjust-ment of the growth direction. Experiments under microgravity conditions have significantly contributed to our understanding of plant gravity-sensing and gravitropic reorientation. For a gravity-sensing lower plant cell type, the rhizoid of the green alga Chara, and for statocytes of higher plant roots, it was shown that the interactions between statoliths and the actomyosin system consisting of the actin cytoskeleton and motor proteins (myosins) are the basis for highly efficient gravity-sensing processes. In Chara rhizoids, the actomyosin represents a guid-ing system that directs sedimenting statoliths to a specific graviperception site. Parabolic flight experiments aboard the airbus A300 Zero-G have provided evidence that lower and higher plant cells use principally the same statolith-mediated gravireceptor-activation mechanism. Graviper-ception is not dependent on mechanical pressure mediated through the weight of the sedimented statoliths, but on direct interactions between the statoliths's surface and yet unknown gravire-ceptor molecules. In contrast to Chara rhizoids, in the gravity-sensing cells of higher plants, the actin cytoskeleton is not essentially involved in the early phases of gravity sensing. Dis-rupting the actomyosin system did not impair the sedimentation of statoliths and did not prevent the activation of gravireceptors. However, experiments in microgravity and inhibitor experiments have demonstrated that the actomyosin system optimizes the statolith-receptor interactions by keeping the sedimented statoliths in motion causing a consistent activation of different gravireceptor molecules. Thereby, a triggered gravitropic signal is created which is the basis for a highly sensitive control and readjustment mechanism. In addition, the results of recent parabolic flight studies on the effects of altered gravity conditions on the gene expres-sion pattern of Arabidopsis seedlings support these findings and provide new insight into the molecular basis of the plants response to different acceleration conditions. The work was financially supported by DLR on behalf of Bundesministerium für Wirtschaft und Technologie (50WB0815).

  15. Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration.

    PubMed

    Avenhaus, Ulrike; Cabeza, Ricardo A; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

    2015-01-01

    Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be induced by increased formation of NCR peptides and necessitates an efficient iron supply to the bacteroid, which is probably mediated by nicotianamine. The paper is dedicated to the 85th birthday of Prof. Dr. Günther Schilling, University of Halle/Wittenberg, Germany, https://de.wikipedia.org/wiki/Günther_Schilling. PMID:26779207

  16. Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration

    PubMed Central

    Avenhaus, Ulrike; Cabeza, Ricardo A.; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

    2016-01-01

    Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be induced by increased formation of NCR peptides and necessitates an efficient iron supply to the bacteroid, which is probably mediated by nicotianamine. The paper is dedicated to the 85th birthday of Prof. Dr. Günther Schilling, University of Halle/Wittenberg, Germany, https://de.wikipedia.org/wiki/Günther_Schilling PMID:26779207

  17. Gene Expression Profiles of the NCI-60 Human Tumor Cell Lines Define Molecular Interaction Networks Governing Cell Migration Processes

    PubMed Central

    Kohn, Kurt W.; Zeeberg, Barry R.; Reinhold, William C.; Sunshine, Margot; Luna, Augustin; Pommier, Yves

    2012-01-01

    Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes. PMID:22570691

  18. Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes.

    PubMed

    Kohn, Kurt W; Zeeberg, Barry R; Reinhold, William C; Sunshine, Margot; Luna, Augustin; Pommier, Yves

    2012-01-01

    Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes. PMID:22570691

  19. Cloud droplet collisions under different turbulent intensities

    NASA Astrophysics Data System (ADS)

    Chen, Sisi; Zwijzen, Kevin; Vaillancourt, Paul; Bartello, Peter; Yau, Man-kong

    2015-04-01

    Turbulence has long been postulated to have a large contribution in accelerating cloud droplet growth through the collision-coalescence process. Previous studies have shown that turbulence can enhance the collision kernel and may speed up the warm rain processes and even increase the precipitation. We use the Direct Numerical Simulation (DNS) model from Franklin et al. (2005) to simulate the motion of cloud droplets and their collisions under the effects of turbulence. In order to expand the range of investigated Reynolds number, we parallelize the code using MPI technique, so that larger and more energetic scales in the flow can be resolved. Previous DNS studies either span a narrow range of Reynolds number or just a few dissipation rates. This work will be based on a wide range of Reynolds number (Rλ is from 63 to 589) and eddy dissipation rates (from 50 to 1500 cm2 s-3). The purpose is to quantify the influence of Reynolds number (box size) and turbulence intensity (i.e. eddy dissipation rate) on the collision statistics (for example, the relative radial velocity, the radial distribution function, and the collision kernel) to shed light on future microphysics parameterizations for collision statistics under different turbulent conditions. The droplet radii range from 5 to 25 μm because these sizes are crucial to the formation of larger droplets important for effective gravitational collisional growth. The collision statistics between pairs of those sizes are studied. The results show no dependency of collision statics on Reynolds number, in contrast to the conclusions of some previous studies. On the other hand the collision kernel increases monotonically with dissipation rate in a close-to-linear manner.

  20. Capture of K-shell electrons by ?-particles in ?-decay of superheavy nuclei: I. Charge transfer in collisions of ?-particles with He+(1 s) ions

    NASA Astrophysics Data System (ADS)

    Nikulin, V. K.; Gushchina, N. A.

    2015-08-01

    We consider a process in which ?-particles after ?-decay ionize K-shell of daughter atoms and capture electrons. We first have performed similar calculations for collisions of ?-particles with He+(1 s) ions. This charge transfer process is studied for the collision energy region 0.04-400 keV. The transition amplitudes are calculated in the impact parameter approximation with the use of the close coupling equations method for a basis consisting of eight molecular states. Total and partial charge-transfer cross sections to the 1 s and, for the first time, to the 2 s and 2 p 0, 2 p 1 states of the He+ ion are obtained. Angular differential cross sections for the elastic scattering and charge-transfer processes are calculated in the eikonal approximation for a wide range of scattering angles for the collision energy of 1 keV. Results of calculations are in an excellent agreement with experimental data.

  1. Spatial Kerr soliton collisions at arbitrary angles.

    PubMed

    Chamorro-Posada, P; McDonald, G S

    2006-09-01

    The theory of spatial Kerr solitons is extended to colliding beams that are neither almost-exactly copropagating nor almost-exactly counterpropagating. Our new Helmholtz formalism yields results that are consistent with the inherent symmetry of the collision process and that are not predicted by existing paraxial descriptions. Full numerical and approximate analytical results are presented. These show excellent agreement. In particular, Kerr solitons are found to be remarkably robust under nonparaxial collisions. PMID:17025766

  2. Atomic and molecular theory

    SciTech Connect

    Inokuti, Mitio.

    1990-01-01

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

  3. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  4. Investigating Students' Ability to Transfer Ideas Learned from Molecular Animations of the Dissolution Process

    ERIC Educational Resources Information Center

    Kelly, Resa M.; Jones, Loretta L.

    2008-01-01

    Animations of the particulate level of matter are widely available for use in chemistry classes and are often the primary means of representing molecular behavior. These animations may also be viewed by individual students using textbook Web sites, although without reinforcement or feedback. It is not known to what extent the material in these…

  5. Investigating Students' Ability to Transfer Ideas Learned from Molecular Animations of the Dissolution Process

    ERIC Educational Resources Information Center

    Kelly, Resa M.; Jones, Loretta L.

    2008-01-01

    Animations of the particulate level of matter are widely available for use in chemistry classes and are often the primary means of representing molecular behavior. These animations may also be viewed by individual students using textbook Web sites, although without reinforcement or feedback. It is not known to what extent the material in these

  6. Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise

    PubMed Central

    Cifuentes, Oscar E.; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things. PMID:21123698

  7. Teaching the process of molecular phylogeny and systematics: a multi-part inquiry-based exercise.

    PubMed

    Lents, Nathan H; Cifuentes, Oscar E; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things. PMID:21123698

  8. Molecular Chaperones of Leishmania: Central Players in Many Stress-Related and -Unrelated Physiological Processes

    PubMed Central

    Requena, Jose M.; Montalvo, Ana M.; Fraga, Jorge

    2015-01-01

    Molecular chaperones are key components in the maintenance of cellular homeostasis and survival, not only during stress but also under optimal growth conditions. Folding of nascent polypeptides is supported by molecular chaperones, which avoid the formation of aggregates by preventing nonspecific interactions and aid, when necessary, the translocation of proteins to their correct intracellular localization. Furthermore, when proteins are damaged, molecular chaperones may also facilitate their refolding or, in the case of irreparable proteins, their removal by the protein degradation machinery of the cell. During their digenetic lifestyle, Leishmania parasites encounter and adapt to harsh environmental conditions, such as nutrient deficiency, hypoxia, oxidative stress, changing pH, and shifts in temperature; all these factors are potential triggers of cellular stress. We summarize here our current knowledge on the main types of molecular chaperones in Leishmania and their functions. Among them, heat shock proteins play important roles in adaptation and survival of this parasite against temperature changes associated with its passage from the poikilothermic insect vector to the warm-blooded vertebrate host. The study of structural features and the function of chaperones in Leishmania biology is providing opportunities (and challenges) for drug discovery and improving of current treatments against leishmaniasis. PMID:26167482

  9. Biodegradability enhancement and detoxification of cork processing wastewater molecular size fractions by ozone.

    PubMed

    Santos, Diana C; Silva, Lúcia; Albuquerque, António; Simões, Rogério; Gomes, Arlindo C

    2013-11-01

    Cork boiling wastewater pollutants were fractionated by sequential use of four ultrafiltration membranes and five fractions were obtained: four retentates (>100, 50-100, 20-50 and 10-20 kDa) and one permeate (<10 kDa); which were used to study the correlation of molecular size with biodegradability and toxicity before and after ozonation. The results show that molecular size is correlated with organic load and restrains biodegradability. The fraction with >100 kDa corresponds to 56% of the organic load and the one with <10 kDa only 8%. The biodegradability of fractions increased 182% with fractions molecular size reduction from >100 to <10 kDa and the chemical oxygen demand (COD) was from 3436 to 386 mg L(-1). For biodegradability enhancement the best outcome of ozonation was obtained with compounds having molecular size >20 kDa and range from 5% up to 175% for applied ozone doses to COD ratios between 0.15 and 0.38. PMID:23994696

  10. Basins in ARC-continental collisions

    USGS Publications Warehouse

    Draut, Amy E.; Clift, Peter D.

    2012-01-01

    Arc-continent collisions occur commonly in the plate-tectonic cycle and result in rapidly formed and rapidly collapsing orogens, often spanning just 5-15 My. Growth of continental masses through arc-continent collision is widely thought to be a major process governing the structural and geochemical evolution of the continental crust over geologic time. Collisions of intra-oceanic arcs with passive continental margins (a situation in which the arc, on the upper plate, faces the continent) involve a substantially different geometry than collisions of intra-oceanic arcs with active continental margins (a situation requiring more than one convergence zone and in which the arc, on the lower plate, backs into the continent), with variable preservation potential for basins in each case. Substantial differences also occur between trench and forearc evolution in tectonically erosive versus tectonically accreting margins, both before and after collision. We examine the evolution of trenches, trench-slope basins, forearc basins, intra-arc basins, and backarc basins during arc-continent collision. The preservation potential of trench-slope basins is low; in collision they are rapidly uplifted and eroded, and at erosive margins they are progressively destroyed by subduction erosion. Post-collisional preservation of trench sediment and trench-slope basins is biased toward margins that were tectonically accreting for a substantial length of time before collision. Forearc basins in erosive margins are usually floored by strong lithosphere and may survive collision with a passive margin, sometimes continuing sedimentation throughout collision and orogeny. The low flexural rigidity of intra-arc basins makes them deep and, if preserved, potentially long records of arc and collisional tectonism. Backarc basins, in contrast, are typically subducted and their sediment either lost or preserved only as fragments in melange sequences. A substantial proportion of the sediment derived from collisional orogenesis ends up in the foreland basin that forms as a result of collision, and may be preserved largely undeformed. Compared to continent-continent collisional foreland basins, arc-continent collisional foreland basins are short-lived and may undergo partial inversion after collision as a new, active continental margin forms outboard of the collision zone and the orogen whose load forms the basin collapses in extension.

  11. Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte-Carlo processes.

    PubMed

    Francis, Z; Incerti, S; Capra, R; Mascialino, B; Montarou, G; Stepan, V; Villagrasa, C

    2011-01-01

    This paper presents a study of energy deposits induced by ionising particles in liquid water at the molecular scale. Particles track structures were generated using the Geant4-DNA processes of the Geant4 Monte-Carlo toolkit. These processes cover electrons (0.025 eV-1 MeV), protons (1 keV-100 MeV), hydrogen atoms (1 keV-100 MeV) and alpha particles (10 keV-40 MeV) including their different charge states. Electron ranges and lineal energies for protons were calculated in nanometric and micrometric volumes. PMID:20810287

  12. Applications of neural networks to real-time data processing at the Environmental and Molecular Sciences Laboratory (EMSL)

    SciTech Connect

    Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1993-06-01

    Detailed design of the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory (PNL) is nearing completion and construction is scheduled to begin later this year. This facility will assist in the environmental restoration and waste management mission at the Hanford Site. This paper identifies several real-time data processing applications within the EMSL where neural networks can potentially be beneficial. These applications include real-time sensor data acquisition and analysis, spectral analysis, process control, theoretical modeling, and data compression.

  13. Spectroscopic investigation of the NO C 2? de-excitation process by collision with O2 X 3?g? in a low-pressure N2O2 mixture microwave discharge

    NASA Astrophysics Data System (ADS)

    Tan, Hao; Nezu, Atsushi; Akatsuka, Hiroshi

    2016-01-01

    We use a spectroscopic method to diagnose the microwave discharge plasma of N2O2 mixtures. We succeed in observing NO ?-band radiation peaks when the oxygen partial pressure is smaller than 3%. In order to quantitatively investigate the de-excitation processes of the NO C 2? excited state, we improve our self-consistent kinetic model to include some of the main excited states of NO molecules. In providing our numerical results, we discuss a reasonable NO C 2? de-population process by that involves collision with the O2 X 3?g? state molecule, which leads to the disappearance of ?-band radiation. We propose an indirect proof that this de-population process results in an increase in the vibrational temperature of NO A 2?+.

  14. Investigation on growth process and tribological behavior of mixed alkylsilane self-assembled molecular films in aqueous solution

    NASA Astrophysics Data System (ADS)

    Liu, Yuhong; Liu, Pengxiao; Xiao, Yuqi; Luo, Jianbin

    2012-09-01

    In this paper, we investigated the frictional behaviors of the mixed self-assembled molecular films of the fluoroalkylsilane (FAS) molecules and non-fluoroalkylsilane (n-FAS) molecules with different chain length covalently absorbed on silicon surfaces, characterized by the universal ball-disk UMT-2 experimental tester under aqueous solution conditions. The surfaces of the substrate modified by mixed self-assembled molecular films were examined by X-ray photoelectron spectroscopy (XPS) and contact angle measurements. The formation processes of the molecular films were characterized by quartz crystal microbalance (QCM). The results indicated that it would take a longer time to reach the adsorption equilibrium of the molecular films with the increment of carbon chain length. The measured tribological results showed that the mixing of the fluoroalkylsilane and non-fluoroalkylsilane enhance the lubrication and decrease the friction and wear compared to the one-component thin films. This may be caused by the reduced excitation of the energy dissipation channels.

  15. Experimental study of the reactive processes in the gas phase K+ + i-C3H7Cl collisions: A comparison with Li and Na ions

    NASA Astrophysics Data System (ADS)

    Aguilar, J.; Lucas, J. M.; de Andrés, J.; Albertí, M.; Bassi, D.; Aguilar, A.

    2013-05-01

    Reactive collisions between alkali ions (Li+, Na+, and K+) and halogenated hydrocarbon molecules have been studied recently in our research group. In this paper, we have reported on the K+ + i-C3H7Cl system in the 0.20-14.00 eV center-of-mass energy range using a radio frequency guided-ion beam apparatus developed in our laboratory. Aiming at increasing our knowledge about this kind of reactions, we compare our latest results for K+ with those obtained previously for Li+ and Na+. While the reaction channels are the same in all three cases, their energy profiles, reactivity, measured reactive cross-section energy dependences, and even their reaction mechanisms, differ widely. By comparing experimentally measured reactive cross-sections as a function of the collision energy with the ab initio calculations for the different potential energy surfaces, a qualitative interpretation of the dynamics of the three reactive systems is presented in the present work.

  16. Clinical, pathological and molecular prognostic factors in prostate cancer decision-making process.

    PubMed

    Pugliese, Dario; Palermo, Giuseppe; Totaro, Angelo; Bassi, Pier Francesco; Pinto, Francesco

    2016-03-01

    Prostate cancer is the most common urologic neoplasm and the second leading cause of cancer-related death among men in many developed countries. Given the highly heterogeneous behaviour of the disease, there is a great need for prognostic factors, in order to stratify the clinical risk and give the best treatment options to the patient. Clinical factors, such as prostate-specific antigen value and derivatives, and pathological factors, such as stage and Gleason grading, are well kown prognostic factors. Nomograms can provide useful prediction in each clinical sceario. The field of molecular biomarkers is briskly evolving towards personalized medicine. TMPRSS2-ERG fusion, deletion of PTEN ed and gene panels are some of the more extensively explored molecular features in prostate cancer outcome prediction. In the near future, circulating tumour cells, exosomes and microRNAs could give us further, not invasive important tools. PMID:26917215

  17. Molecular and physiological characterization of dominant bacterial populations in traditional mozzarella cheese processing

    PubMed

    Morea; Baruzzi; Cocconcelli

    1999-10-01

    The development of the dominant bacterial populations during traditional Mozzarella cheese production was investigated using physiological analyses and molecular techniques for strain typing and taxonomic identification. Analysis of RAPD fingerprints revealed that the dominant bacterial community was composed of 25 different biotypes, and the sequence analysis of 16S rDNA demonstrated that the isolated strains belonged to Leuconostoc mesenteroides subsp. mesenteroides, Leuc. lactis, Streptococcus thermophilus, Strep. bovis, Strep. uberis, Lactococcus lactis subsp. lactis, L. garviae, Carnobacterium divergens, C. piscicola, Aerococcus viridans, Staphylococcus carnosus, Staph. epidermidis, Enterococcus faecalis, Ent. sulphureus and Enterococcus spp. The bacterial populations were characterized for their physiological properties. Two strains, belonging to Strep. thermophilus and L. lactis subsp. lactis, were the most acidifying; theL. lactis subsp. lactis strain was also proteolytic and eight strains were positive to citrate fermentation. Moreover, the molecular techniques allowed the identification of potential pathogens in a non-ripened cheese produced from raw milk. PMID:10583686

  18. Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

    NASA Technical Reports Server (NTRS)

    Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

    2006-01-01

    A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

  19. Cross Sections for Electron Collisions with Carbon Monoxide

    SciTech Connect

    Itikawa, Yukikazu

    2015-03-15

    Cross section data are collected and reviewed for electron collisions with carbon monoxide. Collision processes included are total scattering, elastic scattering, momentum transfer, excitations of rotational, vibrational and electronic states, ionization, and dissociation. For each process, recommended values of the cross sections are presented, when possible. The literature has been surveyed through to the end of 2013.

  20. Rotational state-changing cold collisions of hydroxyl ions with helium

    NASA Astrophysics Data System (ADS)

    Hauser, Daniel; Lee, Seunghyun; Carelli, Fabio; Spieler, Steffen; Lakhmanskaya, Olga; Endres, Eric S.; Kumar, Sunil S.; Gianturco, Franco; Wester, Roland

    2015-06-01

    Cold molecules are important for many applications, from fundamental precision measurements, quantum information processing, quantum-controlled chemistry, to understanding the cold interstellar medium. Molecular ions are known to be cooled efficiently in sympathetic collisions with cold atoms or ions. However, little knowledge is available on the elementary cooling steps, because the determination of quantum state-to-state collision rates at low temperature is very challenging for both experiment and theory. Here we present a method to manipulate molecular quantum states by non-resonant photodetachment. Based on this we provide absolute quantum scattering rate coefficients under full quantum state control for the rotationally inelastic collision of hydroxyl anions with helium. Experiment and quantum scattering theory show excellent agreement without adjustable parameters. Very similar rate coefficients are obtained for two different isotopes, which is linked to several quantum scattering resonances appearing at different energies. The presented method is also applicable to polyatomic systems and will help elucidate non-radiative processes in polyaromatic hydrocarbons and protein chromophores.