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Sample records for molecular collision processes

  1. 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.

  2. Molecular collision processes in the presence of picosecond laser pulses

    NASA Technical Reports Server (NTRS)

    Lee, H. W.; George, T. F.

    1979-01-01

    Radiative transitions in molecular collision processes taking place in the presence of picosecond pulses are studied within a semiclassical formalism. An expression for adiabatic potential surfaces in the electronic-field representation is obtained, which directly leads to the evaluation of transition probabilities. Calculations with a Landau-Zener-type model indicate that picosecond pulses can be much more effective in inducing transitions than a single long pulse of the same intensity and the same total energy, if the intensity is sufficiently high that the perturbation treatment is not valid.

  3. Is photon angular momentum important in molecular collision processes occurring in a laser field

    NASA Technical Reports Server (NTRS)

    Devries, P. L.; George, T. F.

    1978-01-01

    The importance of the rigorous treatment of photon angular momentum in molecular-collision processes occurring in the presence of intense radiation is investigated. An alternate approximate treatment, which essentially neglects the angular momentum coupling between the photon and the molecular degrees of freedom by averaging over the angular dependence of the interaction matrix elements, is presented and applied to a model calculation. The degeneracy-averaged results of this calculation compare remarkably well with the results of a rigorous calculation, from which we conclude (with reservation) that the explicit consideration of photoangular momentum coupling in molecular-collision problems is unnecessary.

  4. Machine learning for molecular scattering dynamics: Gaussian Process models for improved predictions of molecular collision observables

    NASA Astrophysics Data System (ADS)

    Krems, Roman; Cui, Jie; Li, Zhiying

    2016-05-01

    We show how statistical learning techniques based on kriging (Gaussian Process regression) can be used for improving the predictions of classical and/or quantum scattering theory. In particular, we show how Gaussian Process models can be used for: (i) efficient non-parametric fitting of multi-dimensional potential energy surfaces without the need to fit ab initio data with analytical functions; (ii) obtaining scattering observables as functions of individual PES parameters; (iii) using classical trajectories to interpolate quantum results; (iv) extrapolation of scattering observables from one molecule to another; (v) obtaining scattering observables with error bars reflecting the inherent inaccuracy of the underlying potential energy surfaces. We argue that the application of Gaussian Process models to quantum scattering calculations may potentially elevate the theoretical predictions to the same level of certainty as the experimental measurements and can be used to identify the role of individual atoms in determining the outcome of collisions of complex molecules. We will show examples and discuss the applications of Gaussian Process models to improving the predictions of scattering theory relevant for the cold molecules research field. Work supported by NSERC of Canada.

  5. 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.

  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. Origin of collision-induced molecular orientation.

    PubMed

    Brouard, M; Hornung, B; Aoiz, F J

    2013-11-01

    Collision-induced rotational angular momentum orientation is a fundamental property of molecular scattering, which is sensitive to the balance between attractive and repulsive forces at play during collision. Here, we quantify a new mechanism leading to orientation, which is purely quantum mechanical in origin. Although the new mechanism is quite general, and will operate more widely in atomic and molecular scattering, it is observed here for impulsive hard shell collisions, for which the orientation vanishes classically. The quantum mechanism can thus be studied in isolation from other processes. The orientation is proposed to originate from the nonlocal nature of the quantum mechanical collision encounter.

  8. Molecular collisions coming into focus.

    PubMed

    Onvlee, Jolijn; Vogels, Sjoerd N; von Zastrow, Alexander; Parker, David H; van de Meerakker, Sebastiaan Y T

    2014-08-14

    The Stark deceleration method exploits the concepts of charged particle accelerator physics to produce beams of neutral polar molecules with an almost perfect quantum state purity, a tunable velocity and a narrow velocity distribution. These monochromatic molecular beams offer interesting perspectives for precise studies of molecular scattering processes, in particular when used in conjunction with state-of-the-art laser-based detection techniques such as velocity map imaging. Here, we describe crossed beam scattering experiments in which the Stark deceleration method is combined with the velocity map imaging technique. The narrow velocity spread of Stark-decelerated molecular beams results in scattering images with unprecedented velocity and angular resolution. We demonstrate this by resolving quantum diffraction oscillations in state-to-state inelastic differential scattering cross sections for collisions between NO radicals and rare gas atoms. We describe the future prospects of this "best-of-two-worlds" combination, ranging from scattering studies at low collision energies to bimolecular scattering using two decelerators, and discuss the challenges that lie ahead to achieve these goals.

  9. Electron Capture Processes Following Collisions of He^2+ Ions with Molecular Targets

    NASA Astrophysics Data System (ADS)

    Abu-Haija, O.

    2005-05-01

    Energy-gain spectra, absolute state-selective and total cross sections have been measured for single-electron capture processes in collisions of He^2+ ions with O2, H2O, CO2, N2, and NH3 at impact energies between 100 eV and 1600 eV and scattering angles between 0^o and 6^o using the translational energy-gain spectroscopy (TES) technique. As apparent from the translational energy-gain measurements, single-electron capture (SEC) from O2 and H2O proceeds by both dissociative and non-dissociative channels, whereas for N2 and CO2 only dissociative SEC has been observed. However, for NH3 the non-dissociative SEC channel is found to be predominantly populated. Total cross sections have also been compared with available measurements and theoretical calculations based on Landua-Zener model and Demkov model.

  10. 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.

  11. Molecular Dissociation Induced by Electron Collisions

    NASA Astrophysics Data System (ADS)

    Wolf, Andreas

    2009-05-01

    Free electrons can efficiently break molecules or molecular ions in low-energy collisions by the processes of dissociative recombination or attachment. These processes make slow electrons efficient chemical agents in many environments. For dissociative recombination, in particular, studies of the underlying reaction paths and mechanisms have become possible on a uniquely elementary level in recent years both for theory and experiment. On the experimental side, collisions can be prepared at resolved collision energies down to the meV (10 Kelvin) level, increasingly gaining control also over the initial molecular quantum level, and individual events are detected and kinematically analyzed by fast-beam coincidence fragment imaging. Experiments are reported from the ion cooler ring TSR in Heidelberg. Stored beams of molecular ions cooled in their external and internal degrees of freedom are collinearly merged with intense and cold electron beams from cryogenic GaAs photocathodes, recently shown to yield fast cooling of the center-of-mass motion also for heavy and correspondingly slow molecular ion beams. To reconstruct the molecular fragmentation events multiparticle imaging can now be used systematically with collision energies set a wide range, especially aiming at specific electron capture resonances. Thus, for CF^+ it is found that the electronic state of the C fragment (^3P or ^1D) switches resonantly when the collision energy is changed by only a small fraction. As a new powerful tool, an energy-sensitive multi-strip surface-barrier detector (EMU) has been set up to measure with near-unity efficiency the masses of all fragments together with their hit positions in high-multiplicity events. Among many uses, this device allows internal molecular excitations to be derived for individual chemical channels in polyatomic fragmentation. New results will be presented in particular on the breakup of the hydronium ion (D3O^+).

  12. 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

  13. 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.

  14. Division B Commission 14 Working Group: Collision Processes

    NASA Astrophysics Data System (ADS)

    Peach, Gillian; Dimitrijevic, Milan S.; Barklem, Paul S.

    2016-04-01

    Since our last report (Peach & Dimitrijević 2012), a large number of new publications on the results of research in atomic and molecular collision processes and spectral line broadening have been published. Due to the limited space available, we have only included work of importance for astrophysics. Additional relevant papers, not included in this report, can be found in the databases at the web addresses provided in Section 6. Elastic and inelastic collisions between electrons, atoms, ions, and molecules are included, as well as charge transfer in collisions between heavy particles which can be very important.

  15. Continuum and molecular-dynamics simulation of nanodroplet collisions.

    PubMed

    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 (Kn_{gas}=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 (Kn_{liquid}=0.01 for D=36nm) 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

  16. A new perspective: imaging the stereochemistry of molecular collisions.

    PubMed

    Aoiz, F J; Brouard, M; Gordon, S D S; Nichols, B; Stolte, S; Walpole, V

    2015-11-11

    The concept of the steric effect in molecular collisions is central to chemistry. In this Perspective article we review some of the progress made in studying the steric effect in inelastic and reactive collisions involving relatively small isolated atomic and molecular species. We overview the theoretical framework used to quantify the steric effect, and outline some of the key experimental approaches that can be employed to study the dynamics and mechanism of collisions involving oriented and aligned molecules. We illustrate the discussion by highlighting a few recent studies of inelastic and reactive scattering. Finally, we conclude with some reflections on possible future directions of interest.

  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. 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.

  19. Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

    PubMed

    Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

    2015-05-07

    The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

  20. Benchmark Calculations of Atomic Collision Processes

    NASA Astrophysics Data System (ADS)

    Bartschat, Klaus

    2012-02-01

    The rapid development of computational resources has resulted in enormous improvements in the accuracy of numerical calculations of atomic collision processes. This talk will concentrate on recent advances in the computational treatment of charged-particle and intense short-pulse laser interactions with atoms, ions, and small molecules. Examples include electron collisions with heavy complex targets that are of significant importance in many modelling applications in plasma and astrophysics, fundamental studies of highly correlated 4-body Coulomb processes such as simultaneous ionization with excitation, and the accurate solution of the time-dependent Schr"odinger equation in the presence of intense femto/attosecond laser fields, which paves the way for quantum dynamic imaging and coherent control.

  1. Gaussian Process Model for Collision Dynamics of Complex Molecules.

    PubMed

    Cui, Jie; Krems, Roman V

    2015-08-14

    We show that a Gaussian process model can be combined with a small number (of order 100) of scattering calculations to provide a multidimensional dependence of scattering observables on the experimentally controllable parameters (such as the collision energy or temperature) as well as the potential energy surface (PES) parameters. For the case of Ar-C_{6}H_{6} collisions, we show that 200 classical trajectory calculations are sufficient to provide a ten-dimensional hypersurface, giving the dependence of the collision lifetimes on the collision energy, internal temperature, and eight PES parameters. This can be used for solving the inverse scattering problem, for the efficient calculation of thermally averaged observables, for reducing the error of the molecular dynamics calculations by averaging over the PES variations, and for the analysis of the sensitivity of the observables to individual parameters determining the PES. Trained by a combination of classical and quantum calculations, the model provides an accurate description of the quantum scattering cross sections, even near scattering resonances.

  2. Exchange effects and collision mechanisms in (e, 2e) processes

    NASA Astrophysics Data System (ADS)

    Zhang-jin, Chen; Zhi-xiang, Ni; Qi-cun, Shi; Ke-zun, Xu

    1998-07-01

    In this work the triple differential cross sections for electron impact ionization of helium at an incident energy of 64.6 eV is considered in the coplanar symmetric energy-sharing and fixed relative angles of the two out-going electrons kinematics. A new collision process called triple-binary collision is identified. It has been shown that the ordinary double-binary collision process is excluded from the collision kinematics considered here. It has also been shown how the exchange effects symmetrically contribute to the peaks in the cross sections.

  3. Optimal separable bases and molecular collisions

    SciTech Connect

    Poirier, Lionel 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 + H2 → 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.

  4. Shielding ultracold dipolar molecular collisions with electric fields

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Bohn, John

    2016-05-01

    The prospect for shielding ultracold dipolar molecules from inelastic and reactive collisions is 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. This repulsion can safely allow the molecules to scatter while reducing the risk of inelastic or chemically reactive collisions. Several molecular species of molecules of experimental interest such as NaRb, NaK, 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. We acknowledge the financial support of the COPOMOL project (ANR-13-IS04-0004) from Agence Nationale de la Recherche and the ARO MURI Grant No. W911NF-12-1-0476.

  5. 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.

  6. 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

  7. 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

  8. A novel molecular synchrotron for cold collision and EDM experiments

    PubMed Central

    Hou, Shunyong; Wei, Bin; Deng, Lianzhong; Yin, Jianping

    2016-01-01

    Limited by the construction demands, the state-of-the-art molecular synchrotrons consist of only 40 segments that hardly make a good circle. Imperfections in the circular structure will lead to the appearance of unstable velocity regions (i.e. stopbands), where molecules of certain forward velocity will be lost from the structure. In this paper, we propose a stopband-free molecular synchrotron. It contains 1570 ring electrodes, which nearly make a perfect circle, capable of confining both light and heavy polar molecules in the low-field-seeking states. Molecular packets can be conveniently manipulated with this synchrotron by various means, like acceleration, deceleration or even trapping. Trajectory calculations are carried out using a pulsed 88SrF molecular beam with a forward velocity of 50 m/s. The results show that the molecular beam can make more than 500 round trips inside the synchrotron with a 1/e lifetime of 6.2 s. The synchrotron can find potential applications in low-energy collision and reaction experiments or in the field of precision measurements, such as the searches for electric dipole moment of elementary particles. PMID:27600539

  9. 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.

  10. 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.

  11. Studies of Fluctuation Processes in Nuclear Collisions

    SciTech Connect

    Ayik, Sakir

    2016-04-14

    The standard one-body transport approaches have been extensively applied to investigate heavy-ion collision dynamics at low and intermediate energies. At low energies the approach is the mean-field description of the time-dependent Hartree-Fock (TDHF) theory. At intermediate energies the approach is extended by including a collision term, and its application has been carried out mostly in the semi-classical framework of the Boltzmann-Uhling-Uhlenbeck (BUU) model. The standard transport models provide a good understanding of the average properties of the collision dynamics in terms of the effective interactions in both low and intermediate energies. However, the standard models are inadequate for describing the fluctuation dynamics of collective motion at low energies and disassembling of the nuclear system into fragments at intermediate energies resulting from the growth of density fluctuations in the spinodal region. Our tasks have been to improve the standard transport approaches by incorporating fluctuation mechanisms into the description. There are mainly two different mechanisms for fluctuations: (i) Collisional fluctuations generated by binary nucleon collisions, which provide the dominant mechanism at intermediate energies, and (ii) One-body mechanism or mean-field fluctuations, which is the dominant mechanism at low energies. In the first part of our project, the PI extended the standard transport model at intermediate energies by incorporating collisional mechanism according to the “Generalized Langevin Description” of Mori formalism. The PI and his collaborators carried out a number of applications for describing dynamical mechanism of nuclear multi fragmentations, and nuclear collective response in the semi-classical framework of the approach, which is known as the Boltzmann-Langevin model. In the second part of the project, we considered dynamical description at low energies. Because of the effective Pauli blocking, the collisional dissipation and

  12. 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.

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

    PubMed

    Andrienko, Daniil A; Boyd, Iain D

    2016-07-07

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

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

    NASA Astrophysics Data System (ADS)

    Andrienko, Daniil A.; Boyd, Iain D.

    2016-07-01

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

  15. Applications of cross sections for electron-molecule collision processes

    SciTech Connect

    Cartwright, D.C.

    1985-01-01

    The role of electron-molecule collision cross sections is discussed for the study of the ionospheric and auroral processes in planetary atmospheres and of discharge-pumped lasers. These two areas emphasize the importance of further theoretical and experimental studies concerning electron-impact processes. 13 refs., 3 figs., 2 tabs. (WRF)

  16. Molecular processes in comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1988-01-01

    The transition dipole moments of the c 3 Pi u - a 3 Sigma g +, i 3 Pi g - c 3 Pi u, and i 3 Pi g - b 3 Sigma u + transitions of molecular hydrogen were calculated over a wide range of internuclear distances R. Calculations of the emission spectra are nearing completion. Substantial progress was made in the calculation of the absorption coefficient of a colliding pair of hydrogen atoms in the binary encounter approximation. Detailed calculations were performed on the continuum emission arising from the excitation of the a 3 sigma g + state of H2 by the impact of electrons of various energies. Each curve is labelled by the electron energy in electron volts. The strong emission near Lyman alpha is interesting in that it is produced by excitation of molecular hydrogen.

  17. 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.

  18. Heavy-ion peripheral collisions in the Fermi energy domain : Fragmentation processes or dissipative collisions ?

    NASA Astrophysics Data System (ADS)

    Borderie, B.; Rivet, M. F.; Tassan-Got, L.

    For several years a new field in nuclear physics has been opened by the opportunity to accelerate heavy ions through an energy domain including the Fermi energy of nucleons. The new domain has to be seen as a link between dissipative processes observed at low energies, dominated by mean field considerations, and high energy collisions for which nucleon-nucleon collisions play an important role. This paper reviews our present knowledge on peripheral collisions. A reminder of contiguous energy domains is done as well as their extension in the new field. Specific calculations are also presented. Finally a wide comparison between experiments and calculations is performed. A fast dissipative stage proves to be responsible for the dominant mechanisms involved, at least when the incident energy is lower than 50 MeV/nucleon. Un nouveau champ d'études de la physique nucléaire s'est ouvert depuis quelques années avec la possibilité de réaliser des collisions noyau-noyau dans un domaine en énergie franchissant l'énergie de Fermi des nucléons. Ce nouveau domaine constitue le lien entre les processus dissipatifs observés à basse énergie, dominés par le concept de champ moyen, et les réactions à grande énergie pour lesquelles les collisions nucléon-nucléon jouent un rôle important. Cet article sur les collisions périphériques fait le point sur l'état actuel de nos connaissances. Après un rappel des domaines en énergie connexes, de leurs eventuelles extensions dans le domaine considéré, des calculs spécifiques au domaine sont décrits. Enfin une importante comparaison calculs théoriques-expériences est présentée. Une dissipation en énergie très rapide est responsable des processus dominants observés jusqu'à des énergies incidentes d'environ 50 MeV/nucléon.

  19. Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes.

    PubMed

    Delcorte, Arnaud

    2005-10-07

    This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.

  20. Super-Penrose process due to collisions inside ergosphere

    NASA Astrophysics Data System (ADS)

    Zaslavskii, O. B.

    If two particles collide inside the ergosphere, the energy in the center of mass frame can be made unbound provided at least one of particles has a large negative angular momentum [A. A. Grib and Yu. V. Pavlov, Europhys. Lett. 101 (2013) 20004]. We show that the same condition can give rise to unbounded Killing energy of debris at infinity, i.e. super-Penrose process. Proximity of the point of collision to the black hole horizon is not required.

  1. Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

    The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Universal four-Boson states in ultracold molecular gases: resonant effects in dimer-dimer collisions.

    PubMed

    D'Incao, J P; von Stecher, J; Greene, Chris H

    2009-07-17

    We study the manifestations of universal four-body physics in ultracold dimer-dimer collisions. We show that resonant features associated with three-body Efimov physics and dimer-dimer scattering lengths are universally related. The emergence of universal four-boson states allows for the tunability of the dimer-dimer interaction, thus enabling the future study of ultracold molecular gases with both attractive and repulsive interactions. Moreover, our study of the interconversion between dimers and Efimov trimers shows that B2+B2-->B3+B rearrangement reactions can provide an efficient trimer formation mechanism. Our analysis of the temperature dependence of this reaction provides an interpretation of the available experimental data and sheds light on the possible experimental realization of rearrangement processes in ultracold gases.

  7. Collisional and dissociative processes involving molecular free radicals

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.; Alexander, Millard H.

    1995-04-01

    A collaborative experimental and theoretical study of a number of elementary collisional processes involving small molecular free radicals of importance in combustion and in the decomposition of propellants has been carried out. These have involved chemical reactions and photodissociation, as well as nonreactive collision-induced rotational and electronic transitions. Information on non-bonding interactions involving free radicals was also obtained from analysis of the electronic spectrum of van der Waals complexes of these species.

  8. 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.

  9. Frequency modulated spectroscopy as a probe of molecular collision dynamics.

    PubMed

    Alagappan, Azhagammai; Costen, Matthew L; McKendrick, Kenneth G

    2006-04-01

    We describe the application of frequency modulated spectroscopy (FMS) with an external cavity tuneable diode laser to the study of the scalar and vector properties of inelastic collisions. CN X(2)Sigma(+) radicals are produced by polarized photodissociation of ICN at 266 nm, with a sharp velocity and rotational angular momentum distribution. The collisional evolution of the distribution is observed via sub-Doppler FMS on the A(2)Pi-X(2)Sigma(+) (2,0) band. He, Ar, N(2), O(2) and CO(2) were studied as collider gases. Doppler profiles were acquired in different experimental geometries of photolysis and probe laser propagation and polarization, and on different spectroscopic branches. These were combined to give composite Doppler profiles from which the speed distributions and specific speed-dependent vector correlations could be determined. The angular scattering dynamics with species other than He are found to be very similar, dominated by backward scattering which accompanies transfer of energy between rotation and translation. The kinematics of collisions with He are not conducive to the determination of differential scattering and angular momentum polarization correlations. Angular momentum correlations show interesting differences between reactive and non-reactive colliders. We propose that this reflects differences in the potential energy surfaces, in particular, the nature and depth of attractive potential wells.

  10. Atomic data on inelastic processes in low-energy beryllium-hydrogen collisions

    NASA Astrophysics Data System (ADS)

    Yakovleva, Svetlana A.; Voronov, Yaroslav V.; Belyaev, Andrey K.

    2016-08-01

    Aims: Inelastic processes in low-energy Be + H and Be+ + H- collisions are treated for the states from the ground and up to the ionic state with the aim to provide rate coefficients needed for non-local thermodynamic equilibrium (non-LTE) modeling of beryllium spectra in cool stellar atmospheres. Methods: The electronic molecular structure is determined by using a recently proposed model quantum approach that is based on an asymptotic method. Nonadiabatic nuclear dynamics is treated by means of multichannel formulas, based on the Landau-Zener model for nonadiabatic transition probabilities. Results: The cross sections and the rate coefficients for inelastic processes in Be + H and Be+ + H- collisions are calculated for all transitions between 13 low-lying covalent states plus the ionic state. It is shown that the highest rate coefficient values correspond to the mutual neutralization processes with the final states Be(2s3s 1S), Be(2s3p 1,3P), Be(2s3d 3D). These processes, as well as some of the excitation, de-excitation and ion-pair formation processes, are likely to be important for non-LTE modeling. Tables A.1-A.10 are also available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/593/A27

  11. On the orbital dependence of the asteroidal collision process

    NASA Technical Reports Server (NTRS)

    Ip, W.-H.

    1977-01-01

    Collision of asteroids with the main-belt asteroid population is considered with the effect of the impact kinetic energy taken into account. It is found that objects in eccentric orbits have a larger probability of destructive collision as compared to objects in orbits with mean values of eccentricity (equal to 0.15) and inclination (equal to 10 deg); also orbits with small semimajor axes (about 2.3 AU) are found to have peak values of the probability of destructive collision.

  12. 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.

  13. Cold state-selected molecular collisions and reactions.

    PubMed

    Stuhl, Benjamin K; Hummon, Matthew T; Ye, Jun

    2014-01-01

    Over the past decade, and particularly the past five years, a quiet revolution has been building at the border between atomic physics and experimental quantum chemistry. The rapid development of techniques for producing cold and even ultracold molecules without a perturbing rare-gas cluster shell is now enabling the study of chemical reactions and scattering at the quantum scattering limit with only a few partial waves contributing to the incident channel. Moreover, the ability to perform these experiments with nonthermal distributions comprising one or a few specific states enables the observation and even full control of state-to-state collision rates in this computation-friendly regime: This is perhaps the most elementary study possible of scattering and reaction dynamics.

  14. Radii broadening due to molecular collision in focused ion beams

    NASA Astrophysics Data System (ADS)

    Komuro, Masanori

    1988-01-01

    Point exposures of poly(methyl methacrylate) resist are carried out with focused ion beams of Si++ and Au++ from a liquid AuSi ion source in order to obtain a current density distribution in the probe. All the distributions are composed of a main Gaussian distribution and a long tail dependent on r-3.3 (r means radial distance). The magnitude of this tail increases with the increase in ambient pressure of the ion-drifting space. When the probe is steered at the corner of deflection field, two types of clear ghost patterns appear: (1) circular patterns and (2) lines trailing from the main spot toward the deflection center. It is revealed that they are produced by exposures to ions or energetic neutrals generated with charge transfer collision of the primary ions with residual gas molecules. It is shown that the long tail in the current density distribution is also due to scattering with the residual gas molecules.

  15. 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.

  16. 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.

  17. Vibrational relaxation in H/sub 2/ molecules by wall collisions: applications to negative ion source processes

    SciTech Connect

    Karo, A.M.; Hiskes, J.R.; Hardy, R.J.

    1984-10-01

    In the volume of a hydrogen discharge, H/sub 2/ molecules, excited to high vibrational levels (v'' > 6), are formed either by fast-electron collisions or from H/sub 2//sup +/ ions that are accelerated across the discharge-wall potential that undergo Auger neutralization prior to impact with the discharge chamber wall. We have used computer molecular dynamics to study the de-excitation and re-excitation of vibrationally-excited H/sub 2/ molecules undergoing repeated wall collisions. The initial translational energies range from thermal to 100 eV and the initial vibrational states range from v'' = 2 to v'' = 12. The average loss or gain of vibrational, rotational, translational, and total molecular energies and the survival rates of the molecules have been evaluated. At thermal energies vibrational de-excitation is the predominant process, and a consistent picture emerges of rapid energy redistribution into all the molecular degrees of freedom and a slower rate of loss of total molecular energy to the wall. At higher translational energies (1 to 100 eV) a substantial fraction of the molecules survive with large (v'' > 6) vibrational energy. This vibrational population provides a contribution to the total excited vibrational population comparable to that from the fast-electron collision process.

  18. Theoretical investigation of rotationally inelastic collisions of CH(X2Π ) with molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Dagdigian, Paul J.

    2016-12-01

    We report calculations of state-to-state cross sections for collision-induced rotational transitions of CH(X2Π ) with molecular hydrogen. These calculations employed the diabatic matrix elements of the interaction potential determined by Dagdigian [J. Chem. Phys. 145, 114301 (2016)], which employed the multi-reference configuration-interaction method [MRCISD+Q(Davidson)]. Because of the presence of a deep well on the lower potential energy surface, the scattering calculations were carried out using the quantum statistical method of Manolopoulos and co-workers [Chem. Phys. Lett. 343, 356 (2001)]. The computed cross sections included contributions from direct scattering, as well as from the formation and decay of a collision complex. The magnitude of latter contribution was found to decrease significantly with increasing collision energy. Rotationally energy transfer rate constants were computed for this system since these are required for astrochemical modeling.

  19. 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.

  20. 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.

  1. Effect of collision cascades on dislocations in tungsten: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Fu, B. Q.; Fitzgerald, S. P.; Hou, Q.; Wang, J.; Li, M.

    2017-02-01

    Tungsten (W) is the prime candidate material for the divertor and other plasma-facing components in DEMO. The point defects (i.e. vacancies and self-interstitials) produced in collision cascades caused by incident neutrons aggregate into dislocation loops (and voids), which strongly affect the mechanical properties. The point defects also interact with existing microstructural features, and understanding these processes is crucial for modelling the long term microstructural evolution of the material under fusion conditions. In this work, we performed molecular dynamics simulations of cascades interacting with initially straight edge dislocation dipoles. It was found that the residual vacancy number usually exceeds the residual interstitial number for cascades interacting with vacancy type dipoles, but for interstitial type dipoles these are close. We observed that a cascade near a dislocation promotes climb, i.e. it facilitates the movement of point defects along the climb direction. We also observed that the dislocations move easily along the glide direction, and that kinks are formed near the centre of the cascade, which then facilitate the movement of the dipoles. Some dipoles are sheared off by the cascade, and this is dependent on PKA energy, position, direction, and the width of dipole.

  2. The Conference on the Dynamics of Molecular Collisions Held in Oglebay Park, Wheeling, West Virginia on 12-17 July 1987.

    DTIC Science & Technology

    1987-07-17

    reactive collisions, molecular energy transfer, gas-surface interactions, photodissociation, van der Waals molecules. 12& AMSY onvowers 860 it vseun...transfer processes, and gas-surface interactions, as well as a special session on photiodissociation and van der Waals molecules. There were 240... der Waals Molecules Chairman/Discussion Leader: J. M. Lisy 8:45 G. G. Balint-Kurti, "Theory of Photodissociation Processes and Its Application to van

  3. 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.

  4. 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.

  5. Visual processing of the impending collision of a looming object: time to collision revisited.

    PubMed

    Yan, Jing-Jiang; Lorv, Bailey; Li, Hong; Sun, Hong-Jin

    2011-10-14

    As an object approaches an observer's eye, the optical variable tau, defined as the inverse relative expansion rate of the object's image on the retina (D. N. Lee, 1976), approximates the time to collision (TTC). Many studies have provided support that human observers use TTC, but evidence for the exclusive use of TTC generated by tau remains inconclusive. In the present study, observers were presented with a visual display of two sequentially approaching objects and asked to compare their TTCs at the moment these objects vanished. Upon dissociating several variables that may have potentially contributed to TTC perception, we found that observers were most sensitive to TTC information when completing the task and less sensitive to non-time variables, such as those that specified distance to collision, speed, and object size. Moreover, when we manipulated presented variables to provide conflicting TTC information, TTC specified by tau was weighted much more than TTC derived from distance and speed. In conclusion, our results suggested that even in the presence of other monocular sources of information, observers still had a greater tendency to specifically use optical tau when making relative TTC judgments.

  6. Charge-transfer processes in F{sup 2+}+H{yields}F{sup +}+H{sup +} collisions and the reverse process at low-keV energies

    SciTech Connect

    Dutta, C. M.; Nordlander, P.; Gu, J. P.; Hirsch, G.; Buenker, R. J.; Kimura, M.

    2005-11-15

    Theoretical investigations on single charge-transfer processes in collisions of F{sup 2+}+H{yields}F{sup +}+H{sup +} and its reverse process have been carried out at collision energies from 20 eV/u to 10 keV/u. The molecular orbital expansion method within the semiclassical impact parameter formalism has been employed for the scattering dynamics, while the ab initio multireference single- and double-excitation configuration interaction (MRD-CI) method was adopted for determination of molecular electronic states. The initial channels correspond to the quintet and triplet states for the corresponding collision processes, respectively. Four molecular states in the quintet manifold and eight molecular states in the triplet manifold were coupled. In the quintet manifold, the charge-transfer cross sections for F{sup 2+}+H{yields}F{sup +}+H{sup +} range from 1.3x10{sup -22} cm{sup 2} at 20 eV/u to 2.5x10{sup -15}cm{sup 2} at 10 keV/u. The cross sections of the reverse process, F{sup +}+H{sup +}{yields}F{sup 2+}+H, range from 3.0x10{sup -22} cm{sup 2}to 2.3x10{sup -15} cm{sup 2} in the same energy range. In the triplet states, the charge-transfer cross sections for F{sup 2+}+H{yields}F{sup +}+H{sup +} range from 1.1x10{sup -18} cm{sup 2} to 2.5x10{sup -16} cm{sup 2}, and its reverse process gives charge-transfer cross sections ranging from 1.7x10{sup -24} cm{sup 2} to 1.5x10{sup -17} cm{sup 2}.

  7. 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.

  8. 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.

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

    DTIC Science & Technology

    2016-06-06

    molecular ions has emerged as a new discipline within AMO to bring molecules under control. It is now clear that a trapped sample of ultracold molecular...Angeles Office of Contract and Grant Administration 11000 Kinross Avenue, Suite 211 Los Angeles, CA 90095 -1406 ABSTRACT Final Report: Understanding...ions has emerged as a new discipline within AMO to bring molecules under control. It is now clear that a trapped sample of ultracold molecular ions

  10. An angular momentum approximation for molecular collisions in the presence of intense laser radiation

    NASA Technical Reports Server (NTRS)

    Devries, P. L.; George, T. F.

    1979-01-01

    An approximation to a previously presented rigorous description of molecular (atom-atom) collisions occurring in the presence of intense radiation is investigated. This rigorous description explicitly considers the angular momentum transferred between the molecule and the radiation field in the absorption or emission of a photon, but involves a complicated system of close-coupled equations which must be solved independently for each projection M of the initial, total molecular angular momentum. (This is a direct consequence of the lack of rotational invariance in the molecule-field problem). These equations are solved for a model system which mimics the collision of a halogen with a rare gas atom. Empirical observations made in the course of performing these calculations lead to the development of an approximation which avoids the repeated calculations for each initial M. This orientational average approximation greatly reduces the effort required to describe the system, and for the model calculation, yields accurate results for field intensities as high as 10 GW/sq cm.

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

    SciTech Connect

    Swaminathan-Gopalan, Krishnan; Stephani, Kelly A.

    2016-02-15

    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.

  12. Molecular thermodynamics for chemical process design.

    PubMed

    Prausnitz, J M

    1979-08-24

    Chemical process design requires quantitative information on the equilibrium properties of a variety of fluid mixtures. Since the experimental effort needed to provide this information is often prohibitive in cost and time, chemical engineers must utilize rational estimation techniques based on limited experimental data. The basis for such techniques is molecular thermodynamics, a synthesis of classical and statistical thermodynamics, molecular physics, and physical chemistry.

  13. HH 110: the grazing collision of a Herbig-Haro flow with a molecular cloud core.

    NASA Astrophysics Data System (ADS)

    Reipurth, B.; Raga, A. C.; Heathcote, S.

    1996-07-01

    The HH 110 jet is a major collimated Herbig-Haro flow in Orion. Despite careful searches at optical, infrared and sub-mm wavelengths, attempts to find the driving source along its well defined flow axis have failed. We present deep large-field interference-filter CCD images which reveal the presence of another fainter HH flow, here labelled HH 270, to the north-east of HH 110. This flow is driven by an embedded near-infrared source, which is possibly identical to the 5Lsun_ embedded class I source IRAS 05489+0256. We propose that the source driving HH 270 is also responsible for HH 110, and that the HH 270 flow suffers a grazing collision with the dense molecular cloud core from which HH 110 is seen to emerge. This collision deflects and shocks the flow so that it re-appears as HH 110. This scenario is supported by geometric and kinematic evidence: firstly, the HH 270 flow axis points towards the beginning of HH 110; secondly, proper motion measurements of the brightest knot in HH 270, knot A, reveal a large tangential motion of 300km/s directly towards HH 110 knot A, the apex of this flow; thirdly, HH 110 knot A has a two-component structure consisting of a head and a neck, the former moving in the direction defined by the HH 270 flow, and the latter in the direction of the HH 110 flow, suggesting that we here see directly the point of impact and deflection. Moreover, there is evidence for weak shocks approximately parallel with the HH 110 flow, which appear to be due to separate collisions with obstructions in the flow. We assume that the HH 270/110 flow is not far from the plane of the sky, an assumption supported by the high proper motion of HH 270 A and the low radial velocity of HH 110. The observed angle between HH 270 and HH 110 (58deg), is then close to the true deflection angle which results from the flow collision. Using the observed velocities and the analytical models of Canto et al. (1988), we find theoretically that the deflection angle should be

  14. A rear-end collision risk assessment model based on drivers' collision avoidance process under influences of cell phone use and gender-A driving simulator based study.

    PubMed

    Li, Xiaomeng; Yan, Xuedong; Wu, Jiawei; Radwan, Essam; Zhang, Yuting

    2016-12-01

    Driver's collision avoidance performance has a direct link to the collision risk and crash severity. Previous studies demonstrated that the distracted driving, such as using a cell phone while driving, disrupted the driver's performance on road. This study aimed to investigate the manner and extent to which cell phone use and driver's gender affected driving performance and collision risk in a rear-end collision avoidance process. Forty-two licensed drivers completed the driving simulation experiment in three phone use conditions: no phone use, hands-free, and hand-held, in which the drivers drove in a car-following situation with potential rear-end collision risks caused by the leading vehicle's sudden deceleration. Based on the experiment data, a rear-end collision risk assessment model was developed to assess the influence of cell phone use and driver's gender. The cell phone use and driver's gender were found to be significant factors that affected the braking performances in the rear-end collision avoidance process, including the brake reaction time, the deceleration adjusting time and the maximum deceleration rate. The minimum headway distance between the leading vehicle and the simulator during the rear-end collision avoidance process was the final output variable, which could be used to measure the rear-end collision risk and judge whether a collision occurred. The results showed that although cell phone use drivers took some compensatory behaviors in the collision avoidance process to reduce the mental workload, the collision risk in cell phone use conditions was still higher than that without the phone use. More importantly, the results proved that the hands-free condition did not eliminate the safety problem associated with distracted driving because it impaired the driving performance in the same way as much as the use of hand-held phones. In addition, the gender effect indicated that although female drivers had longer reaction time than male drivers in

  15. Computation of Collision-Induced Absorption by Simple Molecular Complexes, for Astrophysical Applications

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Frommhold, Lothar; Li, Xiaoping; Hunt, Katharine L. C.

    2012-06-01

    The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of various types of planets and cool stars, such as late stars, low-mass stars, brown dwarfs, cool white dwarf stars, the ambers of the smaller, burnt out main sequence stars, exoplanets, etc., and therefore of special astronomical interest The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. First results for H_2-He complexes have already been applied to astrophysical models have shown great improvements in these models. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin, Int. J. of Spect., vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin, J. Phys. Chem. A, 115, 6805-6812, 2011} L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Infrared absorption by collisional H_2-He complexes

  16. 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.

  17. Molecular Collision Processes in Gases and at Surfaces.

    DTIC Science & Technology

    1987-12-12

    principle that has been understood since Le Chatelier and undeniable since Gibbs. The results seem to reveal promising possibilities for VUV sources of...for public release; 2b. DECLASSiFICATIONIOOWNGRADING SCHEDULE distribution unlimited. & 4. PERFORMING ORGANIZATION REPORT NUMBER( S ) 5. MONITORING...ORGANIZATION REPORT NUMBER( S ). AFOSR.TR. 8 -0 132 6a. NAME OF PERFORMING ORGANIZATION 6b OFFICE SYMBOL 7a. NAME OF MONITORING ORGANIZATION Yale University

  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. 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.

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

    DTIC Science & Technology

    2014-02-03

    Schowalter, Svetlana Kotochigova, Kuang Chen, Eric R. Hudson. Evidence for sympathetic vibrational cooling of translationally cold molecules, Nature...03 2013): 0. doi: 10.1038/nature11937 Wade G. Rellergert, Scott T. Sullivan, Svetlana Kotochigova, Eric R. Hudson. Role of Electronic Excitations...109.223002 Kuang Chen, Steven Schowalter, Svetlana Kotochigova, Alexander Petrov, Wade Rellergert, Scott Sullivan, Eric Hudson. Molecular-ion trap

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    Charge exchange in collisions of C6+ ions with H and H2 is investigated theoretically at projectile energies 0.1 < E < 10 keV/amu, using electron nuclear dynamics (END) - a semi-classical approximation which not only includes electron translation factors for avoiding spurious couplings but also employs full dynamical trajectories to treat nuclear motions. Both the total and partial cross sections are reported for the collision of C6+ ions with atomic and molecular hydrogen. A comparison with other theoretical and experimental results shows, in general good agreement except at very low energy, considered here. For H2, the one- and two-electron charge exchange cross sections are calculated and compared with other theoretical and experimental results. Small but non-negligible isotope effects are found at the lowest energy studied in the charge transfer of C6+ with H. In low energy region, it is observed that H2 has larger isotope effects than H atom due to the polarizability effect which is larger than the mass effect.

  3. Ionization processes in collisions of open-shell atoms. III - The autoionizing states of nitrogen

    NASA Technical Reports Server (NTRS)

    Boumsellek, S.; Esaulov, V. A.

    1990-01-01

    Results of a study of the energy spectra of electrons produced in collisions of N atoms with inert gases at low keV energies are reported. Ionization here is partly due to production of the (1Dnl) autoionizing states of nitrogen and partly due to another mechanism, which is presumably quasi molecular Auger ionization. A discussion of the assignments of the autoionizing states is presented.

  4. 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.

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

    PubMed

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

    2012-09-14

    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)(X(3)B(1))] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH(2)(X(3)B(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 CH(2), CHD, and CD(2) 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)(X(3)B(1)) molecules in a magnetic trap. Furthermore, we find that ortho-CH(2) undergoes collision-induced spin relaxation much more slowly than para-CH(2), which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.

  6. 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.

  7. Space Object Collision Probability via Monte Carlo on the Graphics Processing Unit

    NASA Astrophysics Data System (ADS)

    Vittaldev, Vivek; Russell, Ryan P.

    2017-03-01

    Fast and accurate collision probability computations are essential for protecting space assets. Monte Carlo (MC) simulation is the most accurate but computationally intensive method. A Graphics Processing Unit (GPU) is used to parallelize the computation and reduce the overall runtime. Using MC techniques to compute the collision probability is common in literature as the benchmark. An optimized implementation on the GPU, however, is a challenging problem and is the main focus of the current work. The MC simulation takes samples from the uncertainty distributions of the Resident Space Objects (RSOs) at any time during a time window of interest and outputs the separations at closest approach. Therefore, any uncertainty propagation method may be used and the collision probability is automatically computed as a function of RSO collision radii. Integration using a fixed time step and a quartic interpolation after every Runge Kutta step ensures that no close approaches are missed. Two orders of magnitude speedups over a serial CPU implementation are shown, and speedups improve moderately with higher fidelity dynamics. The tool makes the MC approach tractable on a single workstation, and can be used as a final product, or for verifying surrogate and analytical collision probability methods.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Plasma and collision processes of hypervelocity meteorite impact in the prehistory of life

    NASA Astrophysics Data System (ADS)

    Managadze, G.

    2010-07-01

    have been explained by an identical process occurring in the plasma torch of hypervelocity collisions between submicron size dust particles. It is assumed that the processes occurred in the highly unbalanced hot plasma simultaneously with the synthesis of simple and complicated organic compounds, thereby ensuring their ordering and assembly. Bona fide experimental evidence presented below indicates that the physical fields generated in the plasma environment in the process of the formation and expansion of the torch meet the main requirements toward “true” local chiral fields. These fields were very likely to be capable to trigger the initial, weak breaking of enantiomer symmetry and determine the “sign” of the asymmetry of the bioorganic world. These fields could have worked as “trapping” fields influencing spontaneous processes occurring in highly overheated and nonequilibrium plasma in the state that is far from the thermodynamical branch of equilibrium and may have contributed to the formation of an environment needed for the synthesis of homochiral molecular structures, which, in turn, were needed for the emergence of the primary forms of living matter. It has been shown experimentally that the plasma-chemical processes in the torch have high catalytic properties and assure the rise of the chemical reaction rates by 10-100 million times. In the process of the plasma flyaway this in turn can assure the fast formation of simple and complicated organic compounds, including hyper-branched polymers. It is possible to assume that predominantly inorganic substances from meteorites were used for the synthesis of complicated organic compounds on early Earth. A laboratory experiment with hypervelocity impact plasma torch modelling by a laser with a Q-switch mode has shown the possibility of high-molecular organic compound synthesis, with mass of approximately 5000 a.m.u. by meteorite impact with an effective diameter of 100 mkm. The target contained only H, C, N

  13. 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.

  14. Molecular processes in cellular arsenic metabolism

    SciTech Connect

    Thomas, David J.

    2007-08-01

    Elucidating molecular processes that underlie accumulation, metabolism and binding of iAs and its methylated metabolites provides a basis for understanding the modes of action by which iAs acts as a toxin and a carcinogen. One approach to this problem is to construct a conceptual model that incorporates available information on molecular processes involved in the influx, metabolism, binding and efflux of arsenicals in cells. This conceptual model is initially conceived as a non-quantitative representation of critical molecular processes that can be used as a framework for experimental design and prediction. However, with refinement and incorporation of additional data, the conceptual model can be expressed in mathematical terms and should be useful for quantitative estimates of the kinetic and dynamic behavior of iAs and its methylated metabolites in cells. Development of a quantitative model will be facilitated by the availability of tools and techniques to manipulate molecular processes underlying transport of arsenicals across cell membranes or expression and activity of enzymes involved in methylation of arsenicals. This model of cellular metabolism might be integrated into more complex pharmacokinetic models for systemic metabolism of iAs and its methylated metabolites. It may also be useful in development of biologically based dose-response models describing the toxic and carcinogenic actions of arsenicals.

  15. MOLECULAR PROCESSES IN CELLULAR ARSENIC METABOLISM

    EPA Science Inventory

    Elucidating molecular processes that underlie accumulation, metabolism, and binding of iAs and its methylated metabolites provides a basis for understanding the modes of action by which iAs acts as a toxin and a carcinogen. One approach to this problem is to construct a conceptu...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Energy Transfer Collisional Process Involving Heteromolecular Collisions Between Methyl Fluoride and N_2, Ar, He, CO_2, and Air

    NASA Astrophysics Data System (ADS)

    Phillips, Dane J.; Everitt, Henry O.

    2013-06-01

    Time resolved IR/THz double resonance (DR) spectroscopy has been performed with a Q-switched CO_2 laser and heterodyne THz detection. The rate constants associated with allowed rotational- and vibrational-state changing collisions of CH_3F with N_2, Ar, He, CO_2, and air are measured by monitoring the temporal evolution of the absorption strength for numerous rotational transitions as a function of pressure. Collision partner dependent energy transfer processes are studied and compared with homomolecular collisions. Energy transfer maps and associated collisional cross sections will be presented for each collision partner.

  1. Molecular Dynamic Simulation of Collision-Induced Third-Body Formation in Hydrogen-Free Diamond-Like Carbon Asperities.

    PubMed

    von Lautz, Julian; Pastewka, Lars; Gumbsch, Peter; Moseler, Michael

    The collision of two cylindrical hydrogen-free diamond-like carbon (DLC) asperities with approximately 60 % sp(3) hybridization has been studied using classical molecular dynamics. The severity of the collision can be controlled by the impact parameter b that measures the width of the projected overlap of the two cylinders. For a cylinder radius of R = 23 nm, three collisions with b = 0.5 nm, b = 1 nm and b = 2.0 nm are compared. While for the two small b a single shear band between the collision partners and a strongly localized sp(2)/sp(1) hybridised third-body zone between the asperities is observed, the b = 2 nm collision is accompanied by pronounced plastic deformation in both asperities that destabilize the metastable sp(3)-rich phase leading to a drastic increase in the amount of rehybridized tribomaterial. In addition, pronounced roughening of the cylinder surfaces, asymmetric material transfer and the generation of wear debris are found in this case. For the b = 0.5 and 1 nm collision, the evolution of third-body volume can be quantitatively described by a simple geometric overlap model that assumes a sliding-induced phase transformation localized between both asperities. For b = 2 nm, this model underestimates the third-body volume by more than 150 % indicating that plasticity has to be taken into account in simple geometric models of severe DLC/DLC asperity collisions.

  2. Collision processes at the northern margin of the Black Sea

    NASA Astrophysics Data System (ADS)

    Gobarenko, V. S.; Murovskaya, A. V.; Yegorova, T. P.; Sheremet, E. E.

    2016-07-01

    Extended along the Crimea-Caucasus coast of the Black Sea, the Crimean Seismic Zone (CSZ) is an evidence of active tectonic processes at the junction of the Scythian Plate and Black Sea Microplate. A relocation procedure applied to weak earthquakes (mb ≤ 3) recorded by ten local stations during 1970-2013 helped to determine more accurately the parameters of hypocenters in the CSZ. The Kerch-Taman, Sudak, Yuzhnoberezhnaya (South Coast), and Sevastopol subzones have also been recognized. Generalization of the focal mechanisms of 31 strong earthquakes during 1927-2013 has demonstrated the predominance of reverse and reverse-normal-faulting deformation regimes. This ongoing tectonic process occurs under the settings of compression and transpression. The earthquake foci with strike-slip component mechanisms concentrate in the west of the CSZ. Comparison of deformation modes in the western and eastern Crimean Mountains according to tectonophysical data has demonstrated that the western part is dominated by strike-slip and normal- faulting, while in the eastern part, reverse-fault and strike-slip deformation regimes prevail. Comparison of the seismicity and gravity field and modes of deformation suggests underthusting of the East Black Sea Microplate with thin suboceanic crust under the Scythian Plate. In the Yuzhnoberezhnaya Subzone, this process is complicated by the East Black Sea Microplate frontal part wedging into the marginal part of the Scythian Plate crust. The indentation mechanism explains the strong gravity anomaly in the Crimean Mountains and their uplift.

  3. 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.

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

    PubMed

    Tscherbul, T V; Dalgarno, A

    2010-11-14

    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)Σ and (3)Σ electronic states with structureless atoms and with unlike (2)Σ and (3)Σ molecules. The cross sections for elastic scattering and Zeeman relaxation in low-temperature collisions of CaH((2)Σ(+)) and NH((3)Σ(-)) molecules with (3)He 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.

  5. Application of molecular modeling to biological processing

    NASA Astrophysics Data System (ADS)

    Lowrey, Alfred H.; Famini, George R.; Wick, Charles

    1993-07-01

    Detailed understanding of the molecular basis for biological processes is now available through computational modeling techniques. Advances in computational algorithms and technology allow applications to large biological macromolecules and permits the study of such problems as binding mechanisms, chemical reactivity, structural and conformational effects, and simulations of molecular motions. Recent crystallographic data provides access to detailed structural information that allows analysis and comparison of various computational techniques. Preliminary semiempirical studies on N-acetylneuraminic acid are presented as an example of computational studies on binding mechanisms. N-acetylneuraminic acid is a substituted carbohydrate, which is a recognition site for binding of proteins (i.e., cholera toxin). These calculations provide some insight into electronic effects on bin in a crystal complex and the effect of the molecular charge on hydrogen bonding the crystal complex.

  6. 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.

  7. Potential curves and nonadiabatic matrix elements for collisions involving fragments of the HeN + molecular ion

    NASA Astrophysics Data System (ADS)

    Gu, Jian-ping; Buenker, Robert J.; Hirsch, Gerhard; Kimura, Mineo

    1995-05-01

    Ab initio multireference CI calculations have been carried out for the HeN+ molecular ion in order to describe collision processes between its constituent neutral and ionized atoms. The accuracy of these calculations is evaluated by means of a comparison of results obtained at large internuclear separations with the corresponding asymptotic energies deduced from atomic spectral data. Energy values are computed for the eleven lowest He++N and He+N+ atomic limits and average discrepancies relative to the experimental excitation energies up to 110 000 cm-1 are found to lie in the 1000-3000 cm-1 range, of which only 200 cm-1 appears to be the fault of the configuration interaction (CI) technique itself, with the main portion of the error stemming from the choice of atomic orbital (AO) basis instead. The HeN+ X 3Σ- ground state is calculated to have a De value of only 1414 cm-1, but the excited 2 3Π state has a much larger value of 22 133 cm-1 by virtue of an avoided crossing with the lower state of this symmetry. The corresponding radial nonadiabatic coupling is responsible for a large cross section for an excitation process between the N+(3Pg)+He and N+(3Du)+He channels which indirectly provides an efficient electron-capture mechanism leading to the N(4Su)+He+ exit channel. Additional nonadiabatic matrix elements for rotational and spin-orbit coupling have also been obtained and analyzed, as well as transition moments between the various HeN+ molecular states calculated.

  8. 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.

  9. High-speed collision of copper nanoparticle with aluminum surface: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Pogorelko, Victor V.; Mayer, Alexander E.; Krasnikov, Vasiliy S.

    2016-12-01

    We investigate the effect of the high-speed collision of copper nanoparticles with aluminum surface by means of molecular dynamic simulations. Studied diameter of nanoparticles is varied within the range 7.2-22 nm and the velocity of impact is equal to 500 or 1000 m/s. Dislocation analysis shows that a large quantity of dislocations is formed within the impact area. Overall length of dislocations is determined, first of all, by the impact velocity and by the size of incident copper nanoparticle, in other words, by the kinetic energy of the nanoparticle. Dislocations occupy the total volume of the impacted aluminum single crystal layer (40.5 nm in thickness) in the form of intertwined structure in the case of large kinetic energy of the incident nanoparticle. Decrease in the initial kinetic energy or increase in the layer thickness lead to restriction of the penetration depth of the dislocation net; formation of separate dislocation loops is observed in this case. Increase in the initial system temperature slightly raises the dislocation density inside the bombarded layer and considerably decreases the dislocation density inside the nanoparticle. The temperature increase also leads to a deeper penetration of the copper atoms inside the aluminum. Additional molecular dynamic simulations show that the deposited particles demonstrate a very good adhesion even in the case of the considered relatively large nanoparticles. Medium energy of the nanoparticles corresponding to velocity of about 500 m/s and elevated temperature of the system about 700-900 K are optimal parameters for production of high-quality layers of copper on the aluminum surface. These conditions provide both a good adhesion and a less degree of the plastic deformation. At the same time, higher impact velocities can be used for combined treatment consisting of both the plastic deformation and the coating.

  10. Molecular-dynamics simulations of collisions between energetic clusters of atoms and metal substrates

    SciTech Connect

    Hsieh, H.; Averback, R.S. ); Sellers, H. ); Flynn, C.P. )

    1992-02-15

    The collisional dynamics between clusters of Cu, Ni, or Al atoms, with energies of 92 eV to 1.0 keV and sizes of 4 to 92 atoms, and substrates of these same metals were studied using molecular-dynamics computer simulations. A diverse behavior was observed, depending sensitively on the size and energy of the cluster, the elastic and chemical properties of the cluster-substrate combination, and the relative mass of the cluster and substrate atoms. For the 92-atom Cu clusters impacting a Cu substrate, the cluster can form a glob'' on the surface at low energy, while penetrating the substrate and heavily deforming it at high energies. When the cluster energy exceeds {approx}25 eV/atom, the substrate suffers radiation damage. The 92-atom Al clusters do not much deform Ni substrates, but rather tend to spread epitaxially over the surface, despite the 15% lattice mismatch. For 1-keV collisions, several Al atoms dissociate from the cluster, either reflecting into the vacuum or scattering over the surface. 326-eV Ni clusters embed themselves almost completely within Al substrates and form localized amorphous zones. The potentials for these simulations were derived from the embedded-atom method, although modified to treat the higher-energy events. IAb initioP linear-combination-of-atomic-orbitals--molecular-orbitals calculations were employed to test these potentials over a wide range of energies. A simple model for the expected macroscopic behavior of cluster-solid interactions is included as an appendix for a comparison with the atomistic description offered by the simulations.

  11. 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

  12. 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.

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  16. 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.

  17. 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.

  18. 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

    2010-03-03

    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

  19. Star Formation Activity in the Molecular Cloud G35.20–0.74: Onset of Cloud–Cloud Collision

    NASA Astrophysics Data System (ADS)

    Dewangan, L. K.

    2017-03-01

    To probe star formation (SF) processes, we present results of an analysis of the molecular cloud G35.20‑0.74 (hereafter MCG35.2) using multi-frequency observations. The MCG35.2 is depicted in a velocity range of 30–40 km s‑1. An almost horseshoe-like structure embedded within the MCG35.2 is evident in the infrared and millimeter images and harbors the previously known sites, ultra-compact/hyper-compact G35.20‑0.74N H ii region, Ap2-1, and Mercer 14 at its base. The site, Ap2-1, is found to be excited by a radio spectral type of B0.5V star where the distribution of 20 cm and Hα emission is surrounded by the extended molecular hydrogen emission. Using the Herschel 160–500 μm and photometric 1–24 μm data analysis, several embedded clumps and clusters of young stellar objects (YSOs) are investigated within the MCG35.2, revealing the SF activities. A majority of the YSOs clusters and massive clumps (500–4250 {M}ȯ ) are seen toward the horseshoe-like structure. The position–velocity analysis of 13CO emission shows a blueshifted peak (at 33 km s‑1) and a redshifted peak (at 37 km s‑1) interconnected by lower intensity intermediate velocity emission, tracing a broad bridge feature. The presence of such a broad bridge feature suggests the onset of a collision between molecular components in the MCG35.2. A noticeable change in the H-band starlight mean polarization angles has also been observed in the MCG35.2, probably tracing the interaction between molecular components. Taken together, it seems that the cloud–cloud collision process has influenced the birth of massive stars and YSOs clusters in the MCG35.2.

  20. Transdifferentiation: a cell and molecular reprogramming process.

    PubMed

    Sisakhtnezhad, Sajjad; Matin, Maryam M

    2012-06-01

    Evidence has emerged recently indicating that differentiation is not entirely a one-way process, and that it is possible to convert one cell type to another, both in vitro and in vivo. This phenomenon is called transdifferentiation, and is generally defined as the stable switch of one cell type to another. Transdifferentiation plays critical roles during development and in regeneration pathways in nature. Although this phenomenon occurs rarely in nature, recent studies have been focused on transdifferentiation and the reprogramming ability of cells to produce specific cells with new phenotypes for use in cell therapy and regenerative medicine. Thus, understanding the principles and the mechanism of this process is important for producing desired cell types. Here some well-documented examples of transdifferentiation, and their significance in development and regeneration are reviewed. In addition, transdifferentiation pathways are considered and their potential molecular mechanisms, especially the role of master switch genes, are considered. Finally, the significance of transdifferentiation in regenerative medicine is discussed.

  1. 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.

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

    PubMed

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

    2016-06-16

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

  3. Mixed Quantum/Classical Approach for Description of Molecular Collisions in Astrophysical Environments.

    PubMed

    Semenov, Alexander; Babikov, Dmitri

    2015-05-21

    An efficient and accurate mixed quantum/classical theory approach for computational treatment of inelastic scattering is extended to describe collision of an atom with a general asymmetric-top rotor polyatomic molecule. Quantum mechanics, employed to describe transitions between the internal states of the molecule, and classical mechanics, employed for description of scattering of the atom, are used in a self-consistent manner. Such calculations for rotational excitation of HCOOCH3 in collisions with He produce accurate results at scattering energies above 15 cm(-1), although resonances near threshold, below 5 cm(-1), cannot be reproduced. Importantly, the method remains computationally affordable at high scattering energies (here up to 1000 cm(-1)), which enables calculations for larger molecules and at higher collision energies than was possible previously with the standard full-quantum approach. Theoretical prediction of inelastic cross sections for a number of complex organic molecules observed in space becomes feasible using this new computational tool.

  4. 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.

  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. Interaction of Radiation with Matter: Atomic Collision Processes Occurring in the Presence of Radiation Fields

    DTIC Science & Technology

    1988-09-15

    Degenerate Four -Wave Mixing,* Saturation Spectroscopy,’ Dressed Atom,’ Photon Echo: Bloch Equations’, Collision Kernel; Collisions; Optical Noise, 20...information regarding high resolution laser spectroscopy. The initial problem which was studied involved the four -wave mixing signals generated in Na vapor...in four -wave mixing. If the ground and excited state collision rates for a two-level atom differ, collisions result in non-conservation of population

  7. Elastic and inelastic processes in H{sup +}+C{sub 2}H{sub 6} collisions below the 10-keV regime

    SciTech Connect

    Suzuki, Reiko; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.; Pichl, Lukas; Kimura, Mineo

    2005-11-15

    Charge-transfer processes in collisions of H{sup +} ions with C{sub 2}H{sub 6} molecules are investigated theoretically below 10-keV collision energies within a molecular representation. Converged total as well as differential cross sections are obtained in this energy range within a discrete basis of electronic states computed by ab inito methods. The present collision system suggests that the combination of the Demkov-type and Landau-Zener-type mechanisms primarily governs the scattering dynamics for the flux exit from the initial channel. The present charge-transfer cross sections determined are found to agree very well with all available experimental data below a few keV, but begin to deviate above 3 keV, in which the present results slowly decrease, while measurements stay nearly constant. From the study of the electronic state calculation, we provide some information on fragmented species, which should help shed some light on the fragmentation mechanism and process of C{sub 2}H{sub 6}{sup +} ions produced after charge transfer. In addition, the vibrational effect of the initial target to charge transfer is examined.

  8. 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…

  9. 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 ω ≈ 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 ΔJ 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.

  10. Matter-wave entanglement and teleportation by molecular dissociation and collisions.

    PubMed

    Opatrný, T; Kurizki, G

    2001-04-02

    We propose dissociation of cold diatomic molecules as a source of atom pairs with highly correlated (entangled) positions and momenta, approximating the original quantum state introduced by Einstein, Podolsky, and Rosen (EPR) [Phys. Rev. 47, 777 (1935)]. Wave packet teleportation is shown to be achievable by its collision with one of the EPR correlated atoms and manipulation of the other atom in the pair.

  11. Formation rate for Rb 2 + molecular ions created in collisions of Rb Rydberg and ground-state atoms

    NASA Astrophysics Data System (ADS)

    Stanojevic, Jovica; Côté, Robin

    2016-05-01

    We calculate the formation rate of the molecular Rb2+ion in its various bound states produced in the associative ionization of a Rydberg and a ground-state atom. Before the formation takes place, the colliding atoms are accelerated by an attractive force between the collision partners. In this way the ground-state atom is first captured by the Rydberg electron and then guided towards the positive ion-core where a molecular ion is subsequently formed. As recently demonstrated, this process results in giant collisional cross sections for the molecular ion formation, with the cross sections essentially determined by the size of the Rydberg atom. For sufficient high principal quantum numbers and atomic densities, many ground-state atoms are already located inside the Rydberg atom and ready to participate in the associative ionization. The same process can occur between a Rydberg and a ground-state atom that form a long-range Rydberg molecule, possibly contributing to the shortening of the lifetimes of Rydberg atoms and molecules. Partial support from the US Army Research Office (ARO-MURI W911NF-14-1-0378), and from NSF (Grant No. PHY-1415560).

  12. Atomic and molecular collision aspects of thermospheric uranium-vapor releases. Technical report, 15 February 1980-31 December 1985

    SciTech Connect

    Hamlin, D.A.

    1990-05-01

    The DNA Uranium (Oxides) LWIR Review Committee considered the effectiveness of field measurements of the LWIR from uranium oxides produced by (hypothetical) controlled releases of uranium vapor from rockets in the thermosphere. Collated here is the writer's work supporting the committee on atomic and molecular collision aspects of such releases. Included is an essential auxiliary study to (a) understand, in terms of atomic and molecular parameters, coefficients for Ba+ diffusion along the magnetic field as measured and predicted for Ba-release events and (b) apply that (limited) understanding to U-release studies. For particles colliding with neutral atmospheric species, several interaction potentials are used to compute velocity-dependent momentum-transfer cross sections, stopping power and range versus energy, and diffusion coefficients. The momentum-transfer cross sections are also compared with cross sections for certain uranium oxide reactions specially atom-transfer reactions.

  13. Single- and Multiple-Electron Removal Processes in Proton-Water Vapor Collisions

    NASA Astrophysics Data System (ADS)

    Murakami, Mitsuko; Kirchner, Tom; Horbatsch, Marko; Jürgen Lüdde, Hans

    2012-06-01

    Charge-state correlated cross sections for single- and multiple-electron removal processes due to capture and ionization in proton-H2O collisions are calculated by using the non-perturbative basis generator method adapted for ion-molecule collisions [1]. Orbital-specific cross sections for vacancy production are evaluated using this method to predict the yields of charged fragments (H2O^+, OH^+, H^+, O^+) according to branching ratios known to be valid at high impact energies. At intermediate and low energies, we obtain fragmentation results on the basis of predicted multi-electron removal cross sections, and explain most of the available experimental data [2]. The cross sections for charge transfer and for ionization are also compared with recent multi-center classical-trajectory Monte Carlo calculations [3] for impact energies from 20keV to several MeV. [4pt] [1] H.J. L"udde et al, Phys. Rev. A 80, 060702(R) (2009)[0pt] [2] M. Murakami et al, to be submitted to Phys. Rev. A (2012)[0pt] [3] C. Illescas et al, Phys. Rev. A 83, 052704 (2011)

  14. Modeling of collision and coalescence of droplets during microgravity processing of Zn-Bi immiscible alloys

    NASA Technical Reports Server (NTRS)

    Davis, R. H.; Rogers, J. R.

    1990-01-01

    A population balance model is presented for the coarsening of the dispersed phase of liquid-liquid two-phase mixtures in microgravity due to gravity sedimentation and Marangoni migration, which lead to the collision and coalescence of droplets. The model is used to predict the evolution of the size distribution of the dispersed phase in a liquid-phase miscibility gap system, Zn-Bi, which has been used in a number of experimental microgravity processing studies in which significant phase segregation has been observed. The analysis shows that increasing the temperature gradient, gravity level, volume fraction of the dispersed phase, initial average drop radius, initial standard deviation of droplet radii, or the temperature coefficient of the interfacial tension leads to an increase in the rate of droplet growth due to collision and coalescence. Comparison of the distribution evolutions for unimodal and bimodal initial distributions shows that the latter yield significantly more rapid droplet growth. Finally, it is shown that droplet growth can be dramatically reduced with antiparallel orientation of the gravity vector and the temperature gradient, provided that the relative magnitude of these two vectors is properly chosen.

  15. Mechanochemical models of processive molecular motors

    NASA Astrophysics Data System (ADS)

    Lan, Ganhui; Sun, Sean X.

    2012-05-01

    Motor proteins are the molecular engines powering the living cell. These nanometre-sized molecules convert chemical energy, both enthalpic and entropic, into useful mechanical work. High resolution single molecule experiments can now observe motor protein movement with increasing precision. The emerging data must be combined with structural and kinetic measurements to develop a quantitative mechanism. This article describes a modelling framework where quantitative understanding of motor behaviour can be developed based on the protein structure. The framework is applied to myosin motors, with emphasis on how synchrony between motor domains give rise to processive unidirectional movement. The modelling approach shows that the elasticity of protein domains are important in regulating motor function. Simple models of protein domain elasticity are presented. The framework can be generalized to other motor systems, or an ensemble of motors such as muscle contraction. Indeed, for hundreds of myosins, our framework can be reduced to the Huxely-Simmons description of muscle movement in the mean-field limit.

  16. 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.

  17. 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

    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.

  18. A SIMPLE METHOD FOR MODELING COLLISION PROCESSES IN PLASMAS WITH A KAPPA ENERGY DISTRIBUTION

    SciTech Connect

    Hahn, M.; Savin, D. W.

    2015-08-20

    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.

  19. 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.

  20. 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.

  1. Kinematics of the CS method for the treatment of molecular collisions

    NASA Astrophysics Data System (ADS)

    Hahne, G. E.

    1984-08-01

    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.

  2. 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

    2001-02-05

    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.

  3. 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

  4. Charge Transport Processes in Molecular Junctions

    NASA Astrophysics Data System (ADS)

    Smith, Christopher Eugene

    Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires

  5. 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.

  6. Femtosecond laser field induced modifications of electron-transfer processes in Ne{sup +}-He collisions

    SciTech Connect

    Lu Zhenzhong; Chen Deying; Fan Rongwei; Xia Yuanqin

    2012-01-02

    We demonstrate the presence of femtosecond laser induced charge transfer in Ne{sup +}-He collisions. Electron transfer in ion-atom collisions is considerably modified when the collision is embedded in a strong laser field with the laser intensity of {approx}10{sup 15} W/cm{sup 2}. The observed anisotropy of the He{sup +} angular distribution confirms the prediction of early work that the capture probability varies significantly with the laser polarization angle.

  7. R-matrix approach with proper boundary conditions for dissipative and nondissipative collision processes

    NASA Astrophysics Data System (ADS)

    Xu, Hao; Shakeshaft, Robin

    2011-01-01

    We develop an R-matrix approach to treating collision processes which explicitly takes into account, by means of a simple energy-dependent analytic function, the out-of-phase oscillations of the incident and scattered standing waves in the interior region. Thereby we avoid the use of the Bloch operator. In place of the Bloch operator the incident wave provides the source term in an inhomogeneous equation for the scattered wave. We take those subchannels not treated exactly into account via the optical potential, which is generally non-Hermitian due to dissipation at the boundary. The optical potential is constructed on a real analytic basis using a resolvent that satisfies outgoing-wave boundary conditions. The use of an analytic basis together with the direct determination of the K matrix, rather than the R matrix, at the boundary (this is done by matching the interior wave function to the nearly exact analytic solution beyond the boundary) makes the method particularly well suited to the treatment of ultracold collisions. We have tested our method by applying it to one-photon single-ionization of (He1s2) accompanied by excitation to He+(2s) or He+(2p) for photon energies above the complete breakup threshold, where the optical potential is non-Hermitian. Excellent agreement with experiment is obtained for the cross sections for photoionization to both He+(n=1) and to He+(n=2). The 2s-to-2p branching ratio is strongly influenced by both the optical potential and, at photon energies less than a few tens of eV above the breakup threshold, the nonadiabatic dipole mixing of the 2s and 2p states.

  8. Drell-Yan process in p A collisions: Path-integral treatment of coherence effects

    NASA Astrophysics Data System (ADS)

    Goncalves, Victor P.; Krelina, Michal; Nemchik, Jan; Pasechnik, Roman

    2016-12-01

    In this work, we investigate production of Drell-Yan (DY) pairs in proton-nucleus collisions in kinematic regions where the corresponding coherence length does not exceed the nuclear radius, RA, and the quantum coherence effects should be treated with special care. The results for the nucleus-to-nucleon production ratio available in the literature so far are usually based on the assumption of a very long coherence length (LCL) lc≫RA. Since the onset of coherence effects is controlled by the coherence length lc, we estimated its magnitude in various kinematic regions of the DY process and found that the LCL approximation should not be used at small and medium c.m. collision energies (√{s }≲200 GeV ) as well as at large dilepton invariant masses. In order to obtain realistic predictions, we computed for the first time the DY cross section using the generalized color dipole approach based on the rigorous Green function formalism, which naturally incorporates the color transparency and quantum coherence effects and hence allows us to estimate the nuclear shadowing with no restrictions on the CL. In addition to the shadowing effect, we studied a complementary effect of initial state interactions (ISI) that causes an additional suppression at large values of the Feynman variable. Numerical results for the nuclear modification factor accounting for the ISI effect and the finite lc are compared to the data available from the fixed-target Fermi National Laboratory measurements and a good agreement has been found. Besides, we present new predictions for the nuclear suppression as a function of dilepton rapidity and invariant mass in the kinematic regions that can be probed by the RHIC collider as well as by the planned AFTER@LHC and LHCb fixed-target experiments.

  9. Nanoparticle-electrode collision processes: the underpotential deposition of thallium on silver nanoparticles in aqueous solution.

    PubMed

    Zhou, Yi-Ge; Rees, Neil V; Compton, Richard G

    2011-08-01

    The electrochemistry of collisions between metal nanoparticles (NPs) and electrode surfaces has been of recent interest with the development of anodic particle coulometry as a characterisation method. For the first time the underpotential deposition of metal ions from solution onto metal nanoparticles during collisions between the NPs and an inert electrode is reported.

  10. Photon from the annihilation process with CGC in the pA collision

    NASA Astrophysics Data System (ADS)

    Benić, Sanjin; Fukushima, Kenji

    2017-02-01

    We discuss the photon production in the pA collision in a framework of the color glass condensate (CGC) with expansion in terms of the proton color source ρp. We work in a regime where the color density ρA of the nucleus is large enough to justify the CGC treatment, while soft gluons in the proton could be dominant over quark components but do not yet belong to the CGC regime, so that we can still expand the amplitude in powers of ρp. The zeroth-order contribution to the photon production is known to appear from the Bremsstrahlung process and the first-order corrections consist of the Bremsstrahlung diagrams with pair produced quarks and the annihilation diagrams of quarks involving a gluon sourced by ρp. Because the final states are different there is no interference between these two processes. In this work we elucidate calculation procedures in details focusing on the annihilation diagrams only. Using the McLerran-Venugopalan model for the color average we numerically calculate the photon production rate and discuss functional forms that fit the numerical results.

  11. Application of Molecular Modeling to Biological Processes

    DTIC Science & Technology

    1993-07-01

    informa- tion. DNA is the storehouse for the information that ultimately governs the synthesis of all biomolecules. It is generally found in the Watson ... Crick double helix . Breakthroughs in computer graphics and simulations have discovered that intercalation of flat aromatic rings is a major mechanism...for mutations.’ 0 Using molecular mechanics, docking studies show that molecules (e.g., acridine) can insert through the edge of the DNA helix . This

  12. Unraveling Cold Molecular Collisions: Stark Decelerators in Crossed-Beam Experiments.

    PubMed

    Onvlee, Jolijn; Vogels, Sjoerd N; van de Meerakker, Sebastiaan Y T

    2016-11-18

    In the last two decades, enormous progress has been made in the manipulation of molecular beams. In particular, molecular decelerators have been developed with which advanced control over neutral molecules in a beam can be achieved. By using arrays of inhomogeneous and time-varying electric (or magnetic) fields, bunches of molecules can be produced with a tunable velocity, narrow velocity spreads, and almost perfect quantum-state purity. These monochromatic or "tamed" molecular beams are ideally suited to be used in crossed-molecular-beam scattering experiments. Here, we review the first generation of these "cold and controlled" scattering experiments that have been conducted in the last decade and discuss the prospects for this emerging field of research in the years to come.

  13. Classical model for electronically non-adiabatic collision processes resonance effects in electronic-vibrational energy transfer

    SciTech Connect

    Orel, Ann E.; Ali, Dominic P.; Miller, William H.

    1981-02-01

    In this paper, a classical model for electronically non-adiabatic collision processes is applied to E → V energy transfer in a collinear system, A + BC (v = 1) → A* + BC (v = 0), resembling Br-H2. Finally, the model, which treats electronic as well as translational, rotational, and vibrational degrees of freedom by classical mechanics, describes the resonance features in this process reasonably well.

  14. Charmonium production in ultra-peripheral heavy ion collisions with two-photon processes

    NASA Astrophysics Data System (ADS)

    Yu, Gong-Ming; Yu, Yue-Chao; Li, Yun-De; Wang, Jian-Song

    2017-04-01

    We calculate the production of large-pT charmonium and narrow resonance state (exotic charmonium) in proton-proton, proton-nucleus, and nucleus-nucleus collisions with the semi-coherent two-photon interactions at Relativistic Heavy Ion Collider (RHIC), Large Hadron Collider (LHC), and Future Circular Collider (FCC) energies. Using the large quasi-real photon fluxes, we present the γγ → H differential cross section for charmonium and narrow resonance state production at large transverse momentum in ultra-peripheral heavy ion collisions. The numerical results demonstrate that the experimental study of ultra-peripheral collisions is feasible at RHIC, LHC, and FCC energies.

  15. 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.

  16. Estimating Bird / Aircraft Collision Probabilities and Risk Utilizing Spatial Poisson Processes

    DTIC Science & Technology

    2012-06-10

    collisions of birds and objects in motion is wind turbine rotors. When a bird flies through the disc swept out by blades of a wind turbine rotor, the...Mathematical Model of Bird Collisions With Wind Turbine Rotors." Solar Energy Engineering 118 (1996): 253-262. 49 U.S. Air Force. "Air Force Instruction...Altitude Band] .............................................................. 44 viii List of Tables Table 1 USAF Wildlife Strikes by Phase of

  17. 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)

  18. Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Hunt, Katharine L. C.; Li, Xiaoping; Frommhold, Lothar

    2010-03-01

    The interaction-induced absorption by collisional pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets and cool stars [1]. The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H2---H2, H2---He, and H2---H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H2 pairs exist only at temperatures below 300 K. We show that our results reproduce these measurements closely so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. This work has been supported in part by the National Science Foundation through Grants AST-0709106 and AST-0708496.[4pt] [1] L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006

  19. Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin

    NASA Astrophysics Data System (ADS)

    Abel, Martin; Hunt, Katharine L. C.; Li, Xiaoping; Frommhold, Lothar

    2010-03-01

    The interaction-induced absorption by collisional pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets and cool stars.ootnotetextL. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H2---H2, H2---He, and H2---H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H2 pairs exist only at temperatures below 300 K. We show that our results reproduce these measurements closely so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. This work has been supported in part by the National Science Foundation through Grants AST-0709106 and AST-0708496.

  20. A novel framework for molecular characterization of atmospherically relevant organic compounds based on collision cross section and mass-to-charge ratio

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan; Krechmer, Jordan E.; Groessl, Michael; Xu, Wen; Graf, Stephan; Cubison, Michael; Jayne, John T.; Jimenez, Jose L.; Worsnop, Douglas R.; Canagaratna, Manjula R.

    2016-10-01

    A new metric is introduced for representing the molecular signature of atmospherically relevant organic compounds, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio (m/z), a two-dimensional Ω - m/z space is developed to facilitate the comprehensive investigation of the complex organic mixtures. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω - m/z space. Species of the same chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of atmospheric transformation mechanisms of organic species. The characteristics of trend lines for a variety of functionalities that are commonly present in the atmosphere can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω - m/z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision-induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Nanoparticle-electrode collision processes: The electroplating of bulk cadmium on impacting silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhou, Yi-Ge; Rees, Neil V.; Compton, Richard G.

    2011-08-01

    We report, for the first time, the bulk deposition (electroplating) of a metal onto nanoparticles during collisions with an inert electrode surface. Experiments show that for silver nanoparticles, multiple layers of Cd atoms can be electroplated onto the AgNPs from aqueous Cd 2+ during collisions with a glassy carbon electrode held at a suitably reducing potential, and an average of 19 atomic layers of cadmium are found to be deposited in the few milliseconds that the NP is in contact with the electrode. For comparison, results are also presented for the underpotential deposition of Cd onto AgNPs under similar conditions.

  6. Fractional processes and nuclear disassembly in very-heavy-ion collisions in the Fermi energy regime

    SciTech Connect

    Schroeder, W.U.

    1991-01-01

    Exclusive measurements of charged products and neutrons were performed for the reactions {sup 197}Au + (29 MeV/u) {sup 208}Pb and {sup 209}Bi + (28.2 MeV/u) {sup 136}Xe. The multiplicities of neutrons and charged particles are found to indicate collision impact parameters with different sensitivities. Characteristic correlations observed between massive products and light particles suggest the dominance of the damped-reaction mechanism in the Fermi energy domain. For central collisions, massive fragments are no longer observed, and a considerable fraction of the mass of the system is found disassembled into light particles and clusters. 75 refs., 19 figs.

  7. 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.

  8. Effects of adsorption and roughness upon the collision processes at the convertor surface of a plasma sputter negative ion sourcea)

    NASA Astrophysics Data System (ADS)

    Kenmotsu, T.; Wada, M.

    2012-02-01

    Atomic collision processes associated with surface production of negative hydrogen ions (H-) 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+ ion and Cs+ 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.

  9. 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.

  10. Precision measurements of cross-sections for inelastic processes in collisions of alkali metal ions with atoms of rare gases

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

    A multifaceted experimental study of collisions of Na+ and K+ ions in the energy range of 0.5-10 keV with He and Ar atoms is presented. Absolute cross-sections for charge-exchange, ionization, stripping and excitation processes were measured using a refined version of the transfer electric field method, angle- and energy-dependent collection of product ions, energy loss and optical spectroscopy methods. The experimental data and the schematic correlation diagrams are employed to analyze and determine the mechanisms for these processes.

  11. Changes in Drivers’ Visual Performance during the Collision Avoidance Process as a Function of Different Field of Views at Intersections

    PubMed Central

    Yan, Xuedong; Zhang, Xinran; Zhang, Yuting; Li, Xiaomeng; Yang, Zhuo

    2016-01-01

    The intersection field of view (IFOV) indicates an extent that the visual information can be observed by drivers. It has been found that further enhancing IFOV can significantly improve emergent collision avoidance performance at intersections, such as faster brake reaction time, smaller deceleration rate, and lower traffic crash involvement risk. However, it is not known how IFOV affects drivers’ eye movements, visual attention and the relationship between visual searching and traffic safety. In this study, a driving simulation experiment was conducted to uncover the changes in drivers’ visual performance during the collision avoidance process as a function of different field of views at an intersection by using an eye tracking system. The experimental results showed that drivers’ ability in identifying the potential hazard in terms of visual searching was significantly affected by different IFOV conditions. As the IFOVs increased, drivers had longer gaze duration (GD) and more number of gazes (NG) in the intersection surrounding areas and paid more visual attention to capture critical visual information on the emerging conflict vehicle, thus leading to a better collision avoidance performance and a lower crash risk. It was also found that female drivers had a better visual performance and a lower crash rate than male drivers. From the perspective of drivers’ visual performance, the results strengthened the evidence that further increasing intersection sight distance standards should be encouraged for enhancing traffic safety. PMID:27716824

  12. Changes in Drivers' Visual Performance during the Collision Avoidance Process as a Function of Different Field of Views at Intersections.

    PubMed

    Yan, Xuedong; Zhang, Xinran; Zhang, Yuting; Li, Xiaomeng; Yang, Zhuo

    2016-01-01

    The intersection field of view (IFOV) indicates an extent that the visual information can be observed by drivers. It has been found that further enhancing IFOV can significantly improve emergent collision avoidance performance at intersections, such as faster brake reaction time, smaller deceleration rate, and lower traffic crash involvement risk. However, it is not known how IFOV affects drivers' eye movements, visual attention and the relationship between visual searching and traffic safety. In this study, a driving simulation experiment was conducted to uncover the changes in drivers' visual performance during the collision avoidance process as a function of different field of views at an intersection by using an eye tracking system. The experimental results showed that drivers' ability in identifying the potential hazard in terms of visual searching was significantly affected by different IFOV conditions. As the IFOVs increased, drivers had longer gaze duration (GD) and more number of gazes (NG) in the intersection surrounding areas and paid more visual attention to capture critical visual information on the emerging conflict vehicle, thus leading to a better collision avoidance performance and a lower crash risk. It was also found that female drivers had a better visual performance and a lower crash rate than male drivers. From the perspective of drivers' visual performance, the results strengthened the evidence that further increasing intersection sight distance standards should be encouraged for enhancing traffic safety.

  13. Novel experimental setup for time-of-flight mass spectrometry ion detection in collisions of anionic species with neutral gas-phase molecular targets.

    PubMed

    Oller, J C; Ellis-Gibbings, L; da Silva, F Ferreira; Limão-Vieira, P; García, G

    We report a novel experimental setup for studying collision induced products resulting from the interaction of anionic beams with a neutral gas-phase molecular target. The precursor projectile was admitted into vacuum through a commercial pulsed valve, with the anionic beam produced in a hollow cathode discharge-induced plasma, and guided to the interaction region by a set of deflecting plates where it was made to interact with the target beam. Depending on the collision energy regime, negative and positive species can be formed in the collision region and ions were time-of-flight (TOF) mass-analysed. Here, we present data on O2 precursor projectile, where we show clear evidence of O(-) and O2(-) formation from the hollow cathode source as well as preliminary results on the interaction of these anions with nitromethane, CH3NO2. The negative ions formed in such collisions were analysed using time-of-flight mass spectrometry. The five most dominant product anions were assigned to H(-), O(-), NO(-), CNO(-) and CH3NO2(-).

  14. 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.

  15. 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.

  16. 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.

  17. 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).

  18. 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.

  19. Measurements of scattering processes in negative ion: Atom collisions. Technical progress report, 1 September 1991--31 December 1994

    SciTech Connect

    Kvale, T.J.

    1994-09-27

    This report describes the progress made on the research objectives during the past three years of the grant. This research project is designed to study various scattering processes which occur in H{sup {minus}} collisions with atomic (specifically, noble gas and atomic hydrogen) targets in the intermediate energy region. These processes include: elastic scattering, single- and double-electron detachment, and target excitation/ionization. For the elastic and target inelastic processes where H{sup {minus}} is scattered intact, the experimental technique of Ion Energy-Loss Spectroscopy (IELS) will be employed to identify the final target state(s). In most of the above processes, cross sections are unknown both experimentally and theoretically. The measurements will provide total cross sections (TCS) initially, and once the angular positioning apparatus is installed, will provide angular differential cross sections (ADCS).

  20. 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.

  1. CLOUD–CLOUD COLLISION AS A TRIGGER OF THE HIGH-MASS STAR FORMATION: A MOLECULAR LINE STUDY IN RCW 120

    SciTech Connect

    Torii, K.; Hasegawa, K.; Hattori, Y.; Sano, H.; Ohama, A.; Yamamoto, H.; Tachihara, K.; Soga, S.; Shimizu, S.; Fukui, Y.; Okuda, T.; Mizuno, N.; Onishi, T.; Mizuno, A.

    2015-06-10

    RCW 120 is a Galactic H ii region that has a beautiful ring shape that is bright in the infrared. Our new CO J = 1–0 and J = 3–2 observations performed with the NANTEN2, Mopra, and ASTE telescopes have revealed that two molecular clouds with a velocity separation of 20 km s{sup −1} are both physically associated with RCW 120. The cloud at −8 km s{sup −1} apparently traces the infrared ring, while the other cloud at −28 km s{sup −1} is distributed just outside the opening of the infrared ring, interacting with the H ii region as suggested by the high kinetic temperature of the molecular gas and by the complementary distribution with the ionized gas. A spherically expanding shell driven by the H ii region is usually considered to be the origin of the observed ring structure in RCW 120. Our observations, however, indicate no evidence of the expanding motion in the velocity space, which is inconsistent with the expanding shell model. We postulate an alternative that, by applying the model introduced by Habe and Ohta, the exciting O star in RCW 120 was formed by a collision between the present two clouds at a collision velocity of ∼30 km s{sup −1}. In the model, the observed infrared ring can be interpreted as the cavity created in the larger cloud by the collision, whose inner surface is illuminated by the strong ultraviolet radiation after the birth of the O star. We discuss that the present cloud–cloud collision scenario explains the observed signatures of RCW 120, i.e., its ring morphology, coexistence of the two clouds and their large velocity separation, and absence of the expanding motion.

  2. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    PubMed

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

    2015-02-13

    Biological transport is supported by 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 analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and 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 motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  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. Transition of the Taiwan-Ryukyu collision-subduction process as revealed by ocean-bottom seismometer observations

    NASA Astrophysics Data System (ADS)

    Chin, Shao-Jinn; Lin, Jing-Yi; Chen, Yen-Fu; Wu, Wen-Nan; Liang, Chin-Wei

    2016-10-01

    Located at the arc-continental collision region between the Eurasian (EP) and Philippine Sea Plates (PSP), Taiwan is usually considered to have a complex tectonic environment, particularly along the eastern coast of the island. To gain a better understanding of the geological evolution of the east Taiwan area, the data from 8 Ocean Bottom Seismometers (OBS) acquired during the Across Taiwan Strait Explosion Experiment in 2012 and 14 inland seismic stations were used to determine a more detailed and accurate distribution of marine earthquakes. Based on the 333 relocated earthquakes and available geophysical data, we suggest two main tectonic boundaries for eastern Taiwan. South of 23.25°N, the homogeneous distribution of earthquakes in the crustal portion for both the inland and offshore areas suggests an ongoing collisional process. North of this location, between approximately 23.25°N and 23.8°N, the abrupt increasing of seismicity depth infers that the underthrusted arc/fore-arc material is deforming due to the collisional compression at depth. In this segment, the subsidence of the arc/fore-arc area determines the transition from collision to subduction. North of 23.8°N, the northwestern dipping PSP is well illustrated by the seismicity both onshore and offshore, indicating a dominant subduction process.

  5. A role for pre-collision processes in the origin of the aseismic zone of the southern Taiwan Central Range

    NASA Astrophysics Data System (ADS)

    Lewis, J. C.; Cavallotti, C. J.; Rau, R. J.

    2015-12-01

    Although Taiwan is one of the most seismically active areas on Earth, two areas on the island are notable for their lack of earthquakes, the coastal plain of central western Taiwan and an elongate area centered on the eastern flank of the southern Central Range. I focus on the latter area and suggest that pre-collision processes may have contributed to its development. Seismogenic strain offshore southeastern Taiwan reveals that the west side of the Luzon arc hosts a forearc sliver that was initially uplifted during basin inversion then tectonically thinned by pull-apart basin formation as collision initiated. This pre-collision history favors the tectonic insertion of a sliver of oceanic crust at depth in the orogenic suture zone. The presence of oceanic crust in this region is consistent with high seismic velocity observations as well as existing analog models. Strain inversions spanning the aseismic zone broadly show crustal thickening and NW-directed shortening to the east, and crustal thinning and SW-directed stretching to the west. Oceanic crust at depth could contribute to the aseismic zone by acting as a relatively strong body sandwiched between the accreted arc and weaker transitional continental crust to the west. In this scenario the aseismic zone is largely composed of forearc rocks that are not internally deforming by elastic deformation mechanisms. Alternatively the sliver may act as a west-pointing wedge (in profile view) that is promoting weaker transitional continental material to detach, imbricate or delaminate in front of the colliding continental promontory (i.e., the Peikang high) that appears to contribute to the low rates of seismicity in western Taiwan. In any of these latter scenarios it would be reasonable to expect changes in crustal architecture that might promote shallowing of the brittle-plastic transition as is observed around the aseismic zone. The specific mechanism for this shallowing remains unresolved and clearly the presence of

  6. Hydrogen Atom Collision Processes in Cool Stellar Atmospheres: Effects on Spectral Line Strengths and Measured Chemical Abundances in Old Stars

    NASA Astrophysics Data System (ADS)

    Barklem, Paul S.

    2012-12-01

    The precise measurement of the chemical composition of stars is a fundamental problem relevant to many areas of astrophysics. State-of-the-art approaches attempt to unite accurate descriptions of microphysics, non-local thermodynamic equilibrium (non-LTE) line formation and 3D hydrodynamical model atmospheres. In this paper I review progress in understanding inelastic collisions of hydrogen atoms with other species and their influence on spectral line formation and derived abundances in stellar atmospheres. These collisions are a major source of uncertainty in non-LTE modelling of spectral lines and abundance determinations, especially for old, metal-poor stars, which are unique tracers of the early evolution of our galaxy. Full quantum scattering calculations of direct excitation processes X(nl) + H leftrightarrow X(n'l') + H and charge transfer processes X(nl) + H leftrightarrow X+ + H- have been done for Li, Na and Mg [1,2,3] based on detailed quantum chemical data, e.g. [4]. Rate coefficients have been calculated and applied to non-LTE modelling of spectral lines in stellar atmospheres [5,6,7,8,9]. In all cases we find that charge transfer processes from the first excited S-state are very important, and the processes affect measured abundances for Li, Na and Mg in some stars by as much as 60%. Effects vary with stellar parameters (e.g. temperature, luminosity, metal content) and so these processes are important not only for accurate absolute abundances, but also for relative abundances among dissimilar stars.

  7. Classical trajectory models for electronically nonadiabatic collision processes: A classical valence bond model for electronic degrees of freedom

    SciTech Connect

    Miller, William H.; Orel, Ann E.

    1981-06-01

    A classical interpretation of the Dirac–Van Vleck spin version of valence bond theory is used in this research to obtain a classical model for electronic degrees of freedom within the valence bond framework. The approach is illustrated by deriving the explicit forms of the classical Hamiltonians, involving electronic and heavy particle degrees of freedom, for the H–H2, F–H2, and O–H2 systems. It is also shown how the initial conditions for both electronic and heavy particle degrees of freedom are chosen to carry out a classical trajectory simulation of collision processes. In addition, the attractive feature of this model is that it is as easily applicable to electronically nonadiabatic processes as it is to adiabatic ones.

  8. Visual displays that directly interface and provide read-outs of molecular states via molecular graphics processing units.

    PubMed

    Poje, Julia E; Kastratovic, Tamara; Macdonald, Andrew R; Guillermo, Ana C; Troetti, Steven E; Jabado, Omar J; Fanning, M Leigh; Stefanovic, Darko; Macdonald, Joanne

    2014-08-25

    The monitoring of molecular systems usually requires sophisticated technologies to interpret nanoscale events into electronic-decipherable signals. We demonstrate a new method for obtaining read-outs of molecular states that uses graphics processing units made from molecular circuits. Because they are made from molecules, the units are able to directly interact with molecular systems. We developed deoxyribozyme-based graphics processing units able to monitor nucleic acids and output alphanumerical read-outs via a fluorescent display. Using this design we created a molecular 7-segment display, a molecular calculator able to add and multiply small numbers, and a molecular automaton able to diagnose Ebola and Marburg virus sequences. These molecular graphics processing units provide insight for the construction of autonomous biosensing devices, and are essential components for the development of molecular computing platforms devoid of electronics.

  9. Ultrafast molecular processes at the short-wavelength regime

    NASA Astrophysics Data System (ADS)

    Picon, A.; Lehmann, C. S.; Bostedt, C.; Rudenko, A.; Rolles, D.; Marinelli, A.; Young, L.; Pratt, S. T.; Southworth, S. H.

    2016-05-01

    Fundamental molecular processes that underlie chemical reactivity and biological processes typically involve intramolecular dynamics consisting of nuclear motion and the flow of charge and energy across atomic sites. Examples include photosynthesis, electron transfer in biomolecules, and molecular fragmentation. Molecular phenomena initiated by the absorption of an XUV/x-ray photon is one of the most challenging questions for the new generation of XUV/x-ray sources. New capabilities at accelerator-based are continuously being developed, being possible to nowadays generate two-color XUV/x-ray pulses with controlled time delay. The site-specificity of those photons allow the excitation of inner-shell electrons in a particular site of the molecule and, with a controlled time delay, the probing of the induced intramolecular dynamics in another site of the same molecule, opening the door to the unexplored field of intramolecular processes initiated by short-wavelength photons. Also, novel XUV/x-ray sources allow the generation of two-color pulses with a high spatio-temporal degree of coherence, suitable for quantum control schemes involving inner-shell electrons. In this talk, we present new theoretical and experimental results towards this direction. This work is funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, under Contract No. DE-AC02-06CH11357.

  10. Role of molecular dynamics on descriptions of shock front processes

    NASA Astrophysics Data System (ADS)

    Karo, A. M.

    1981-07-01

    A computational approach, based on classical molecular dynamics, is used to form a realistic picture of shock induced processes occurring at the shock front and resulting from the detailed, violent motion associated with shock motion on an atomic scale. Prototype studies of phase transitions are discussed. The interaction of the shock front with defects, surfaces, voids, and inclusions, and across grain boundaries are summarized. The critical question of how mechanical energy imparted to a condensed material by shock loading is converted to the activation energy required to overcome some initial energy barrier in an initiation process, is addressed.

  11. 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.

  12. 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.

  13. Understanding molecular-level effects during post-exposure processing

    NASA Astrophysics Data System (ADS)

    Schmid, Gerard M.; Smith, Mark D.; Mack, Chris A.; Singh, Vivek K.; Burns, Sean D.; Willson, C. Grant

    2001-08-01

    The perpetual advancement of materials and equipment for microlithography has resulted in reduction of critical dimensions to scales approaching the size of the molecules that constitute a photoresist. As a result, molecular scale effects such as line edge roughness have become an increasing concern for resist manufacturers and process engineers alike. Computer simulation of lithography has become an integral tool for both process optimization and development of new technologies. However, these simulation tools are generally based upon continuum approximation of the resist material, and are therefore unable to investigate molecular level variations. In this work we investigate the increasing importance of molecular level effects, especially in terms of the contributions of the post exposure bake (PEB) to feature roughness. A linkage has been made between a previously reported mesoscale simulation of the post exposure bake. The mesoscale simulation models discrete transport and reaction events during the post exposure bake to determine solubility variations on the scale of a single oligomeric chain. These solubility variations are then imported into PROLITH and transformed into photoresist topography using the familiar Mack dissolution model. This method has been used to simulate line-edge formation in an APEX-type resist. It is found that the distribution of photoproducts produced during exposure can lead to significant solubility variations during the PEB. These solubility variations can become manifest as roughness of resist feature topogrpahy.

  14. Information processing by simple molecular motifs and susceptibility to noise.

    PubMed

    Mc Mahon, Siobhan S; Lenive, Oleg; Filippi, Sarah; Stumpf, Michael P H

    2015-09-06

    Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that facilitate these essential processes are however subject to a range of random effects and stochastic processes, which jointly affect the reliability of information transmission between receptors and, for example, the physiological downstream response. Information is mathematically defined in terms of the entropy; and the extent of information flowing across an information channel or signalling system is typically measured by the 'mutual information', or the reduction in the uncertainty about the output once the input signal is known. Here, we quantify how extrinsic and intrinsic noise affects the transmission of simple signals along simple motifs of molecular interaction networks. Even for very simple systems, the effects of the different sources of variability alone and in combination can give rise to bewildering complexity. In particular, extrinsic variability is apt to generate 'apparent' information that can, in extreme cases, mask the actual information that for a single system would flow between the different molecular components making up cellular signalling pathways. We show how this artificial inflation in apparent information arises and how the effects of different types of noise alone and in combination can be understood.

  15. Single-electron capture processes in slow collisions of He{sup 2+} ions with O{sub 2}, NH{sub 3}, N{sub 2}, and CO{sub 2}

    SciTech Connect

    Abu-Haija, O.; Kamber, E.Y.; Ferguson, S.M.; Stolterfoht, N.

    2005-10-15

    Using the translational energy-gain spectroscopy technique, we have measured the energy-gain spectra and absolute total cross sections for single-electron capture (SEC) in collisions of He{sup 2+} ions with O{sub 2}, NH{sub 3}, N{sub 2}, and CO{sub 2} at laboratory impact energies between 25 and 400 eV/amu. The measured spectra for the He{sup 2+}-N{sub 2} and CO{sub 2} collision systems show that the dominant reaction channel is due to dissociative transfer ionization (i.e., SEC accompanied by ionization of the molecular target ion). In the case of the He{sup 2+}-NH{sub 3} collision system, nondissociative single-electron capture into n=2 states of He{sup +} with production of NH{sub 3}{sup +} in the ground state is predominantly populated. These processes are observed to be the dominant reaction channels over the entire impact energy region studied and at laboratory scattering angles between 0 deg. and 8 deg. The energy dependence of total cross sections for SEC are also measured and found to slowly increase with increasing impact energies. The measured cross sections are also compared with the available measurements and theoretical results based on the Demkov and Landau-Zener models.

  16. Theoretical Studies Relating to the Interaction of Radiation with Matter: Atomic Collision Processes Occurring in the Presence of Radiation Fields

    DTIC Science & Technology

    1981-09-01

    Two-Level System, Aromic Coherence, Zeeman Coherence, Dressed-Atom Picture, Degenerate Four -Wave Mixing. S20 ABSTRACT (Continue on reverse, *Ida If...Coherences: (S) Effects of Collisions on Zeeman Coherences (1r) Collision Effects in Degenerate- Four -Wave-Mixing, ~ (5) Dressed-Atom Picture in Laser...Effects of collisions on Zeeman coherences, (4) Colision effects in degenerate- four -wave-mixing, and (5) Dressed-atom picture in laser spectroscopy. 1. Two

  17. 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.

  18. 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.

  19. 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.

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

    PubMed

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

    2014-08-07

    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.

  1. 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.

  2. 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.

  3. 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

    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

  4. 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

  5. Collision limited reaction rates for arbitrarily shaped particles across the entire diffusive Knudsen number range.

    PubMed

    Gopalakrishnan, Ranganathan; Thajudeen, Thaseem; Hogan, Christopher J

    2011-08-07

    Aerosol particle reactions with vapor molecules and molecular clusters are often collision rate limited, hence determination of particle-vapor molecule and particle-molecular cluster collision rates are of fundamental importance. These collisions typically occur in the mass transfer transition regime, wherein the collision kernel (collision rate coefficient) is dependent upon the diffusive Knudsen number, Kn(D). While this alone prohibits analytical determination of the collision kernel, aerosol particle- vapor molecule collisions are further complicated when particles are non-spherical, as is often the case for particles formed in high temperature processes (combustion). Recently, through a combination of mean first passage time simulations and dimensional analysis, it was shown that the collision kernel for spherical particles and vapor molecules could be expressed as a dimensionless number, H, which is solely a function of Kn(D). In this work, it is shown through similar mean first passage times and redefinitions of H and Kn(D) that the H(Kn(D)) relationship found for spherical particles applies for particles of arbitrary shape, including commonly encountered agglomerate particles. Specifically, it is shown that to appropriately define H and Kn(D), two geometric descriptors for a particle are necessary: its Smoluchowski radius, which defines the collision kernel in the continuum regime (Kn(D)→0) and its orientationally averaged projected area, which defines the collision kernel in the free molecular regime (Kn(D)→∞). With these two parameters, as well as the properties of the colliding vapor molecule (mass and diffusion coefficient), the particle-vapor molecule collision kernel in the continuum, transition, and free molecular regimes can be simply calculated using the H(Kn(D)) relationship.

  6. Evidence of molecular fragmentation inside the charged droplets produced by electrospray process.

    PubMed

    Banerjee, Shibdas; Prakash, Halan; Mazumdar, Shyamalava

    2011-10-01

    The behavior of the analyte molecules inside the neutral core of the charged droplet produced by the electrospray (ES) process is not unambiguously known to date. We have identified interesting molecular transformations of two suitably chosen analytes inside the ES droplets. The highly stable Ni(II) complex of 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane (1) that consists of a positive charge at the metal center, and the allyl pendant armed tertiary amine containing macrocycle 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetraallyl-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-diene (M(4p)) have been studied by ESI mass spectrometry as the model analytes. We have shown that these two molecules are not representatively transferred from solution to gas phase by ESI; rather, they undergo fragmentation inside the charged droplets. The results indicated that a charged analyte such as 1 was possibly unstable inside the neutral core of the ES droplet and undergoes fragmentation due to the Coulombic repulsion imparted by the surface protons. Brownian motion of the neutral analyte such as M(4p) inside the droplet, on the other hand, may lead to proton attachment on interaction with the charged surface causing destabilization that leads to fragmentation of M(4p) and release of resonance stabilized allyl cations from the core of the droplet. Detailed solvent dependence and collision-induced dissociation (CID) studies provided compelling evidences that the fragmentation of the analytes indeed occurs inside the charged ES droplets. A viable model of molecular transformations inside the ES droplet was proposed based on these results to rationalize the behavior of the analyte molecules inside the charged ES droplets.

  7. 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

    SciTech Connect

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

    2016-03-20

    We present distributions of two molecular clouds having velocities of 2 and 14 km s{sup −1} toward RCW 38, the youngest super star cluster in the Milky Way, in the {sup 12}CO J = 1–0 and 3–2 and {sup 13}CO 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{sup −1} cloud. We suggest that the collision is currently continuing toward part of the 2 km s{sup −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.

  8. Classical molecular dynamics simulation of electronically non-adiabatic processes.

    PubMed

    Miller, William H; Cotton, Stephen J

    2016-12-22

    Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

  9. Effect of the collision-induced trajectory curvature on molecular line shifts in the visible region of the spectrum

    NASA Astrophysics Data System (ADS)

    Bykov, A. D.; Lavrent'eva, N. N.; Sinitsa, L. N.

    1992-09-01

    The paper is concerned with the effect of trajectory curvature in calculations of the vibrational-rotational lines of molecules. The first-order term of the interruption function is calculated using exact solutions of classical dynamic equations. A universal function for two reduced arguments is obtained which is independent of the potential parameter and initial collision conditions; the function is capable of accounting for actual trajectories. Errors resulting from the use of a linear trajectory model are estimated for water vapor and methane expanded by various gases.

  10. 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.

  11. Vibrational effect on charge-transfer processes in collisions of H{sup +} and O{sup +} ions with C{sub 2}H{sub 4} molecules at energies below 10 keV/u

    SciTech Connect

    Kusakabe, Toshio; Gotanda, Kazushi; Kimura, Mineo; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.

    2007-10-15

    Charge-transfer processes in collisions of H{sup +} and O{sup +} ions with C{sub 2}H{sub 4} molecules have been studied in joint theoretical and experimental approaches for collision energies below 10 keV/u. Since H and O atoms possess nearly identical ionization potentials, these two ions are expected to share similar dynamics and hence to have similar cross-section values for charge transfer, at least for the energy region above 100 eV. In the present experiments, these cross sections of H{sup +} and O{sup +} ions have been derived by the initial growth rate method in the energy range of 0.20 to 3.6 keV, while the present theoretical study has been carried out for H{sup +} impact only. We have examined the vibrational effect on charge transfer, especially the 'temperature effect' of the initial vibrational states of the C{sub 2}H{sub 4} molecule as well as the final vibrational states of the product C{sub 2}H{sub 4}{sup +} molecular ion. Indeed, a strong influence of the initial vibrational states on charge transfer has been observed since these vibrationally excited initial and final states force the process to be more nearly resonant, thus making charge transfer more efficient. This vibrational effect, and perhaps rotational effect as well, that makes the collision process more nearly resonant has not been well investigated previously, and thus the present study is expected to shed much light on this effect in general.

  12. Elastic and inelastic processes in H{sup +}+CH{sub 2} collisions between 0.5 and 1.5 keV

    SciTech Connect

    Suno, Hiroya; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.; Kimura, Mineo; Janev, R.K.

    2004-09-01

    Electron capture and direct elastic scattering in collisions of H{sup +} ions with CH{sub 2} molecules between 0.5 and 1.5 keV are theoretically investigated. A molecular representation is adopted within a fully quantum-mechanical approach. We consider the following four different molecular configurations for collision dynamics: (I) the proton approaches the C atom along the bisector of the H--C--H bond angle, passing the midpoint of the H-H line (II) it comes along the same line as in (I), but in the opposite direction (III) the proton approaches the C atom in the H-C-H plane and perpendicularly to the bisector of the H-C-H bond angle, and (IV) the proton approaches the C atom perpendicularly to the H-C-H plane. Differential cross sections for elastic scattering and electron capture are calculated at 1.5 and 0.5 keV for these different molecular orientations. Total cross sections for these four orientations as well as orientation-averaged total cross sections are also calculated. Our results indicate that electron capture dynamics and corresponding electron-capture cross sections depend substantially on the molecular configuration, thus revealing a strong steric effect.

  13. Elastic and inelastic processes in H{sup +}+NH{sub 2} collisions between 0.5 and 1.5 keV

    SciTech Connect

    Suno, Hiroya; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.; Kimura, Mineo; Pichl, Lukas

    2006-07-15

    Electron capture and direct elastic scattering in collisions of H{sup +} ions with NH{sub 2} molecules between 0.5 and 1.5 keV are theoretically investigated. A molecular representation is adopted within a fully quantum-mechanical approach. We consider the following four different molecular configurations for collision dynamics: (I) the proton approaches the N atom along the bisector of the H-N-H bond angle, passing the midpoint of the H-H line (II) it comes along the same line as in (I), but in the opposite direction (III) the proton approaches the N atom in the H-N-H plane and perpendicularly to the bisector of the H-N-H bond angle, and (IV) the proton approaches the N atom perpendicularly to the H-N-H plane. Differential cross sections for elastic scattering and electron capture are calculated at 1.5 and 0.5 keV for these different molecular orientations. Total cross sections for these four orientations as well as orientation-averaged total cross sections are also calculated. Our results indicate that electron-capture dynamics and corresponding electron-capture cross sections depend substantially on the molecular configuration, thus revealing a strong steric effect.

  14. 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

  15. 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.

  16. Genomic Signal Processing: Predicting Basic Molecular Biological Principles

    NASA Astrophysics Data System (ADS)

    Alter, Orly

    2005-03-01

    Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

  17. Irreversible kinetics on a one-dimensional lattice: Comparison of exact result with a point-process nucleation-growth-collision model

    NASA Astrophysics Data System (ADS)

    Fletcher, S.

    1983-02-01

    In this paper we discuss irreversible kinetics on a one-dimensional lattice. We compare the expectation value of the coverage of the lattice, as a function of time, with that predicted by a point-process nucleation-growth-collision model. We conclude that the nucleation-growth-collision model is only applicable to lattice kinetics when the spreading rate of clusters is much greater than their nucleation rate. Although the kinetics of coverage of a one-dimensional lattice are known exactly, the complete solution turns out to be rather complex. In order to facilitate comparison with the point-process nucleation and growth model, we calculate an approximation to the lattice kinetics which is valid when the collision rate of clusters is very fast. The result is complementary to an earlier approximation of McQuarrie, McTague and Reiss, which described the case when the collision rate of clusters was comparable with the spreading rate. We also consider an integral geometrical approach to discreteness effects in lattice models. The general approach which we suggest is to calculate coefficients of variation of the numbers of lattice sites covered by various geometric shapes as a measure of "discreteness". This method uses some mathematical results of Kendall et al.

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

    NASA Astrophysics Data System (ADS)

    Yang, Wenbing

    -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.

  19. 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

  20. 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.

  1. 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.}

  2. 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

  3. 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.

  4. 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.

  5. Evaluation of the Influence of Amino Acid Composition on the Propensity for Collision-Induced Dissociation of Model Peptides Using Molecular Dynamics Simulations

    SciTech Connect

    Cannon, William R.; Taasevigen, Danny J.; Baxter, Douglas J.; Laskin, Julia

    2007-09-01

    The dynamical behavior of model peptides was evaluated with respect to their ability to form internal proton donor-acceptor pairs using molecular dynamics simulations. The proton donor-acceptor pairs are postulated to be prerequisites for peptide bond cleavage resulting in formation of b and y ions during low energy collision-induced dissociation in tandem mass spectrometry (MS/MS). The simulations for the polyalanine pentamer Ala5H+ were compared to experimental data from collision energy-resolved surface induced dissociation (SID) studies. The results of the simulation are insightful into the events that likely lead up to the fragmentation of peptides. 9-mer polyalanine-based model peptides were used to examine the dynamical effect of each of the 20 common amino acids on the probability to form donor-acceptor pairs at labile peptide bonds. A continuous range of probabilities was observed as a function of the substituted amino acid. However, the location of the peptide bond involved in the donor-acceptor pair plays a critical role in the dynamical behavior. This influence of position on the probability of forming a donor-acceptor pair would be hard to predict from statistical analyses on experimental spectra of aggregate, diverse peptides. In addition, the inclusion of basic side chains in the model peptides alters the probability of forming donor-acceptor pairs across the entire backbone. In this case there are still more ionizing protons than basic residues, but the side chains of the basic amino acids form stable hydrogen bond networks with the peptide carbonyl oxygens and thus act to prevent free access of “mobile protons” to labile peptide bonds. It is clear from the work that the identification of peptides from low-energy CID using automated computational methods should consider the location of the fragmenting bond as well as the amino acid composition.

  6. 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.

  7. Stochastic simulations of cargo transport by processive molecular motors

    NASA Astrophysics Data System (ADS)

    Korn, Christian B.; Klumpp, Stefan; Lipowsky, Reinhard; Schwarz, Ulrich S.

    2009-12-01

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

  8. Stochastic simulations of cargo transport by processive molecular motors.

    PubMed

    Korn, Christian B; Klumpp, Stefan; Lipowsky, Reinhard; Schwarz, Ulrich S

    2009-12-28

    We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.

  9. 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.

  10. 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.

  11. Collision Dynamics of Decimeter Bodies

    NASA Astrophysics Data System (ADS)

    Deckers, Johannes; Teiser, J.

    2013-10-01

    The collision dynamics of decimeter bodies are important for the early phase of planet formation. Planets form by accretion of km-sized objects, the so called planetesimals. These planetesimals evolve from small grains, but their formation process is not yet understood entirely. Two groups of models try to explain the formation process. Decimeter bodies and their collision behavior play a vital role in both groups. The threshold between bouncing and fragmentation is especially interesting for coagulation models, as decimeter bodies are the direct precursors to meter sized bodies. But the collision dynamics are also relevant for the models, which describe planetesimal formation by gravitational collapse in dense regions of the protoplanetary disk. We will present preliminary results of our collision experiments. Previous experiments on mutual collisions of decimeter dust agglomerates showed that the threshold between bouncing and fragmentation lies at a collision velocity of 16.2 cm/s, which corresponds to a specific kinetic energy of 5 mJ/kg. We expand these experiments to investigate the conditions for “catastrophic disruption” of decimeter dust bodies. Here, “catastrophic disruption” means that the largest fragment of a collision partner has only half the mass of the original body. Furthermore, we extend the parameter range to ice aggregates. We will present first experimental results of collisions of ice aggregates in the decimeter range. In these first experiments we will analyze the threshold conditions for solid ice. We will investigate the collision dynamics for both central and non-central collisions.

  12. 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)

  13. Transfer Excitation Processes Observed in N3+-He and O3+-He Collisions at Elab = 33 eV

    NASA Astrophysics Data System (ADS)

    Itoh, Yoh

    2016-09-01

    We measured the relative state-selective differential cross sections (DCSs) for one-electron capture reactions using a crossed-beam apparatus. The scattering angle θlab studied in the laboratory frame ranged from -3.0 to 22° and the laboratory collision energy Elab was 33 eV. Only the transfer excitation processes, i.e., the electron capture reactions with the simultaneous excitation of the projectile, were observed. The DCSs were determined for the following reactions: N3+ (1s2 2s2 1S) + He (1s2 1S) → N2+ (1s2 2s2p2 2D) + He+ (1s 2S) + 10.3 eV, O3+ (1s2 2s2 2p 2P) + He (1s2 1S) → O2+ (1s2 2s 2p3 3P) + He+ (1s 2S) + 12.7 eV, and O3+ (1s2 2s2 2p 2P) + He (1s2 1S) → O2+ (1s2 2s 2p3 3D) + He+ (1s 2S) + 15.5 eV. In the N3+-He system, the DCSs for the reaction are zero at the center-of-mass angle θcm = 0 and show a peak at a certain angle and a shoulder at a larger angle. In the O3+-He system, the DCSs are again zero at θcm = 0. The capture process to the O2+ (1s2 2s 2p3 3P) state is mainly observed at smaller scattering angles, and the reaction to the O2+ (1s2 2s 2p3 3D) state becomes dominant with increasing scattering angle. A classical trajectory analysis within the two-state approximation based on the ab initio potentials for (NHe)3+ revealed that the transfer excitation of a two-electron process takes place through a single crossing of the relevant potentials.

  14. Inelastic collisions of ultracold triplet Rb2 molecules in the rovibrational ground state

    NASA Astrophysics Data System (ADS)

    Drews, Björn; Deiß, Markus; Jachymski, Krzysztof; Idziaszek, Zbigniew; Hecker Denschlag, Johannes

    2017-03-01

    Exploring and controlling inelastic and reactive collisions on the quantum level is a main goal of the developing field of ultracold chemistry. For this, the preparation of precisely defined initial atomic and molecular states in tailored environments is necessary. Here we present experimental studies of inelastic collisions of metastable ultracold Rb2 molecules in an array of quasi-1D potential tubes. In particular, we investigate collisions of molecules in the absolute lowest triplet energy level where any inelastic process requires a change of the electronic state. Remarkably, we find similar decay rates as for collisions between rotationally or vibrationally excited triplet molecules where other decay paths are also available. The decay rates are close to the ones for universal reactions but vary considerably when confinement and collision energy are changed. This might be exploited to control the collisional properties of molecules.

  15. A Hybrid approach to molecular continuum processes combiningGaussian basis functions and the discrete variable representation

    SciTech Connect

    Rescigno, Thomas N.; Horner, Daniel A.; Yip, Frank L.; McCurdy,C. William

    2005-08-29

    Gaussian basis functions, routinely employed in molecular electronic structure calculations, can be combined with numerical grid-based functions in a discrete variable representation to provide an efficient method for computing molecular continuum wave functions. This approach, combined with exterior complex scaling, obviates the need for slowly convergent single-center expansions, and allows one to study a variety of electron-molecule collision problems. The method is illustrated by computation of various bound and continuum properties of H2+.

  16. Distribution and Molecular Characterization of Campylobacter Species at Different Processing Stages in Two Poultry Processing Plants.

    PubMed

    Lee, Soo-Kyoung; Park, Hyun-Jung; Lee, Jin-Hee; Lim, Jong-Soo; Seo, Kun-Ho; Heo, Eun-Jeong; Kim, Young-Jo; Wee, Sung-Hwan; Moon, Jin-San

    2017-03-01

    The present study analyzed the prevalence and molecular characterization of Campylobacter at different processing steps in poultry slaughterhouses to determine where contamination mainly occurs. A total of 1,040 samples were collected at four different stages (preprocessing cloacal swabs, postevisceration, postwashing, and postchilling) in two processing plants. Campylobacter was detected in 5.8% (15 of 260) of the cloacal swabs and in 13.3% (104 of 780) of the processing samples. In both plants, the sampling points with the greatest contamination rates were after evisceration (20.5% and 15.4% for plants A and B, respectively) and significantly decreased after chilling (p < 0.05, from 20.5% to 10.9%) in plant A and after washing (from 15.4% to 2.9%) in plants B. In the result, however, the reduction in Campylobacter contamination was achieved through the sequential processing procedures in both plants. Campylobacter loads (>10(3) colony-forming units [CFUs]/mL) also decreased from 41.7% at evisceration to 20.0% in final carcasses. The genetic relationships of isolates were analyzed by the automated repetitive sequence-based polymerase chain reaction (rep-PCR) system, and the rep-PCR banding pattern was found to be unrelated to the processing plants, species, sampling point, or sampling day. As the gap in the intervention efficacy remains between plant A and B despite several consistencies, a national program for monitoring critical processing stages in poultry processing plants is recommended for the successful exportation of Korean-processed white mini broiler meat.

  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

  18. Electron-capture collisions at keV energies of multiply charged ions of carbon and argon with molecular deuterium

    SciTech Connect

    Bliman, S.; Aubert, J.; Geller, R.; Jacquot, B.; Van Houtte, D.

    1981-04-01

    Single- and double-electron-capture cross sections have been measured for C/sup q/+ with initial charges 2 < or = q < or = 6 and for Ar/sup q/+ with initial charges 2 < or = q < or = 12 incident on molecular deuterium gas targets. The cross sections show little dependence on the incident-ion energy for the range studied 2q to 10q keV. The single-electron-capture cross sections do not vary monotonically with the initial charge, but show an oscillation about a mean curve, reflecting the projectile electronic structure.

  19. 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.

  20. 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.

  1. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

    NASA Astrophysics Data System (ADS)

    Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen

    2017-02-01

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

  2. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

    PubMed

    Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J Valentine, Stephen

    2017-02-16

    Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.

  3. Quantum molecular dynamics approach to heavy ion collisions: Description of the model, comparison with fragmentation data, and the mechanism of fragment formation

    NASA Astrophysics Data System (ADS)

    Aichelin, J.; Peilert, G.; Bohnet, A.; Rosenhauer, A.; Stöcker, H.; Greiner, W.

    1988-06-01

    We present a detailed microscopic quantum molecular dynamic analysis of fragment formation in the reaction Ne(1.05 GeV/nucleon) + Au. The theoretical predictions of the total mass yield, the multiplicity distribution of clusters, their average momentum, and their angular distribution agree well with the available data. We find a rather localized hot participant zone, which predominantly emits protons and neutrons. The multiplicity of light clusters depends strongly on the impact parameter whereas the heavier fragments A>=40 result from the decay of spectator residues. Their yield can provide a good measure for the impact parameter. The hypothesis of a compound system of AP and AT nucleons which is globally heated and equilibrated is not supported by our results. Light and massive fragments occupy different regions in phase space. Semiperipheral reactions do not lead to a stopping of the projectile. We observe a power law behavior of the inclusive mass yield distribution. Its form, however, is caused by averaging over different impact parameters. This rules out inclusive mass yield distributions as candidates for revealing a possible liquid gas phase transition. Light and intermediate mass fragments are formed during the early compressional stage of the reaction. We find that the projectile causes a high density wave to travel through the target. It causes the target to fragment and transfers transverse momentum to the intermediate mass fragments. Lighter fragments receive additional momentum transfer due to n-n collisions.

  4. The continuous and discrete molecular orbital x-ray bands from Xeq+ (12≤q≤29) +Zn collisions

    PubMed Central

    Guo, Yipan; Yang, Zhihu; Hu, Bitao; Wang, Xiangli; Song, Zhangyong; Xu, Qiumei; Zhang, Boli; Chen, Jing; Yang, Bian; Yang, Jie

    2016-01-01

    In this paper, the x-ray emissions are measured by the interaction of 1500–3500 keV Xeq+ (q = 12, 15, 17, 19, 21, 23, 26 and 29) ions with Zn target. When q < 29, we observe Ll, Lα, Lβ1, Lβ2 and Lγ characteristic x-rays from Xeq+ ions and a broad M-shell molecular orbital (MO) x-ray band from the transient quasi-molecular levels. It is found that their yields quickly increase with different rates as the incident energy increases. Besides, the widths of the broad MO x-ray bands are about 0.9–1.32 keV over the energy range studied and are proportional to v1/2 (v = projectile velocity). Most remarkably, when the projectile charge state is 29, the broad x-ray band separates into several narrow discrete spectra, which was never observed before in this field. PMID:27469425

  5. 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.

  6. Gain control in molecular information processing: lessons from neuroscience

    NASA Astrophysics Data System (ADS)

    Nemenman, Ilya

    2012-04-01

    Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitates adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here, we argue that a certain simple mechanism of gain control, understood well in the context of systems neuroscience, also works for molecular signaling. The mechanism allows us to transmit more than 1 bit (on or off) of information about the signal independent of the signal variance. It does not require additional molecular circuitry beyond that already present in many molecular systems, and in particular, it does not depend on existence of feedback loops. The mechanism provides a potential explanation for abundance of ultrasensitive response curves in biological regulatory networks.

  7. Timing and tectonic processes associated to the Late Cretaceous to Paleogene transition from collision to subduction in the Northern margin of Colombia

    NASA Astrophysics Data System (ADS)

    Cardona, A.; Montes, C.; Bayona, G.; Jaramillo, S.; Lopez-Martinez, M.; Silva, J.; Valencia, V.; Vanegas, J.; Zapata, S.

    2013-05-01

    Large scale plate tectonic scale models of the Caribbean-South American interactions have suggest the existence of different Late Cretaceous to Eocene collisional and subduction events associated to the Caribbean and South American plates interactions. We integrate field, petrological and geochronological results from igneous, metamorphic and sedimentary rocks from northeastern Colombia Guajira and Santa Margin in order to accurately discriminate the timing and understand with more details the processes associated to the evolution from collision to subduction and oblique convergence between the Caribbean and South America. Geochronological data from metamorphic units in the Santa Marta and Guajira regions document Late Cretaceous and Early Paleocene deformational events link to the collision of the Caribbean plate margin and the subsequent inversion of the upper plate during subduction initiation. Contemporaneous with these metamorphic events, inland basins experienced two major peaks of subsidence that can be related to the advance and overthrusting of the continental plate within the same tectonic scenario of collision and renewed subductions. This was followed by the construction of an Early Eocene magmatic arc located within the upper plate in a near trench position. Shallow and "fore arc" melting was related to the early astenospheric influx under the upper plate during the early stages of subduction. Another Late Eocene-Oligocene deformation is related to thrusting of the arc, exhumation and inland migration of deformation. This event may be related to major changes in the rates and directions of plate convergence between the Caribbean and South American plates.

  8. High-energy proton emission and Fermi motion in intermediate-energy heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Lin, W.; Liu, X.; Wada, R.; Huang, M.; Ren, P.; Tian, G.; Luo, F.; Sun, Q.; Chen, Z.; Xiao, G. Q.; Han, R.; Shi, F.; Liu, J.; Gou, B.

    2016-12-01

    An antisymmetrized molecular dynamics model (AMD-FM), modified to take into account the Fermi motion explicitly in its nucleon-nucleon collision process, is presented. Calculated high-energy proton spectra are compared with those of 40Ar+51V at 44 MeV/nucleon from Coniglione et al. [Phys. Lett. B 471, 339 (2000), 10.1016/S0370-2693(99)01383-0] and those of 36Ar+181Ta at 94 MeV/nucleon from Germain et al. [Nucl. Phys. A 620, 81 (1997), 10.1016/S0375-9474(97)00146-2]. Both of the experimental data are reasonably well reproduced by the newly added Fermi boost in the nucleon-nucleon collision process without additional processes, such as a three-body collision or a short-range correlation. The production mechanism of high-energy protons in intermediate-energy heavy-ion collisions is discussed.

  9. Electron Collisions with Hydrogen Fluoride

    NASA Astrophysics Data System (ADS)

    Itikawa, Yukikazu

    2017-03-01

    Cross section data are reviewed for electron collisions with hydrogen fluoride. Collision processes considered are total scattering, elastic scattering, excitations of rotational, vibrational, and electronic states, ionization, and dissociative electron attachment. After a survey of the literature, recommended values of the cross sections are determined, as far as possible.

  10. Half collision resonance phenomena in molecules

    SciTech Connect

    Maximo Garcia-Sucre ); Raseev, G. ); Ross, S.C. )

    1991-01-01

    The Escuela Latinoamericana de Fisica (ELAF) is a series of meeting s that for 28 years has played an important role in research-level teaching of physics in Latin America. This book contains the proceedings of ELAF 90 which was held at the Instituto Venezolano de Investigaciones Cientificas (IVIC) in Caracas, Venezuela from July 23 to August 3, 1990, as part of the commemoration of the 30th anniversary of IVIC. In contrast to previous ELAF's that were of general scope, ELAF 90 centered on a particular subject matter: Half Collisional Resonance Phenomena in Molecules, Experimental and Theoretical Approaches. The term Half Collision'' refers to the fragmentation of a molecular system following is excitation by light. The lack of an incident fragmentation of a molecular system following is excitation by light. The lack of an incident particle (other than the photon) in the fragmentation process is what leads to the term. The purpose of this volume is to present current results in the experimental and theoretical study of half collisions and also to include pedagogical papers at an introductory or intermediate level. The contributions are grouped into several sections; light sources; ionization; dissociation-experimental; dissociation-theory; competition between ionization and dissociation; and particle-molecule collisions.

  11. X-RAY EMISSION FROM STELLAR JETS BY COLLISION AGAINST HIGH-DENSITY MOLECULAR CLOUDS: AN APPLICATION TO HH 248

    SciTech Connect

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

    2015-06-10

    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 10{sup 7} 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. X-ray Emission from Stellar Jets by Collision against High-density Molecular Clouds: an Application to HH 248

    NASA Astrophysics Data System (ADS)

    López-Santiago, J.; Bonito, R.; Orellana, M.; Miceli, M.; Orlando, S.; Ustamujic, S.; Albacete-Colombo, J. F.; de Castro, E.; Gómez 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.

  13. 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

  14. 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.

  15. Long Timestep Molecular Dynamics on the Graphical Processing Unit.

    PubMed

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

    2013-08-13

    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 μs/day using implicit solvent models.

  16. Global Franck-Condon breakdown: nonresonant molecular photoionization processes

    NASA Astrophysics Data System (ADS)

    Das, Aloke; Hardy, David; Aguilar, Alejandro; Kilcoyne, A. L. D.; Bozek, John D.; Poliakoff, Erwin D.

    2007-06-01

    We report photoelectron spectroscopy results of nonresonant Franck-Condon breakdown in the photoionization of CO and ICN. Most importantly, the deviations occur over a surprisingly wide range of energies. For the case of CO^+(X^2σ^+), the v^ + = 1/v^ + = 0 vibrational branching ratio is found to vary significantly (>50%) over a 200 eV range. While it is well understood that resonances can lead to coupling between photoelectron and molecular vibration, there is little information on nonresonant sources of coupling. It appears that Cooper minima may be responsible for the observations. Moreover, for ICN, the vibrationally resolved deviations from Franck-Condon behavior are vibrationally mode-specific. Studies on alternative molecular targets are planned to see whether they exhibit photoelectron dynamics that are geometry-dependent.

  17. Nanoparticle-electrode collision processes: Investigating the contact time required for the diffusion-controlled monolayer underpotential deposition on impacting nanoparticles

    NASA Astrophysics Data System (ADS)

    Cutress, Ian J.; Rees, Neil V.; Zhou, Yi-Ge; Compton, Richard G.

    2011-09-01

    Recent work on faradaic processes occurring during thermal nanoparticle-electrode collisions contrasts significantly from analogous research using ultrasonically-driven microparticles, where no faradaic signals were found. It is suggested that this might be explained by the differences in both particle size and contact time. To investigate this, we present results from adapted Monte Carlo random walk simulations. Using the underpotential deposition of thallium onto silver nanoparticles as a model system, it is found that an estimated minimum contact time of ca. 10-4 s is required to deposit a complete monolayer (from a 10 mM solution) onto a nanoparticle of radius 45 nm.

  18. 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.

  19. Elastic and electron-capture processes in H{sup +}+C{sub 2}H{sub 4} collisions below the 10-keV regime

    SciTech Connect

    Suzuki, Reiko; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J.; Pichl, Lukas; Kimura, Mineo

    2005-03-01

    Electron capture and direct elastic scattering in collisions of H{sup +} ions with C{sub 2}H{sub 4} molecules are studied by using a molecular representation within a semiclassical as well as a fully quantum-mechanical approaches below 10 keV. Calculations are carried out at three different molecular configurations, in which H{sup +} approaches (i) parallel and (ii) perpendicular to the C=C axis in the molecular plane, and (iii) perpendicular to this plane. We find that electron capture in the (iii) configuration takes place preferentially over that in the (i) and (ii) configurations at scattering angles above 15 deg., while the results for (i) and (ii) are comparable in magnitude below 10 deg., although (ii) dominates slightly at still smaller angles. Total capture cross sections for the (iii) and (ii) configurations differ by a factor of 4 above 500 eV, while those for (i) lie between these values. Below 500 eV, the results for (i) and (iii) are similar in magnitude, while that for the (ii) configuration sharply decreases.

  20. Neutrino-atom collisions

    NASA Astrophysics Data System (ADS)

    Kouzakov, Konstantin A.; Studenikin, Alexander I.

    2016-05-01

    Neutrino-atom scattering provides a sensitive tool for probing nonstandard interactions of massive neutrinos in laboratory measurements. The ionization channel of this collision process plays an important role in experiments searching for neutrino magnetic moments. We discuss some theoretical aspects of atomic ionization by massive neutrinos. We also outline possible manifestations of neutrino electromagnetic properties in coherent elastic neutrino-nucleus scattering.

  1. Collision-Induced Dissociation of Electrosprayed NaCl Clusters: Using Molecular Dynamics Simulations to Visualize Reaction Cascades in the Gas Phase

    NASA Astrophysics Data System (ADS)

    Schachel, Tilo D.; Metwally, Haidy; Popa, Vlad; Konermann, Lars

    2016-11-01

    Infusion of NaCl solutions into an electrospray ionization (ESI) source produces [Na( n+1)Cl n ]+ and other gaseous clusters. The n = 4, 13, 22 magic number species have cuboid ground state structures and exhibit elevated abundance in ESI mass spectra. Relatively few details are known regarding the mechanisms whereby these clusters undergo collision-induced dissociation (CID). The current study examines to what extent molecular dynamics (MD) simulations can be used to garner insights into the sequence of events taking place during CID. Experiments on singly charged clusters reveal that the loss of small neutrals is the dominant fragmentation pathway. MD simulations indicate that the clusters undergo extensive structural fluctuations prior to decomposition. Consistent with the experimentally observed behavior, most of the simulated dissociation events culminate in ejection of small neutrals ([NaCl] i , with i = 1, 2, 3). The MD data reveal that the prevalence of these dissociation channels is linked to the presence of short-lived intermediates where a relatively compact core structure carries a small [NaCl] i protrusion. The latter can separate from the parent cluster via cleavage of a single Na-Cl contact. Fragmentation events of this type are kinetically favored over other dissociation channels that would require the quasi-simultaneous rupture of multiple electrostatic contacts. The CID behavior of NaCl cluster ions bears interesting analogies to that of collisionally activated protein complexes. Overall, it appears that MD simulations represent a valuable tool for deciphering the dissociation of noncovalently bound systems in the gas phase.

  2. Mixing Diagnostics in Confined, High-Speed Droplet Collisions

    NASA Astrophysics Data System (ADS)

    Carroll, Brian; Hidrovo, Carlos

    2012-11-01

    Fast mixing remains a major challenge in droplet-based microfluidics. The low Reynolds number operating regime of most mixing devices signifies orderly flows that are devoid of any inertial characteristics. To increase droplet mixing rates, a novel technique is under development that uses a high Reynolds number gaseous phase for droplet generation and transport and promotes mixing through binary droplet collisions at velocities near 1m/s. Limitations in existing mixing diagnostic methodologies has persuaded cultivation of a new technique for measuring droplet collision mixing in confined microchannels. The technique employs single fluorophore laser-induced fluorescence, custom image processing, and meaningful statistical analysis for monitoring and quantifying mixing in high-speed droplet collisions. Mixing progress is revealed through two statistics that separate the roles of convective rearrangement and molecular diffusion during the mixing process. The end result is a viewing window into the rich dynamics of droplet collisions with spatial and temporal resolutions of 1 μm and 25 μs, respectively. Experimental results obtained across a decade of Reynolds and Peclet numbers reveal a direct link between droplet mixing time and the collision convective timescale. This work provides valuable insight into the emerging field of two-phase gas-liquid microfluidics and opens the door to fundamental research possibilities not offered by traditional oil-based architectures.

  3. Accelerating molecular docking calculations using graphics processing units.

    PubMed

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2011-04-25

    The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein-ligand or protein-protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein-protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein-ligand interaction potentials. Additionally, we introduce a parallel version of our protein-ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein-protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60.

  4. 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.

  5. 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

  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. 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.

  8. Theoretical Studies of Laser-Induced Molecular Rate Processes: Topics in Line Broadening and Spectroscopy.

    DTIC Science & Technology

    1985-10-01

    GROUP SU. GRF. MOLECULAR RATE PROCESSES MOLECULAR DYNAMICS LASER-INDUCED LINE BROADENING THEORETICAL STUDIES SPECTROSCOPY 19. ABSI*ACT (Continue On...approaches half the band-gap energy. -q 14 This idea of using a laser to "charge" the surface region has fomed the basis of a semiclassical theory of charge

  9. Numerical study of charge transfer processes in collisions of Be^4+ and He^2+ with atomic hydrogen

    NASA Astrophysics Data System (ADS)

    Minami, Tatsuya; Pindzola, Michael S.; Lee, Teck-Gee

    2005-05-01

    We have calculated state-selective charge-transfer cross sections in collisions of Be^(4+ with H(1s) and of He^2+ with H(1s). We have used the lattice time-dependent Schr"odinger equation (LTDSE) approach, the atomic orbital coupled channel (AOCC) method, and the classical trajectory Monte Carlo (CTMC) method. The calculations are performed with impact energy ranging between 1keV/u and 1MeV/u. With a well chosen basis-function set, we have found that AOCC gives good agreement with LTDSE. Also, with regard to Wigner's n-3 law, we have found that CTMC gives good extrapolations to the cross sections calculated by LTDSE and AOCC toward high n levels such as for those greater than 6. Thus, in our presentation, we will propose theoretical values of the total charge-transfer cross sections for these collision systems based on a combination of the most reliable results of the various method. This research used resources of the Center for Computational Sciences at Oak Ridge National Laboratory, which is supported by the Office of Science of the Department of Energy under Contract DE-AC05-00OR22725, and also of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098.

  10. 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.

  11. Vibrationally resolved charge transfer for proton collisions with CO and H collisions with CO{sup +}

    SciTech Connect

    Lin, C. Y.; Stancil, P. C.; Li, Y.; Gu, J. P.; Liebermann, H. P.; Buenker, R. J.; Kimura, M.

    2007-07-15

    Electron capture by protons following collisions with carbon monoxide, and the reverse process, is studied with a quantal molecular-orbital coupled-channel method utilizing the infinite order sudden approximation for collision energies between 0.5 and 1000 eV/u. The potential surfaces and couplings, computed with the multireference single- and double-excitation method for a range of H{sup +}-CO orientation angles and C-O separations, are adopted in the scattering calculations. Results including vibrationally resolved and orientation-angle-dependent cross sections are presented for a range of CO and CO{sup +} vibrational levels. Comparison with experiment is made where possible and the relevance of the reaction in astrophysics and atmospheric physics is discussed.

  12. Post-processing interstitialcy diffusion from molecular dynamics simulations

    SciTech Connect

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

    2016-01-15

    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. -- Graphical abstract:.

  13. 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.

  14. Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

  15. Geochemical Interpretation of Collision Volcanism

    NASA Astrophysics Data System (ADS)

    Pearce, Julian

    2014-05-01

    collision type with extreme LILE and significant HFSE enrichment relative to MORB and with large negative Nb-Ta and Ti anomalies. Post-collision volcanism is usually ascribed to combinations of slab detachment, delamination, and slab roll back (orogenic) and extension (post-orogenic). The magma source is typically conductively-heated, sub-continental mantle lithosphere with composition and depth of melting depending on the nature and evolution of the collision zone in question. Geochemical patterns may be similar to those of syn-collision basalts or of intraplate, continental basalts - or transitional between these. This variability in space and time, though problematic for geochemical fingerprinting, can give clues to the polarity and development of the collision zone, for example by highlighting the distribution of subduction-modified mantle lithosphere and hence of pre-collision subduction zones. One characteristic common to this setting is a high crustal input resulting from the presence of a hot, thick 'crustal chemical filter' which is evident on geochemical projections that highlight AFC-type processes. Using this, and other, geochemical features it is possible to develop methodologies to at least partly see through the complexity of collision terranes.

  16. 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

  17. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control.

    PubMed

    Lebuhn, Michael; Weiß, Stefan; Munk, Bernhard; Guebitz, Georg M

    2015-01-01

    Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

  18. Using a direct simulation Monte Carlo approach to model collisions in a buffer gas cell.

    PubMed

    Doppelbauer, Maximilian J; Schullian, Otto; Loreau, Jerome; Vaeck, Nathalie; van der Avoird, Ad; Rennick, Christopher J; Softley, Timothy P; Heazlewood, Brianna R

    2017-01-28

    A direct simulation Monte Carlo (DSMC) method is applied to model collisions between He buffer gas atoms and ammonia molecules within a buffer gas cell. State-to-state cross sections, calculated as a function of the collision energy, enable the inelastic collisions between He and NH3 to be considered explicitly. The inclusion of rotational-state-changing collisions affects the translational temperature of the beam, indicating that elastic and inelastic processes should not be considered in isolation. The properties of the cold molecular beam exiting the cell are examined as a function of the cell parameters and operating conditions; the rotational and translational energy distributions are in accord with experimental measurements. The DSMC calculations show that thermalisation occurs well within the typical 10-20 mm length of many buffer gas cells, suggesting that shorter cells could be employed in many instances-yielding a higher flux of cold molecules.

  19. Using a direct simulation Monte Carlo approach to model collisions in a buffer gas cell

    NASA Astrophysics Data System (ADS)

    Doppelbauer, Maximilian J.; Schullian, Otto; Loreau, Jerome; Vaeck, Nathalie; van der Avoird, Ad; Rennick, Christopher J.; Softley, Timothy P.; Heazlewood, Brianna R.

    2017-01-01

    A direct simulation Monte Carlo (DSMC) method is applied to model collisions between He buffer gas atoms and ammonia molecules within a buffer gas cell. State-to-state cross sections, calculated as a function of the collision energy, enable the inelastic collisions between He and NH3 to be considered explicitly. The inclusion of rotational-state-changing collisions affects the translational temperature of the beam, indicating that elastic and inelastic processes should not be considered in isolation. The properties of the cold molecular beam exiting the cell are examined as a function of the cell parameters and operating conditions; the rotational and translational energy distributions are in accord with experimental measurements. The DSMC calculations show that thermalisation occurs well within the typical 10-20 mm length of many buffer gas cells, suggesting that shorter cells could be employed in many instances—yielding a higher flux of cold molecules.

  20. Collision partner selection schemes in DSMC: From micro/nano flows to hypersonic flows

    NASA Astrophysics Data System (ADS)

    Roohi, Ehsan; Stefanov, Stefan

    2016-10-01

    The motivation of this review paper is to present a detailed summary of different collision models developed in the framework of the direct simulation Monte Carlo (DSMC) method. The emphasis is put on a newly developed collision model, i.e., the Simplified Bernoulli trial (SBT), which permits efficient low-memory simulation of rarefied gas flows. The paper starts with a brief review of the governing equations of the rarefied gas dynamics including Boltzmann and Kac master equations and reiterates that the linear Kac equation reduces to a non-linear Boltzmann equation under the assumption of molecular chaos. An introduction to the DSMC method is provided, and principles of collision algorithms in the DSMC are discussed. A distinction is made between those collision models that are based on classical kinetic theory (time counter, no time counter (NTC), and nearest neighbor (NN)) and the other class that could be derived mathematically from the Kac master equation (pseudo-Poisson process, ballot box, majorant frequency, null collision, Bernoulli trials scheme and its variants). To provide a deeper insight, the derivation of both collision models, either from the principles of the kinetic theory or the Kac master equation, is provided with sufficient details. Some discussions on the importance of subcells in the DSMC collision procedure are also provided and different types of subcells are presented. The paper then focuses on the simplified version of the Bernoulli trials algorithm (SBT) and presents a detailed summary of validation of the SBT family collision schemes (SBT on transient adaptive subcells: SBT-TAS, and intelligent SBT: ISBT) in a broad spectrum of rarefied gas-flow test cases, ranging from low speed, internal micro and nano flows to external hypersonic flow, emphasizing first the accuracy of these new collision models and second, demonstrating that the SBT family scheme, if compared to other conventional and recent collision models, requires smaller

  1. 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.

  2. 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

  3. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    SciTech Connect

    Yu,P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  4. 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.

  5. Collision-induced fusion of two single-walled carbon nanotubes: A quantitative study

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Mao, Fei; Meng, Xiang-Rui; Wang, Dong-Qi; Zhang, Feng-Shou

    2016-07-01

    The coalescence processes of two (6, 0) single-walled carbon nanotubes are investigated via coaxial collision based on the self-consistent-charge density-functional tight-binding molecular dynamics method. According to the structure characteristics of the nanotubes, five impact cases are studied to explore the coalescence processes of the nanotubes. The simulation shows that various kinds of carbon nanomaterials, such as graphene sheets, graphene nanoribbons, and single-walled carbon nanotubes with larger diameters, are created after collision. Moreover, some defects formed in the carbon nanomaterials can be eliminated, and even the final configurations which are originally fragmented can almost become intact structures by properly quenching and annealing.

  6. 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.

    PubMed

    Ellis, Jenny L; Conklin, Sean D; Gallawa, Christina M; Kubachka, Kevin M; Young, Andrea R; Creed, Patricia A; Caruso, Joseph A; Creed, John T

    2008-04-01

    The simultaneous detection of arsenic and sulfur in thioarsenicals was achieved using xenon-based collision-cell inductively coupled plasma (ICP) mass spectrometry (MS) in combination with high-performance liquid chromatography. In an attempt to minimize the (16)O(16)O(+) interference at m/z 32, both sample introduction and collision-cell experimental parameters were optimized. Low flow rates (0.25 mL/min) and a high methanol concentration (8%) in the mobile phase produced a fourfold decrease in the m/z 32 background. A plasma sampling depth change from 3 to 7 mm produced a twofold decrease in background at m/z 32, with a corresponding fourfold increase in the signal associated with a high ionization surrogate for sulfur. The quadrupole bias and the octopole bias were used as a kinetic energy discriminator between background and analyte ions, but a variety of tuning conditions produced similar (less than twofold change) detection limits for sulfur ((32)S). A 34-fold improvement in the (32)S detection limit was achieved using xenon instead of helium as a collision gas. The optimized xenon-based collision cell ICP mass spectrometer was then used with electrospray ionization MS to provide elemental and molecular-based information for the analysis of a fortified sample of NIST freeze-dried urine. The 3sigma detection limits, based on peak height for dimethylthioarsinic acid (DMTA) and trimethylarsine sulfide (TMAS), were 15 and 12 ng/g, respectively. Finally, the peak area reproducibilities (percentage relative standard deviation) of a 5-ppm fortified sample of NIST freeze dried urine for DMTA and TMAS were 7.4 and 5.4%, respectively.

  7. Nanoparticle collisions in the gas phase in the presence of singular contact potentials

    NASA Astrophysics Data System (ADS)

    Ouyang, Hui; Gopalakrishnan, Ranganathan; Hogan, Christopher J.

    2012-08-01

    Collisional growth and ionization is commonplace for gas phase nanoparticles (i.e., in aerosols). Nanoparticle collisions in atmospheric pressure environments occur in the mass transfer transition regime, and further attractive singular contact potentials (which arise when modeling nanoparticles as condensed matter and for which the potential energy approaches -∞ when two entities contact) often have a non-negligible influence on collision processes. For these reasons collision rate calculations for nanoparticles in the gas phase are not straightforward. We use mean first passage time calculations to develop a simple relationship to determine the collision rate in the gas phase, accounting for the influences of both the transition regime and singular contact potentials (specifically the non-retarded van der Waals and image potentials). In the presented analysis, methods to determine the degree of enhancement in collision rate due to attractive singular potentials in the continuum (diffusive) regime, ηC, and the degree of enhancement in the free molecular (ballistic) regime, ηFM, are first reviewed. Accounting for these enhancement factors, with mean first passage time calculations it is found that the collision rate for gas phase nanoparticles with other gas phase entities can be determined from a relationship between the dimensionless collision rate coefficient, H, and the diffusive Knudsen number, KnD, i.e., the ratio of the mean collision persistence distance to the collision length scale. This coincides with the H(KnD) relationship found to appropriately describe collisions between entities interacting via a hard-sphere potential, but with ηC and ηFM incorporated into the definitions of both H and KnD, respectively. The H(KnD) relationship is compared to the predictions of flux matching theory, used prevalently in prior work for collision rate calculation, and through this comparison it is found that at high potential energy to thermal energy ratios, flux

  8. Dependence of radiative stabilization on the projectile charge state after double-electron-transfer processes in slow, highly charged ion-molecule collisions

    NASA Astrophysics Data System (ADS)

    Krok, Franciszek; Tolstikhina, Inga Yu.; Sakaue, Hiroyuki A.; Yamada, Ichihiro; Hosaka, Kazumoto; Kimura, Masahiro; Nakamura, Nobuyuki; Ohtani, Shunsuke; Tawara, Hiroyuki

    1997-12-01

    We have measured the radiative stabilization probabilities after double-electron-transfer processes in slow (1.5q keV) Iq++CO collisions in the charge-state regime 8<=q<=26 by using the charge-selected-projectile-recoil-ion-coincidence method. It was found that the radiative stabilization probabilities Prad, defined as Prad=TDC/(TDC+ADC) (TDC is true double capture, and ADC autoionizing double capture), increases from about 1% at the lowest charge up to about 10% 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.

  9. Double-Spin Asymmetry A{sub LT} for Polarized Drell-Yan Process in pp-bar Collisions: Wandzura-Wilczek Contribution

    SciTech Connect

    Koike, Yuji; Yoshida, Shinsuke; Tanaka, Kazuhiro

    2009-08-04

    The longitudinal-transverse spin asymmetry A{sub LT} in the polarized Drell-Yan process depends on twist-3 quark distributions of nucleon. In addition to the contributions associated with the twist-3 operators, these distributions contain the 'Wandzura-Wilczek (WW)' part, which is determined by a certain integral of twist-2 distributions. The recently obtained empirical information on the transversity allows a realistic estimate of the WW contribution to A{sub LT} for the polarized pp-bar collisions. Our results indicate that rather large A{sub LT}({approx}10%) can be observed in the proposed spin experiments at GSI, with novel pattern as a function of dilepton mass compared with A{sub TT} and A{sub LL}.

  10. Kinematic slowing and electrostatic guiding of KBr molecules formed by the reactive collision process: K + HBr --> KBr + H.

    PubMed

    Liu, Ning-Ning; Loesch, Hansjürgen

    2010-03-11

    We have generated a beam of translationally cold KBr molecules formed by exoergic reactive collisions in counterpropagating beams of K atoms and HBr molecules. The method relies on the extreme mass ratio of the products and the proper choice of the beam velocities (Liu, N.-N.; Loesch, H. J. Phys. Rev. Lett. 2007, 98, 10300). Here, we report the results of experiments on guiding the slow molecules from the site of their creation to the detector by a linear electrostatic quadrupole field. The device enhances the total intensity by a factor of 2.3 and the intensity at 14.2 m/s (1.4K) by an order of magnitude. The density velocity distributions, deduced directly from the observed time-of-flight profiles, peak at 20 m/s (2.9K). A numerical simulation of the guiding efficiency indicates that the polarization of the nascent molecules is first altered by a sudden change of the quantization axis from parallel to the initial relative velocity to parallel to the fringing field and thereafter follows adiabatically the local field as quantization axis. Drastic differences between the velocity and rotational state distributions of the molecules entering and leaving the energized quadrupole field are predicted. The counterpropagating beams can be used to continuously load an electrostatic trap. The equilibrium density of confined molecules is estimated to 1 x 10(7) cm(-3).

  11. 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.

  12. Statistics of Infima and Stopping Times of Entropy Production and Applications to Active Molecular Processes

    NASA Astrophysics Data System (ADS)

    Neri, Izaak; Roldán, Édgar; Jülicher, Frank

    2017-01-01

    We study the statistics of infima, stopping times, and passage probabilities of entropy production in nonequilibrium steady states, and we show that they are universal. We consider two examples of stopping times: first-passage times of entropy production and waiting times of stochastic processes, which are the times when a system reaches a given state for the first time. Our main results are as follows: (i) The distribution of the global infimum of entropy production is exponential with mean equal to minus Boltzmann's constant; (ii) we find exact expressions for the passage probabilities of entropy production; (iii) we derive a fluctuation theorem for stopping-time distributions of entropy production. These results have interesting implications for stochastic processes that can be discussed in simple colloidal systems and in active molecular processes. In particular, we show that the timing and statistics of discrete chemical transitions of molecular processes, such as the steps of molecular motors, are governed by the statistics of entropy production. We also show that the extreme-value statistics of active molecular processes are governed by entropy production; for example, we derive a relation between the maximal excursion of a molecular motor against the direction of an external force and the infimum of the corresponding entropy-production fluctuations. Using this relation, we make predictions for the distribution of the maximum backtrack depth of RNA polymerases, which follow from our universal results for entropy-production infima.

  13. 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

  14. A local collision probability approximation for predicting momentum transfer cross sections.

    PubMed

    Bleiholder, Christian

    2015-10-21

    The local collision probability approximation (LCPA) method is introduced to compute molecular momentum transfer cross sections for comparison to ion mobility experiments. The LCPA replaces the (non-local) scattering trajectory used in the trajectory method to describe the collision process by a (local) collision probability function. This momentum transfer probability is computed using the exact same analyte-buffer interaction potential as used in the trajectory method. Subsequently, the momentum transfer cross section ΩLCPA(T) is calculated in a projection-type manner (corrected for shape effects through a shape factor). Benchmark calculations on a set of 208 carbon clusters with a range of molecular size and degree of concavity demonstrate that LCPA and trajectory calculations agree closely with one another. The results discussed here indicate that the LCPA is suitable to efficiently calculate momentum transfer cross sections for use in ion mobility spectrometry in conjunction with different buffer gases.

  15. Effects of classical nonlinear resonances in grazing diatom-surface collisions.

    PubMed

    Ruiz, Antonia; Palao, José P

    2012-08-28

    Energy transfer between vibrational, rotational, and translational degrees of freedom of a molecule during a collision process is enhanced when the classical frequencies associated with the initial state are in the proximity of nonlinear resonance conditions. We present an analysis of the classical resonant effects in the collisions of light diatoms with periodic surfaces, and discuss the initial conditions in which these effects can be observed. In particular, we find that for grazing incidence and resonant initial values of the classical frequencies, corresponding to specific vibro-rotational molecular states and translational energies, an efficient energy transfer between the intramolecular vibro-rotational degrees of freedom and the translational degree of freedom along a symmetry direction on the surface can be found. This efficient energy transfer manifests itself in the emergence of specific peaks in the molecular diffraction patterns. The predictions of the resonance analysis are contrasted with the results of classical trajectory calculations obtained in a diatom-rigid surface collision model.

  16. R-matrix calculations of electron molecule collision data for plasma models

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan

    2016-09-01

    Models of low-pressure plasma require electron collision cross sections for many processes. For transient molecular species, almost none of these data are available from laboratory measurements so theory has to be the chosen means of providing the necessary information. The R-matrix method is a well-established fully quantal procedure for computing low-energy electron-collision cross sections. The R-matrix calculations using the UK Molecular R-matrix codes (UKRMol), which are run by the Quantemol-N expert system, are being employed to provide a wide range of collision cross sections. These are augmented by use of suitable high-energy approximations, such as BEB for ionisation, and a novel procedure to give branching ratios for the fragmentation pattern following electron impact ionisation and electron impact dissociation. Examples, such as recently generated complete cross section sets for the molecules NF, NF and NF, will be given at the meeting.

  17. 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.

  18. 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.

  19. 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.

  20. Quantum state-resolved molecular scattering of NO (2Π1 /2) at the gas-[Cnmim][Tf2N] room temperature ionic liquid interface: Dependence on alkyl chain length, collision energy, and temperature

    NASA Astrophysics Data System (ADS)

    Zutz, Amelia; Nesbitt, David J.

    2016-10-01

    Room temperature ionic liquids (RTILs) represent a promising class of chemically tunable, low vapor pressure solvents with myriad kinetic applications that depend sensitively on the nature of gas-molecule interactions at the liquid surface. This paper reports on rovibronically inelastic dynamics at the gas-RTIL interface, colliding supersonically cooled hyperthermal molecular beams of NO (1/2 2Π, N = 0) from 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (or [Cnmim][Tf2N]) and probing the scattered NO molecules via laser induced fluorescence (LIF) from the A(2Σ ) state. Specifically, inelastic energy transfer into NO rovibrational and electronic degrees of freedom is explored as a function of RTIL alkyl chain length (n), incident collision energy (Einc) and surface temperature (Ts). At low collision energies (Einc = 2.7(9) kcal/mol), the scattered NO molecules exhibit a rotational temperature (Trot) systematically colder than Ts for all chain lengths, which signals the presence of non-equilibrium dynamics in the desorption channel. At high collision energies (Einc = 20(2) kcal/mol), microscopic branching into trapping/desorption (TD) and impulsive scattering (IS) pathways is clearly evident, with the TD fraction (α ) exhibiting a step-like increase between short (n = 2, 4) and long (n = 8, 12, 16) alkyl chains consistent with theoretical predictions. For all hydrocarbon chain lengths and RTIL temperature conditions, NO rotational excitation in the IS channel yields hyperthermal albeit Boltzmann-like distributions well described by a "temperature" (TIS = 900 -1200 K) that decreases systematically with increasing n. Non-adiabatic, collision induced hopping between ground and excited spin-orbit states is found to be independent of RTIL alkyl chain length and yet increase with collision energy. The scattering data confirm previous experimental reports of an enhanced presence of the alkyl tail at the gas-RTIL interface with increasing n, as well as

  1. 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.

  2. 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).

  3. Electron Collisions - Looking Back and Looking Forward

    NASA Astrophysics Data System (ADS)

    McConkey, J. William

    2004-05-01

    For almost a century, ever since the pioneering experiments of Franck and Hertz provided one of the foundation stones of the emerging quantum theory, electron scattering has been a versatile tool for diagnosing atomic and molecular structure and interactions. Electron collisions with a wide variety of targets have proved to be fundamental to our understanding of such diverse topics as planetary atmosphere processes, low and high temperature plasma physics, lasers and radiation chemistry. They undergird the efficient operation of a multitude of practical devices and industrial processes. This talk will provide a flavor of what has happened in this field, particularly over the past half-century. It will illustrate some of the current developments and and suggest what might be fruitful areas of research in the future.

  4. Molecular Optics Nonlinear Optical Processes in Organic and Polymeric Crystals and Films

    DTIC Science & Technology

    1988-04-01

    LAr 9B L Appr 1~ forjIbi1893 2 8 I I IE2 Molecular Optics: Nonlinear Optical Processes in Organic and Polymeric Crystals and Films i Professor A. F...frequency dependent local field factors. While there are various prevalent models (Lorentz- Lorenz, Onsager ) all of them give the field factors in terms of

  5. Spatiotemporal Fluctuation Analysis: A Powerful Tool for the Future Nanoscopy of Molecular Processes.

    PubMed

    Di Rienzo, Carmine; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

    2016-08-23

    The enormous wealth of information available today from optical microscopy measurements on living samples is often underexploited. We argue that spatiotemporal analysis of fluorescence fluctuations using multiple detection channels can enhance the performance of current nanoscopy methods and provide further insight into dynamic molecular processes of high biological relevance.

  6. Alignment of H (2 p) in H-He, Ne, Ar collisions

    NASA Astrophysics Data System (ADS)

    Madeheim, H.; Hippler, R.; Lutz, H. O.

    1990-12-01

    The integral alignment A 20 was investigated for H(2 p) excitation in H-He, Ne, Ar collisions at incident energies of 1 25 keV. The experimental results are compared with theoretical calculations based on different theoretical models. Calculations which do not account for the quasi-molecular aspect of the collision process are at variance with the experimental data below incident energies of 10 keV. Above 15 keV, fair agreement is obtained with calculations which include simultaneous excitation of both projectile and target.

  7. 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.

  8. 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?"

  9. 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.

  10. 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

  11. 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.

  12. Collision Induced Velocity Changes from Molecular Dynamic Simulations. Application to the Spectral Shape of the Q(1) Raman Lines of H{_2}/H{_2}

    NASA Astrophysics Data System (ADS)

    Tran, H.; Hartmann, J. M.

    2011-06-01

    Collision induced velocity changes for pure H{_2} have been computed from classical dynamic simulations. The results have been compared with the Keilson-Storer model from four different points of view. The first involves various autocorrelation functions associated with the velocity. The second and third give more detailed information, and are time evolutions of some conditional probabilities for changes of the velocity modulus and orientation and the collision kernels themselves. The fourth considers the evolutions, with density, of the half widths of the Q(1) lines of the isotropic Raman (1-0) fundamental band and of the (2-0) overtone quadrupole band. These spectroscopic data enable an indirect test of the models since velocity changes translate into line-shape modifications through the speed dependence of collisional parameters and the Dicke narrowing of the Doppler contribution to the profile. The results indicate that, while the KS approach gives a poor description of detailed velocity-to-velocty changes, it leads to accurate results for the correlation functions and spectral shapes, quantities related to large averages over the velocity. It is also shown that the use of collision kernels directly derived from MDS lead to an almost perfect prediction of all considered quantities (correlation functions, conditional probabilities, and spectral shapes). Finally, the results stress the need for very accurate calculations of line-broadening and -shifting coefficients from the intermolecular potential to obviate the need for experimental data and permit fully meaningful tests of the models. H. Tran, J.M. Hartmann J. Chem. Phys. 130, 094301, 2009.

  13. Inelastic processes in atomic, molecular and chemical physics (in honour of Andrey K. Belyaev)

    NASA Astrophysics Data System (ADS)

    Barklem, Paul S.; Tscherbul, Timur V.

    2015-11-01

    This Special Issue is dedicated to Professor Andrey K. Belyaev, on the occasion of his 60th birthday and in celebration of his productive career in theoretical atomic, molecular, and chemical physics. It brings together 12 research studies of Inelastic Processes in Atomic, Molecular and Chemical Physics, a research area where Andrey himself made significant contributions. Inelastic processes are central to many different areas of physics, including atmospheric physics, astrophysics, and plasma physics to name a few, as well as in related technological applications such as lasers and fusion reactors. Quantitative understanding of the mechanisms of inelastic processes in atoms and molecules is therefore a problem of fundamental importance in physics, astrophysics, and chemistry. It is precisely this challenging problem that Andrey's research addresses using a broad arsenal of theoretical tools and techniques.

  14. Dynamics of elementary atomic and molecular processes in gases and plasmas

    NASA Astrophysics Data System (ADS)

    Shcheglov, V. A.

    The papers presented in this volume provide an overview of recent theoretical research in the dynamics of atomic-molecular processes in gas and plasma. The theory of bimolecular reactions is developed in the context of a statistical approach. Results of Monte Carlo calculations of two-channel chemical reactions are presented; the cross sections of a number of processes in nuclear, atomic, and molecular physics are calculated within the framework of the quantum theory of scattering. The discussion also covers the ionization of Rydberg atoms colliding with neutral particles, the bremsstrahlung effect associated with the resonance scattering of electrons by atoms, and the elementary process of three-level system decomposition. (No individual items are abstracted in this volume)

  15. Resonant charge transfer process in ion-metal surface collisions: effect of the presence of vacancies on the surface

    NASA Astrophysics Data System (ADS)

    Silva, J. A. M. C.; Wolfgang, J.; Borisov, A. G.; Gauyacq, J. P.; Nordlander, P.; Teillet-Billy, D.

    In this paper an investigation of how the presence of a vacancy on a metal surface influences the energy shift and broadening of negative ion states near the surface is presented. Results for H - and F - ions in the vicinity of a surface vacancy defect on an Al(1 1 1) surface are included. The vacancy-induced electron potential is calculated using a density functional method and the Coupled Angular Mode (CAM) method is used to determine the shift and broadening of H - and F - levels. The results show that the vacancy induces a repulsive potential, shifting the negative ion levels up, while narrowing the width. These two effects have opposite influences on the resonant charge transfer process. Their approximate cancellation makes the RCT process in these systems relatively insensitive to vacancies in the surface layer.

  16. Nonequilibrium phenomena in N{sub 2}-cluster-surface collisions: A molecular-dynamics study of fragmentation, lateral jetting, and nonequilibrium energy distributions

    SciTech Connect

    Zimmermann, Steffen; Urbassek, Herbert M.

    2006-12-15

    Using molecular-dynamics simulation, we study the impact of (N{sub 2}){sub 2869} clusters on a flat rigid wall. We study the cluster fragmentation process, the formation of lateral jets, the energy redistribution among the resulting fragments, and the ratio of internal and translational energy of the emerging free molecules as a function of cluster impact energy in the range of 0.076-1520 meV/molecule. We find the fragmentation threshold energy to be in agreement with that found previously for (N{sub 2}){sub 13} clusters; the (scaled) number of fragments, however, increases more slowly with impact energy. Also the energy redistribution of the cluster impact energy among the internal and translational energy of the fragments is similar to that found for the small cluster. This means in particular that free molecules show a strong nonequilibrium energy partitioning in which the internal degrees of freedom are considerably less excited than the translational degrees of freedom. We also find that at impact energies above the fragmentation threshold the angular distribution of fragments is peaked parallel to the surface--i.e., the formation of lateral surface jets.

  17. Water interactions with condensed organic phases: a combined experimental and theoretical study of molecular-level processes

    NASA Astrophysics Data System (ADS)

    Johansson, Sofia M.; Kong, Xiangrui; Thomson, Erik S.; Papagiannakopoulos, Panos; Pettersson, Jan B. C.; Lovrić, Josip; Toubin, Céline

    2016-04-01

    Water uptake on aerosol particles modifies their chemistry and microphysics with important implications for air quality and climate. A large fraction of the atmospheric aerosol consists of organic aerosol particles or inorganic particles with condensed organic components. Here, we combine laboratory studies using the environmental molecular beam (EMB) method1 with molecular dynamics (MD) simulations to characterize water interactions with organic surfaces in detail. The over-arching aim is to characterize the mechanisms that govern water uptake, in order to guide the development of physics-based models to be used in atmospheric modelling. The EMB method enables molecular level studies of interactions between gases and volatile surfaces at near ambient pressure,1 and the technique may provide information about collision dynamics, surface and bulk accommodation, desorption and diffusion kinetics. Molecular dynamics simulations provide complementary information about the collision dynamics and initial interactions between gas molecules and the condensed phase. Here, we focus on water interactions with condensed alcohol phases that serve as highly simplified proxies for systems in the environment. Gas-surface collisions are in general found to be highly inelastic and result in efficient surface accommodation of water molecules. As a consequence, surface accommodation of water can be safely assumed to be close to unity under typical ambient conditions. Bulk accommodation is inefficient on solid alcohol and the condensed materials appear to produce hydrophobic surface structures, with limited opportunities for adsorbed water to form hydrogen bonds with surface molecules. Accommodation is significantly more efficient on the dynamic liquid alcohol surfaces. The results for n-butanol (BuOH) are particularly intriguing where substantial changes in water accommodation taking place over a 10 K interval below and above the BuOH melting point.2 The governing mechanisms for the

  18. 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.

  19. Effects of weakly coupled and dense quantum plasmas environments on charge exchange and ionization processes in Na+ + Rb(5s) atom collisions

    NASA Astrophysics Data System (ADS)

    Pandey, Mukesh Kumar; Lin, Yen-Chang; Ho, Yew Kam

    2017-02-01

    The effects of weakly coupled or classical and dense quantum plasmas environment on charge exchange and ionization processes in Na+ + Rb(5s) atom collision at keV energy range have been investigated using classical trajectory Monte Carlo (CTMC) method. The interaction of three charged particles are described by the Debye-Hückel screen potential for weakly coupled plasma, whereas exponential cosine-screened Coulomb potential have been used for dense quantum plasma environment and the effects of both conditions on the cross sections are compared. It is found that screening effects on cross sections in high Debye length condition is quite small in both plasma environments. However, enhanced screening effects on cross sections are observed in dense quantum plasmas for low Debye length condition, which becomes more effective while decreasing the Debye length. Also, we have found that our calculated results for plasma-free case are comparable with the available theoretical results. These results are analyzed in light of available theoretical data with the choice of model potentials.

  20. Close-coupling calculations of low-energy inelastic and elastic processes in 4He collisions with H2: A comparative study of two potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Lee, Teck-Ghee; Rochow, C.; Martin, R.; Clark, T. K.; Forrey, R. C.; Balakrishnan, N.; Stancil, P. C.; Schultz, D. R.; Dalgarno, A.; Ferland, Gary J.

    2005-01-01

    The two most recently published potential energy surfaces (PESs) for the HeH2 complex, the so-called MR (Muchnick and Russek) and BMP (Boothroyd, Martin, and Peterson) surfaces, are quantitatively evaluated and compared through the investigation of atom-diatom collision processes. The BMP surface is expected to be an improvement, approaching chemical accuracy, over all conformations of the PES compared to that of the MR surface. We found significant differences in inelastic rovibrational cross sections computed on the two surfaces for processes dominated by large changes in target rotational angular momentum. In particular, the H2(ν=1,j=0) total quenching cross section computed using the BMP potential was found to be a factor of 1000 larger than that obtained with the MR surface. A lesser discrepancy persists over a large range of energies from the ultracold to thermal and occurs for other low-lying initial rovibrational levels. The MR surface was used in previous calculations of the H2(ν=1,j=0) quenching rate coefficient and gave results in close agreement with the experimental data of Audibert et al. which were obtained for temperatures between 50 and 300 K. Examination of the rovibronic coupling matrix elements, which are obtained following a Legendre expansion of the PES, suggests that the magnitude of the anisotropy of the BMP potential is too large in the interaction region. However, cross sections for elastic and pure rotational processes obtained from the two PESs differ typically by less than a factor of 2. The small differences may be ascribed to the long-range and anharmonic components of the PESs. Exceptions occur for (ν=10,j=0) and (ν=11,j=1) where significant enhancements have been found for the low-energy quenching and elastic cross sections due to zero-energy resonances in the BMP PES which are not present in the MR potential.

  1. 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.

  2. Multiscale Molecular Simulation of Solution Processing of SMDPPEH: PCBM Small-Molecule Organic Solar Cells.

    PubMed

    Lee, Cheng-Kuang; Pao, Chun-Wei

    2016-08-17

    Solution-processed small-molecule organic solar cells are a promising renewable energy source because of their low production cost, mechanical flexibility, and light weight relative to their pure inorganic counterparts. In this work, we developed a coarse-grained (CG) Gay-Berne ellipsoid molecular simulation model based on atomistic trajectories from all-atom molecular dynamics simulations of smaller system sizes to systematically study the nanomorphology of the SMDPPEH/PCBM/solvent ternary blend during solution processing, including the blade-coating process by applying external shear to the solution. With the significantly reduced overall system degrees of freedom and computational acceleration from GPU, we were able to go well beyond the limitation of conventional all-atom molecular simulations with a system size on the order of hundreds of nanometers with mesoscale molecular detail. Our simulations indicate that, similar to polymer solar cells, the optimal blending ratio in small-molecule organic solar cells must provide the highest specific interfacial area for efficient exciton dissociation, while retaining balanced hole/electron transport pathway percolation. We also reveal that blade-coating processes have a significant impact on nanomorphology. For given donor/acceptor blending ratios, applying an external shear force can effectively promote donor/acceptor phase segregation and stacking in the SMDPPEH domains. The present study demonstrated the capability of an ellipsoid-based coarse-grained model for studying the nanomorphology evolution of small-molecule organic solar cells during solution processing/blade-coating and provided links between fabrication protocols and device nanomorphologies.

  3. Chemical and entropic control on the molecular self-assembly process

    NASA Astrophysics Data System (ADS)

    Packwood, Daniel M.; Han, Patrick; Hitosugi, Taro

    2017-02-01

    Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process.

  4. 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.

  5. Chemical and entropic control on the molecular self-assembly process

    PubMed Central

    Packwood, Daniel M.; Han, Patrick; Hitosugi, Taro

    2017-01-01

    Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process. PMID:28195175

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

    NASA Astrophysics Data System (ADS)

    Engstrom, James R.; Kummel, Andrew C.

    2017-02-01

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

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

    PubMed

    Engstrom, James R; Kummel, Andrew C

    2017-02-07

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

  8. Formulation and numerical analysis of diatomic molecular dissociation using Boltzmann kinetic equation

    NASA Astrophysics Data System (ADS)

    Yano, Ryosuke; Suzuki, Kojiro; Kuroda, Hisayasu

    2007-01-01

    The direct description of chemical reactions by the Boltzmann equation still involves some difficulties in the kinetic theory. In this paper, we describe diatomic molecular dissociation due to transitions of vibrational quantum states resulting from inelastic collisions. These can be described by the Wang Chang-Uhlenbeck (WCU) equation. To avoid direct evaluation of the strong nonlinear collision kernel of the WCU equation, we used a kinetic equation. For accurate description of the dissociation process, we describe improvements we made to the conventional inelastic collision model (the so-called Morse model). Combining this inelastic collision model with the gas mixture model by Oguchi, we formulated a model for representing diatomic molecular dissociations. We validated this model by simulating a hypersonic shock layer with diatomic molecular dissociation.

  9. 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.

  10. 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.

  11. Dithienogermole-based solution-processed molecular solar cells with efficiency over 9.

    PubMed

    Gupta, Vinay; Lai, Lai Fan; Datt, Ram; Chand, Suresh; Heeger, Alan J; Bazan, Guillermo C; Singh, Surya Prakash

    2016-06-30

    A molecular donor of intermediate dimensions based on dithienogermole (DTG) as the central electron rich unit, coded as DTG(FBT2Th2)2, was designed and synthesized for use in bulk heterojunction, solution-processed organic solar cells. Under optimized conditions, a maximum power conversion efficiency (PCE) of 9.1% can be achieved with [6,6]-phenyl C71-butyric acid methyl ester (PC71BM) as the acceptor semiconductor component.

  12. Molecular Dynamics Simulations of Surface Processes: Oxygen Recombination on Silica Surfaces at High Temperature

    DTIC Science & Technology

    2007-07-01

    size-scalable cluster approach with SixOy clusters of increasing size cleaved from the β- cristobalite unit cell. In this study the hybrid Hartree...values of the β- cristobalite cell and extending the Molecular Dynamics Simulations of Surface Processes: Oxygen Recombination on Silica Surfaces at... cristobalite surface is reported as a function of the distance of the N atom from the Si active atom. The dashed line shows the interaction

  13. Power factor enhancement in solution-processed organic n-type thermoelectrics through molecular design.

    PubMed

    Russ, Boris; Robb, Maxwell J; Brunetti, Fulvio G; Miller, P Levi; Perry, Erin E; Patel, Shrayesh N; Ho, Victor; Chang, William B; Urban, Jeffrey J; Chabinyc, Michael L; Hawker, Craig J; Segalman, Rachel A

    2014-06-04

    A new class of high-performance n-type organic thermoelectric materials, self-doping perylene diimide derivatives with modified side chains, is reported. These materials achieve the highest n-type thermoelectric performance of solution-processed organic materials reported to date, with power factors as high as 1.4 μW/mK(2). These results demonstrate that molecular design is a promising strategy for enhancing organic thermoelectric performance.

  14. Collisions of excited Na atoms with H2 molecules. I. Ab initio potential energy surfaces and qualitative discussion of the quenching process

    NASA Astrophysics Data System (ADS)

    Botschwina, Peter; Meyer, Wilfried; Hertel, Ingolf V.; Reiland, W.

    1981-12-01

    Potential energy surfaces have been calculated for the four lowest electronic states of Na (3 2S, 3 2P)+H2(1Σ+g) by means of the RHF-SCF and PNO-CEPA methods. For the so-called quenching process of Na (3 2P) by H2 at low initial translational energies (E-VRT energy transfer) the energetically most favorable path occurs in C2v symmetry, since—at intermediate Na-H2 separation—the ? 2B2 potential energy surface is attractive. From the CEPA calculations, the crossing point of minimal energy between the ? 2A1 and ? 2B2 surfaces is obtained at Rc = 3.57 a.u. and rc = 2.17 a.u. with an energy difference to the asymptotic limit (R = ∞, r = re) of -0.06 eV. It is thus classically accessible without any initial translational energy, but at low initial translational energies (˜0.1 eV) quenching will be efficient only for arrangements of collision partners close to C2v symmetry. There is little indication of an avoiding crossing with an ionic intermediate correlating asymptotically with Na+ and H2- as was assumed in previous discussions of the quenching process. The dependence of the total quenching cross sections on the initial translational energy is discussed by means of the ''absorbing sphere'' model, taking the initial zero-point vibrational energy of the hydrogen molecule into account. New experimental data of the product channel distribution in H2 for center-of-mass forward scattering are presented. The final vibrational states v' = 3, 2, 1, and 0 of H2 are populated to about 26%, 61%, 13%, and 0%, respectively. The observed distributions in H2 (and D2) may be rationalized by simple dynamic considerations on the basis of the calculated surfaces.

  15. Radiative Association in Li+ + H- collisions

    NASA Astrophysics Data System (ADS)

    Dickinson, A. S.; Gadéa, F. X.

    Radiative association is one of the ways of forming LiH in low density environments. Its formation in collisions of Li(2p) +H(1s) has been shown to be about five orders of magnitude faster than for Li(2s) + H(1s) [1]. We investigate LiH formation in Li+ + H- collisions, considering association on both the C and D Σ states as about 96% of the mutual neutralization is to these states at low energy [2]. A quantal description of the process [3] has been used. The potentials are from ref. [4] and the dipole moments from ref. [5]. Similar results were obtained from both the C and D states. At 1000 K the total radiative association rate coefficient from the D state is 9.2× 10-15 cm3/s, compared to 2.1 × 10-20 cm3/s in Li(2s) + H(1s) collisions [6]. British Council support is gratefully acknowledged. {[1]} Gianturco F.A., Gori Giorgi P., 1996, Phys. Rev. A 54, 4073 {[2]} Croft H., Dickinson A.S., Gadéa F. X., 1999, MNRAS 304, 327 {[3]} Babb J.F., Kirby K.P., 1998, in The Molecular Astrophysics of Stars and Galaxies, Clarendon Press, Oxford, p. 11 {[4]} Gadéa F. X., Boutalib A., 1993, J. Phys. B 26, 61 {[5]} Berriche H., Gadéa F. X., 1995, Chem. Phys. Letts. 247 85 {[6]} Stancil P. C., Dalgarno A., 1997, ApJ 479, 543

  16. 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

    2016-02-01

    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.

  17. The shear flow processing of controlled DNA tethering and stretching for organic molecular electronics.

    PubMed

    Yu, Guihua; Kushwaha, Amit; Lee, Jungkyu K; Shaqfeh, Eric S G; Bao, Zhenan

    2011-01-25

    DNA has been recently explored as a powerful tool for developing molecular scaffolds for making reproducible and reliable metal contacts to single organic semiconducting molecules. A critical step in the process of exploiting DNA-organic molecule-DNA (DOD) array structures is the controlled tethering and stretching of DNA molecules. Here we report the development of reproducible surface chemistry for tethering DNA molecules at tunable density and demonstrate shear flow processing as a rationally controlled approach for stretching/aligning DNA molecules of various lengths. Through enzymatic cleavage of λ-phage DNA to yield a series of DNA chains of various lengths from 17.3 μm down to 4.2 μm, we have investigated the flow/extension behavior of these tethered DNA molecules under different flow strengths in the flow-gradient plane. We compared Brownian dynamic simulations for the flow dynamics of tethered λ-DNA in shear, and found our flow-gradient plane experimental results matched well with our bead-spring simulations. The shear flow processing demonstrated in our studies represents a controllable approach for tethering and stretching DNA molecules of various lengths. Together with further metallization of DNA chains within DOD structures, this bottom-up approach can potentially enable efficient and reliable fabrication of large-scale nanoelectronic devices based on single organic molecules, therefore opening opportunities in both fundamental understanding of charge transport at the single molecular level and many exciting applications for ever-shrinking molecular circuits.

  18. 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.

  19. An anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors.

    PubMed

    Lin, Thy-Hou; Lin, Guan-Liang

    2008-08-01

    A molecular docking method designated as ADDock, anchor-dependent molecular docking process for docking small flexible molecules into rigid protein receptors, is presented in this article. ADDock makes the bond connection lists for atoms based on anchors chosen for building molecular structures for docking small flexible molecules or ligands into rigid active sites of protein receptors. ADDock employs an extended version of piecewise linear potential for scoring the docked structures. Since no translational motion for small molecules is implemented during the docking process, ADDock searches the best docking result by systematically changing the anchors chosen, which are usually the single-edge connected nodes or terminal hydrogen atoms of ligands. ADDock takes intact ligand structures generated during the docking process for computing the docked scores; therefore, no energy minimization is required in the evaluation phase of docking. The docking accuracy by ADDock for 92 receptor-ligand complexes docked is 91.3%. All these complexes have been docked by other groups using other docking methods. The receptor-ligand steric interaction energies computed by ADDock for some sets of active and inactive compounds selected and docked into the same receptor active sites are apparently separated. These results show that based on the steric interaction energies computed between the docked structures and receptor active sites, ADDock is able to separate active from inactive compounds for both being docked into the same receptor.

  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. Infrared absorption by molecular gases as a probe of nanoporous silica xerogel and molecule-surface collisions: Low-pressure results

    NASA Astrophysics Data System (ADS)

    Vander Auwera, J.; Ngo, N. H.; El Hamzaoui, H.; Capoen, B.; Bouazaoui, M.; Ausset, P.; Boulet, C.; Hartmann, J.-M.

    2013-10-01

    Transmission spectra of gases confined (but not adsorbed) within the pores of a 1.4-cm-thick silica xerogel sample have been recorded between 2.5 and 5 μm using a high-resolution Fourier transform spectrometer. This was done for pure CO, CO2, N2O, H2O, and CH4 at room temperature and pressures of a few hectopascals. Least-squares fits of measured absorption lines provide the optical-path lengths within the confined (LC) and free (LF) gas inside the absorption cell and the half width at half maximum ΓC of the lines of the confined gases. The values of LC and LF retrieved using numerous transitions of all studied species are very consistent. Furthermore, LC is in satisfactory agreement with values obtained from independent measurements, thus showing that reliable information on the open porosity volume can be retrieved from an optical experiment. The values of ΓC, here resulting from collisions of the molecules with the inner surfaces of the xerogel pores, are practically independent of the line for each gas and inversely proportional to the square root of the probed-molecule molar mass. This is a strong indication that, for the studied transitions, a single collision of a molecule with a pore surface is sufficient to change its rotational state. A previously proposed simple model, used for the prediction of the line shape, leads to satisfactory agreement with the observations. It also enables a determination of the average pore size, bringing information complementary to that obtained from nitrogen adsorption porosimetry.

  2. 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.

  3. 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.

  4. Theoretical study of charge transfer dynamics in collisions of C6+ carbon ions with pyrimidine nucleobases

    NASA Astrophysics Data System (ADS)

    Bacchus-Montabonel, M. C.

    2012-07-01

    A theoretical approach of the charge transfer dynamics induced by collision of C6+ ions with biological targets has been performed in a wide collision energy range by means of ab-initio quantum chemistry molecular methods. The process has been investigated for the target series thymine, uracil and 5-halouracil corresponding to similar molecules with different substituent on carbon C5. Such a study may be related to hadrontherapy treatments by C6+carbon ions and may provide, in particular, information on the radio-sensitivity of the different bases with regard to ion-induced radiation damage. The results have been compared to a previous analysis concerning the collision of C4+ carbon ions with the same biomolecular targets and significant charge effects have been pointed out.

  5. Stepping and Crowding of Molecular Motors: Statistical Kinetics from an Exclusion Process Perspective

    PubMed Central

    Ciandrini, Luca; Romano, M. Carmen; Parmeggiani, Andrea

    2014-01-01

    Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerization (e.g., RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend contemporary statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of comoving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions. PMID:25185553

  6. Stepping and crowding of molecular motors: statistical kinetics from an exclusion process perspective.

    PubMed

    Ciandrini, Luca; Romano, M Carmen; Parmeggiani, Andrea

    2014-09-02

    Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerization (e.g., RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend contemporary statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of comoving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

  7. Sequential binary collision ionization mechanisms

    NASA Astrophysics Data System (ADS)

    van Boeyen, R. W.; Watanabe, N.; Doering, J. P.; Moore, J. H.; Coplan, M. A.; Cooper, J. W.

    2004-03-01

    Fully differential cross sections for the electron-impact ionization of the magnesium 3s orbital have been measured in a high-momentum-transfer regime wherein the ionization mechanisms can be accurately described by simple binary collision models. Measurements where performed at incident-electron energies from 400 to 3000 eV, ejected-electron energies of 62 eV, scattering angle of 20 °, and momentum transfers of 2 to 5 a.u. In the out-of-plane geometry of the experiment the cross section is observed far off the Bethe ridge. Both first- and second-order processes can be clearly distinguished as previously observed by Murray et al [Ref. 1] and Schulz et al [Ref. 2]. Owing to the relatively large momentum of the ejected electron, the second order processes can be modeled as sequential binary collisions involving a binary elastic collision between the incident electron and ionic core and a binary knock-out collision between the incident electron and target electron. At low incident-electron energies the cross section for both first and second order processes are comparable, while at high incident energies second-order processes dominate. *Supported by NSF under grant PHY-99-87870. [1] A. J. Murray, M. B. J. Woolf, and F. H. Read J. Phys. B 25, 3021 (1992). [2] M. Schulz, R. Moshammer, D. Fischer, H. Kollmus, D. H. Madison. S. Jones and J. Ullrich, Nature 422, 48 (2003).

  8. Collision Repair Campaign

    EPA Pesticide Factsheets

    The Collision Repair Campaign targets meaningful risk reduction in the Collision Repair source category to reduce air toxic emissions in their communities. The Campaign also helps shops to work towards early compliance with the Auto Body Rule.

  9. 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)

  10. Molecular characterization of low molecular weight dissolved organic matter in water reclamation processes using Orbitrap mass spectrometry.

    PubMed

    Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

    2016-09-01

    Reclaimed water has recently become an important water source for urban use, but the composition of dissolved organic matter (DOM) in reclaimed water has rarely been characterized at the compound level because of its complexity. In this study, the transformation and changes in composition of low molecular weight DOM in water reclamation processes, where secondary effluent of the municipal wastewater treatment plant was further treated by biofiltration, ozonation and chlorination, were investigated by "unknown" screening analysis using Orbitrap mass spectrometry (Orbitrap MS). The intense ions were detected over an m/z range from 100 to 450. In total, 2412 formulae with various heteroatoms were assigned, and formulae with carbon (C), hydrogen (H) and oxygen (O) only and C, H, O and sulfur (S) were the most abundant species. During biofiltration, CHO-only compounds with relatively high hydrogen to carbon (H/C) ratio or with saturated structure were preferentially removed, while CHOS compounds were mostly removed. Ozonation induced the greatest changes in DOM composition. CHOS compounds were mostly decreased after ozonation while ozone selectively removed CHO compounds with relatively unsaturated structure and produced compounds that were more saturated and with a higher degree of oxidation. After chlorination, 168 chlorine-containing formulae, chlorinated disinfection by-products (DBPs), were additionally detected. Candidate DBP precursors were determined by tracking chlorinated DBPs formed via electrophilic substitution, half of which were generated during the ozonation.

  11. Profibrillin-1 Maturation by Human Dermal Fibroblasts: Proteolytic Processing and Molecular Chaperones

    PubMed Central

    Wallis, Debra D.; Putnam, Elizabeth A.; Cretoiu, Jill S.; Carmical, Sonya G.; Cao, Shi-Nian; Thomas, Gary; Milewicz, Dianna M.

    2006-01-01

    Fibrillin-1 is synthesized as a proprotein that undergoes proteolytic processing in the unique C-terminal domain by a member of the PACE/furin family of endoproteases. This family of endoproteases is active in the trans-Golgi network (TGN), but metabolic labeling studies have been controversial as to whether profibrillin-1 is processed intracellularly or after secretion. This report provides evidence that profibrillin-1 processing is not an intracellular event. Bafilomycin A1 and incubation of dermal fibroblasts at 22°C were used to block secretion in the TGN to confirm that profibrillin-1 processing did not occur in this compartment. Profibrillin-1 immunoprecipitation studies revealed that two endoplasmic reticulum-resident molecular chaperones, BiP and GRP94, interacted with profibrillin-1. To determine the proprotein convertase responsible for processing profibrillin-1, a specific inhibitor of furin, α-1-antitrypsin, Portland variant, was both expressed in the cells and added to cells exogenously. In both cases, the inhibitor blocked the processing of profibrillin-1, providing evidence that furin is the enzyme responsible for profibrillin-1 processing. These studies delineate the secretion and proteolytic processing of profibrillin-1, and identify the proteins that interact with profibrillin-1 in the secretory pathway. PMID:14523997

  12. Molecular view of an electron transfer process essential for iron–sulfur protein biogenesis

    PubMed Central

    Banci, Lucia; Bertini, Ivano; Calderone, Vito; Ciofi-Baffoni, Simone; Giachetti, Andrea; Jaiswal, Deepa; Mikolajczyk, Maciej; Piccioli, Mario; Winkelmann, Julia

    2013-01-01

    Biogenesis of iron–sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron–sulfur protein assembly machinery, two human key proteins—NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin—form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron–sulfur cluster proteins. The Ndor1–anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells. PMID:23596212

  13. Information theory and signal transduction systems: from molecular information processing to network inference.

    PubMed

    Mc Mahon, Siobhan S; Sim, Aaron; Filippi, Sarah; Johnson, Robert; Liepe, Juliane; Smith, Dominic; Stumpf, Michael P H

    2014-11-01

    Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival and successful reproduction. Developmental processes are marshalled by a diverse set of signalling and control systems, ranging from systems with simple chemical inputs and outputs to complex molecular and cellular networks with non-linear dynamics. Information theory provides a powerful and convenient framework in which such systems can be studied; but it also provides the means to reconstruct the structure and dynamics of molecular interaction networks underlying physiological and developmental processes. Here we supply a brief description of its basic concepts and introduce some useful tools for systems and developmental biologists. Along with a brief but thorough theoretical primer, we demonstrate the wide applicability and biological application-specific nuances by way of different illustrative vignettes. In particular, we focus on the characterisation of biological information processing efficiency, examining cell-fate decision making processes, gene regulatory network reconstruction, and efficient signal transduction experimental design.

  14. 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

  15. Experiments on the Dynamics of Molecular Processes: a Chronicle of Fifty Years

    NASA Astrophysics Data System (ADS)

    Boato, Giovanni; Volpi, Gian Gualberto

    1999-10-01

    This paper reviews the way in which, in the Italy of the years immediately after World War II, interest in the dynamics of molecular processes was awakened. The narrative begins with the work of a small number of chemists and physicists who, in the initial stage, interacted closely. In the course of the years, their interests diverged and younger people joined the newly formed groups. Even now, after half a century, a common approach can still to be seen regarding how to attack problems and perform experiments. Experimental work is discussed, bringing out the common viewpoint of fields as diverse as mass spectrometry, isotope effects, chemical kinetics, molecular beams, molecule-molecule interactions, molecule-ion interactions, molecule-surface interactions, and plasma chemistry.

  16. Variable timestep algorithm for molecular dynamics simulation of non-equilibrium processes

    NASA Astrophysics Data System (ADS)

    Marks, Nigel A.; Robinson, Marc

    2015-06-01

    A simple, yet robust variable timestep algorithm is developed for use in molecular dynamics simulations of energetic processes. Single-particle Kepler orbits are studied to study the relationship between trajectory properties and the critical timestep for constant integration error. Over a wide variety of conditions the magnitude of the maximum force is found to correlate linearly with the inverse critical timestep. Other quantities used in the literature such as the time derivative of the force and the product of the velocity and force also show reasonable correlations, but not to the same extent. Application of the corresponding metric | |Fmax | | Δt in molecular dynamics simulation of radiation damage in graphite shows that the scheme is both straightforward to implement and effective. In tests on a 1 keV cascade the timestep varies by over two orders of magnitude with minimal loss of energy conservation.

  17. The Henry Ford production system: LEAN process redesign improves service in the molecular diagnostic laboratory: a paper from the 2008 William Beaumont hospital symposium on molecular pathology.

    PubMed

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

    2009-09-01

    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.

  18. Molecular and cellular processes underlying the hallmarks of head and neck cancer.

    PubMed

    Bernstein, Jonathan M; Bernstein, Clare R; West, Catharine M L; Homer, Jarrod J

    2013-09-01

    The hallmarks of cancer were updated by Hanahan and Weinberg in 2011. Here we discuss the updated hallmarks in relation to what is known of the molecular and cellular processes underlying the development of head and neck squamous cell carcinoma (HNSCC). Several mechanisms are described, and recent surveys of HNSCC suggest a limited number of mutations, from which more mechanisms may emerge. There are also epigenetic changes to the control of normal processes. More than one mechanism underlies each hallmark. Processes essential to the development of HNSCC need not be essential to the proliferation of the fully developed tumour. Attention is paid to the emerging hallmarks, deregulation of cellular energy metabolism and evasion of immune destruction, and enabling characteristics, genome instability and mutation and tumour-promoting inflammation. HNSCC may adapt to hypoxia, suppress HLA expression, and express Toll-like receptors to facilitate inflammation, which support the proliferation of the tumour.

  19. Haber Process Made Efficient by Hydroxylated Graphene: Ab Initio Thermochemistry and Reactive Molecular Dynamics.

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-07-07

    The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.

  20. Actualities on molecular pathogenesis and repairing processes of cerebral damage in perinatal hypoxic-ischemic encephalopathy.

    PubMed

    Distefano, Giuseppe; Praticò, Andrea D

    2010-09-16

    Hypoxic-ischemic encephalopathy (HIE) is the most important cause of cerebral damage and long-term neurological sequelae in the perinatal period both in term and preterm infant. Hypoxic-ischemic (H-I) injuries develop in two phases: the ischemic phase, dominated by necrotic processes, and the reperfusion phase, dominated by apoptotic processes extending beyond ischemic areas. Due to selective ischemic vulnerability, cerebral damage affects gray matter in term newborns and white matter in preterm newborns with the typical neuropathological aspects of laminar cortical necrosis in the former and periventricular leukomalacia in the latter. This article summarises the principal physiopathological and biochemical processes leading to necrosis and/or apoptosis of neuronal and glial cells and reports recent insights into some endogenous and exogenous cellular and molecular mechanisms aimed at repairing H-I cerebral damage.

  1. Actualities on molecular pathogenesis and repairing processes of cerebral damage in perinatal hypoxic-ischemic encephalopathy

    PubMed Central

    2010-01-01

    Hypoxic-ischemic encephalopathy (HIE) is the most important cause of cerebral damage and long-term neurological sequelae in the perinatal period both in term and preterm infant. Hypoxic-ischemic (H-I) injuries develop in two phases: the ischemic phase, dominated by necrotic processes, and the reperfusion phase, dominated by apoptotic processes extending beyond ischemic areas. Due to selective ischemic vulnerability, cerebral damage affects gray matter in term newborns and white matter in preterm newborns with the typical neuropathological aspects of laminar cortical necrosis in the former and periventricular leukomalacia in the latter. This article summarises the principal physiopathological and biochemical processes leading to necrosis and/or apoptosis of neuronal and glial cells and reports recent insights into some endogenous and exogenous cellular and molecular mechanisms aimed at repairing H-I cerebral damage. PMID:20846380

  2. Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation

    PubMed Central

    Millevoi, Stefania; Vagner, Stéphan

    2010-01-01

    Messenger RNA (mRNA) 3′ end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3′ end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3′ end processing regulation by proposing several overlapping models of regulation. PMID:20044349

  3. Medullary and papillary carcinoma of the thyroid gland occurring as a collision tumour: report of three cases with molecular analysis and review of the literature.

    PubMed

    Rossi, S; Fugazzola, L; De Pasquale, L; Braidotti, P; Cirello, V; Beck-Peccoz, P; Bosari, S; Bastagli, A

    2005-06-01

    We report the simultaneous occurrence of medullary thyroid carcinoma (MTC) and papillary thyroid carcinoma (PTC), presenting as spatially distinct and well-defined tumour components, in three cases. In the first patient, histology, immunohistochemistry and electron microscopy demonstrated an MTC in the one nodule and PTC in two additional lesions. Non-neoplastic thyroid parenchyma separated the three nodules. Metastasis from PTC was diagnosed in a regional lymph node. Genetic analysis of both tumour components showed a distinctive mutational pattern: in the MTC a Cys634Arg substitution in exon 11 of the RET gene and in the two PTC foci a Val600Glu substitution in exon 15 of the BRAF gene. The other two patients are members of a large multigenerational family affected with familial MTC due to a germline mutation of the RET gene (Ala891Ser). Both patients harboured, besides medullary cancer and C-cell hyperplasia, distinct foci of papillary thyroid cancer, which was positive for Val600Glu BRAF mutation. Review of the literature disclosed 18 similar lesions reported and allowed the identification of different patterns of clinical presentation and biological behaviour. So far, the pathogenesis of these peculiar cases of thyroid malignancy has been completely unknown, but an underlying common genetic drive has been hypothesised. This is the first report in which two mutations, in the RET and BRAF genes, have been identified in three cases of MTC/PTC collision tumour, thus documenting the different genetic origin of these two coexisting carcinomas.

  4. Probability of satellite collision

    NASA Technical Reports Server (NTRS)

    Mccarter, J. W.

    1972-01-01

    A method is presented for computing the probability of a collision between a particular artificial earth satellite and any one of the total population of earth satellites. The collision hazard incurred by the proposed modular Space Station is assessed using the technique presented. The results of a parametric study to determine what type of satellite orbits produce the greatest contribution to the total collision probability are presented. Collision probability for the Space Station is given as a function of Space Station altitude and inclination. Collision probability was also parameterized over miss distance and mission duration.

  5. 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

  6. Nonequilibrium processes.

    PubMed

    Polanyi, J C

    1971-08-01

    Nonequilibrium phenomena have been studied for over half a century, particularly as a means to understanding the mechanism of energy transfer. Application of the insights and techniques of molecular physics to chemistry has resulted in a view of chemistry as constituting an aspect of the study of strong collisions, and chemical reaction as a special type of energy transfer. Increasing use has been made in experimental work of nonequilibrium environments for the study of chemical processes. The nature and purpose of such experiments are reviewed here, very briefly, and an attempt is made to point to areas that appear ripe for development over the coming decade.

  7. Differential scattering cross sections for collisions of 0.5-, 1.5-, and 5.0-keV helium atoms with He, H2, N2, and O2. [for atmospheric processes modeling

    NASA Technical Reports Server (NTRS)

    Newman, J. H.; Smith, K. A.; Stebbings, R. F.; Chen, Y. S.

    1985-01-01

    This paper reports the first results of an experimental program established to provide cross section data for use in modeling various atmospheric processes. Absolute cross sections, differential in the scattering angle, have been measured for collisions of 0.5-, 1.5-, and 5.0-keV helium atoms with He, H2, N2, and O2 at laboratory scattering angles between 0.1 deg and 5 deg. The results are the sums of cross sections for elastic and inelastic scattering of helium atoms; charged collision products are not detected. Integration of the differential cross section data yields integral cross sections consistent with measurements by other workers. The apparatus employs a position-sensitive detector for both primary and scattered particles and uses a short target cell with a large exit aperture to ensure a simple and well-defined apparatus geometry.

  8. Molecular alignment effect on the photoassociation process via a pump-dump scheme

    SciTech Connect

    Wang, Bin-Bin; Han, Yong-Chang Cong, Shu-Lin

    2015-09-07

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na{sub 2}) 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 (X{sup 1}Σ{sup +}) is associated into the molecule in the bound states of the excited state (A{sup 1}Σ{sup +}) 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.

  9. 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

  10. 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

    NASA Astrophysics Data System (ADS)

    Misra, Deepankar; Kelkar, A.; Kadhane, U.; Kumar, Ajay; Singh, Y. P.; Tribedi, Lokesh C.; Fainstein, P. D.

    2007-05-01

    We report the energy and angular distribution of electron double differential cross sections (DDCS) in collision of 6-MeV/uC6+ 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 1000eV are detected at about 10 different emission angles between 30° and 150° . 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 H2 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.

  11. 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.

  12. Ab initio molecular dynamics simulation on the formation process of He@C₆₀ synthesized by explosion.

    PubMed

    Li, Jian-Ying; Liu, Li-Min; Jin, Bo; Liang, Hua; Yu, Hai-Jun; Zhang, Hong-Chang; Chu, Shi-Jin; Peng, Ru-Fang

    2013-04-01

    The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C₆₀ at fairly high yield, but the mechanism of He inserting into C₆₀ cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C₆₀ molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C₆₀, and the self-healing capability of the defects was also observed.

  13. 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.

  14. Mandibular arch muscle identity is regulated by a conserved molecular process during vertebrate development.

    PubMed

    Knight, Robert D; Mebus, Katharina; Roehl, Henry H

    2008-06-15

    Vertebrate head muscles exhibit a highly conserved pattern of innervation and skeletal connectivity and yet it is unclear whether the molecular basis of their development is likewise conserved. Using the highly conserved expression of Engrailed 2 (En2) as a marker of identity in the dorsal mandibular muscles of zebrafish, we have investigated the molecular signals and tissues required for patterning these muscles. We show that muscle En2 expression is not dependent on signals from the adjacent neural tube, pharyngeal endoderm or axial mesoderm and that early identity of head muscles does not require bone morphogenetic pathway, Notch or Hedgehog (Hh) signalling. However, constrictor dorsalis En2 expression is completely lost after a loss of fibroblast growth factor (Fgf) signalling and we show that is true throughout head muscle development. These results suggest that head muscle identity is dependent on Fgf signalling. Data from experiments performed in chick suggest a similar regulation of En2 genes by Fgf signalling revealing a conserved mechanism for specifying head muscle identity. We present evidence that another key gene important in the development of mouse head muscles, Tbx1, is also critical for specification of mandibular arch muscle identity and that this is independent of Fgf signalling. These data imply that dorsal mandibular arch muscle identity in fish, chick and mouse is specified by a highly conserved molecular process despite differing functions of these muscles in different lineages.

  15. 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.

  16. How useful is molecular modelling in combination with ion mobility mass spectrometry for 'small molecule' ion mobility collision cross-sections?

    PubMed

    Lapthorn, Cris; Pullen, Frank S; Chowdhry, Babur Z; Wright, Patricia; Perkins, George L; Heredia, Yanira

    2015-10-21

    Ion mobility mass spectrometry is used to measure the drift-time of an ion. The drift-time of an ion can be used to calculate the collision cross-section (CCS) in travelling wave ion mobility (e.g. Waters Synapt and Vion instruments) or directly determine the experimental CCS (e.g. Agilent 6560 instrument and many drift-tube instruments). A comparison of the experimental CCS and theoretical CCS values obtained from trajectory method He(g) parameterised MOBCAL and N2(g) parameterised MOBCAL software, for a range of 20 'small molecules' is presented. This study utilises density functional theory B3LYP methods and the 6-31G+(d,p) basis set to calculate theoretical CCS values. This study seeks to assess the accuracy of a common procedure using CCS calibration with poly-(d/l)-alanine derived from drift-cell measurements and the original release of MOBCAL software and compare it with recent improvements with a drug-like molecule calibration set and a revision of MOBCAL parameterised for N2(g) drift gas. This study represents one of the first quantitative evaluations of the agreement between theoretical CCS and experimental CCS values for a range of small pharmaceutically relevant molecules using travelling wave ion mobility mass spectrometry. Accurate theoretical CCS may allow optimisation of ion mobility separations in silico, provide CCS databases that can confirm structures without the need for alternative analytical tools such as nuclear magnetic resonance spectroscopy (NMR) and assignment of unknowns and positional isomers without requiring reference materials.

  17. 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.

  18. Molecular Dynamics simulations of platinum plasma sputtering. : A comparative case study.

    NASA Astrophysics Data System (ADS)

    Brault, Pascal; Chuon, Sotheara; Bauchire, Jean-Marc

    2016-05-01

    Molecular Dynamics simulations are carried out for investigating atomic processes of platinum sputtering. Sputtered Pt atom energy distribution functions are determined at different sputtering argon ionenergies: 100, 500 and 1000 eV. Calculated energy distribution functions show a cross-over from Thompson theory to binary collision model when increasing argon ion energy and Pt atom sputtered energy. Implanted argon ion number is depending on its kinetic energy, while it is not the case in binary collision approximation. Finally sputtering yields are greater for Thompson theory than for binary collision model at low energy, but converge to the close values at high energy.

  19. 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

  20. Molecular floating-gate organic nonvolatile memory with a fully solution processed core architecture

    NASA Astrophysics Data System (ADS)

    Wu, Chao; Wang, Wei; Song, Junfeng

    2016-11-01

    In this paper, we demonstrated a floating-gate organic thin film transistor based nonvolatile memory, in which the core architecture was processed by a sequential three-step solution spin-coating method. The molecular semiconductor 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-Pen) distributing in the matrix of polymer poly(styrene) (PS), acting as the floating-gate and tunneling layer, respectively, was processed by one-step spin-coating from their blending solution. The effect of the proportion of TIPS-Pen in the matrix of PS on the memory performances of devices was researched. As a result, a good nonvolatile memory was achieved, with a memory window larger than 25 V, stable memory endurance property over 500 cycles and retention time longer than 5000 s with a high memory ratio larger than 102, at an optimal proportion of TIPS-Pen in the matrix of PS.

  1. Fast direct reconstruction strategy of dynamic fluorescence molecular tomography using graphics processing units

    NASA Astrophysics Data System (ADS)

    Chen, Maomao; Zhang, Jiulou; Cai, Chuangjian; Gao, Yang; Luo, Jianwen

    2016-06-01

    Dynamic fluorescence molecular tomography (DFMT) is a valuable method to evaluate the metabolic process of contrast agents in different organs in vivo, and direct reconstruction methods can improve the temporal resolution of DFMT. However, challenges still remain due to the large time consumption of the direct reconstruction methods. An acceleration strategy using graphics processing units (GPU) is presented. The procedure of conjugate gradient optimization in the direct reconstruction method is programmed using the compute unified device architecture and then accelerated on GPU. Numerical simulations and in vivo experiments are performed to validate the feasibility of the strategy. The results demonstrate that, compared with the traditional method, the proposed strategy can reduce the time consumption by ˜90% without a degradation of quality.

  2. 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.

  3. 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

  4. Wavelet analysis of molecular dynamics: efficient extraction of time-frequency information in ultrafast optical processes.

    PubMed

    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.

  5. 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.

  6. 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

  7. Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process.

    PubMed

    Venclovas, Ceslovas; Colvin, Michael E; Thelen, Michael P

    2002-10-01

    Replication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP-driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9-Rad1-Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C-terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21-PCNA interaction, while the RFC3-PCNA binding is proposed to be similar to the E. coli delta-beta interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1-PCNA interaction and compare putative clamp-interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C-terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17-RFC(2-5)/Rad9-Rad1-Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental

  8. 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.

  9. 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 25μl Ep-tube amplified reaction, which indicates a promising clinic molecular diagnostics in the droplet amplification.

  10. 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.

  11. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools

    PubMed Central

    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

  12. Antiproton production in heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Jacak, B. V.

    In high energy p-p and alpha-alpha collisions, baryons are observed predominantly at rapidities near those of target and projectile; the mean rapidity shift of projectile and target nucleons is approximately one unit. In the central rapidity region, the number of baryons is quite small. In fact, the number of baryons and antibaryons is rather similar, indicating that most of these baryons are CREATED particles rather than projectile and target fragments. Antibaryon production is of interest in heavy ion collisions as enhanced antiquark production has been predicted as a potential signature of quark-gluon plasma formation. Antibaryons also provide a sensitive probe of the hadronic environment, via annihilation and/or mean field effects upon their final distributions. However, the collision dynamics also affect the baryon and antibaryon distributions. Baryons are more shifted toward midrapidity in nucleus-nucleus and p-p nucleus collisions than in p-p collisions, increasing the probability of annihilating the antibaryons. The interpretation of antibaryon yields is further complicated by collective processes which may take place in the dense hadronic medium formed in nucleus-nucleus collisions. Jahns and coworkers have shown that multistep processes can increase antibaryon production near threshold. Antiproton production is clearly very interesting, but is sensitive to a combination of processes taking place in the collision. The final number of observed antiprotons depends on the balance between mechanisms for extra antiproton production beyond those from the individual nucleon-nucleon collisions and annihilation with surrounding baryons. We can hope to sort out these things by systematic studies, varying the system size and beam energy. I will review what is known about antiproton production at both the AGS and SPS, and look at trends going from p-p to p-nucleus to nucleus-nucleus collisions.

  13. Diffractive processes in antiproton-proton collision at √s = 1.96 TeV in the D0 experiment

    SciTech Connect

    Otec, Roman

    2006-01-01

    A first study of single diffractive central high-pT dijet events in p$\\bar{p}$ collisions at center-of-mass energy √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-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 |η| ϵ [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 pt central jets. This variable is sensitive to the dynamics of the process. Indeed, the results show the different behavior of ΔΦ distributions between the inclusive and diffractive samples. It is also shown that this difference is bigger for lower pT jets. Other distributions presented in the thesis show that most

  14. 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.

  15. 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.

  16. Stereodynamics: From elementary processes to macroscopic chemical reactions

    SciTech Connect

    Kasai, Toshio; Che, Dock-Chil; Tsai, Po-Yu; Lin, King-Chuen; Palazzetti, Federico; Aquilanti, Vincenzo

    2015-12-31

    This paper aims at discussing new facets on stereodynamical behaviors in chemical reactions, i.e. the effects of molecular orientation and alignment on reactive processes. Further topics on macroscopic processes involving deviations from Arrhenius behavior in the temperature dependence of chemical reactions and chirality effects in collisions are also discussed.

  17. 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

  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

  19. Study the sensitivity of molecular functional groups to bioethanol processing in lipid biopolymer of co-products using DRIFT molecular spectroscopy.

    PubMed

    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=O ester (ca. 1745 cm(-1)) and unsaturated groups (CH attached to C=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=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

  20. Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations.

    PubMed

    Debela, Tekalign T; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z

    2017-03-14

    The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

  1. WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

    PubMed

    McMahon, S

    2016-06-01

    Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

  2. 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.

  3. Molecular reordering processes on ice (0001) surfaces from long timescale simulations

    NASA Astrophysics Data System (ADS)

    Pedersen, Andreas; Wikfeldt, Kjartan T.; Karssemeijer, Leendertjan; Cuppen, Herma; Jónsson, Hannes

    2014-12-01

    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.

  4. 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.

  5. Newton's cradle versus nonbinary collisions.

    PubMed

    Sekimoto, Ken

    2010-03-26

    Newton's cradle is a classical example of a one-dimensional impact problem. In the early 1980s the naive perception of its behavior was corrected: For example, the impact of a particle does not exactly cause the release of the farthest particle of the target particle train, if the target particles have been just in contact with their own neighbors. It is also known that the naive picture would be correct if the whole process consisted of purely binary collisions. Our systematic study of particle systems with truncated power-law repulsive force shows that the quasibinary collision is recovered in the limit of hard core repulsion, or a very large exponent. In contrast, a discontinuous steplike repulsive force mimicking a hard contact, or a very small exponent, leads to a completely different process: the impacting cluster and the targeted cluster act, respectively, as if they were nondeformable blocks.

  6. 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.

  7. Bidirectional transport by molecular motors: enhanced processivity and response to external forces.

    PubMed

    Müller, Melanie J I; Klumpp, Stefan; Lipowsky, Reinhard

    2010-06-02

    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.

  8. 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

  9. A sulfuric-lactic acid process for efficient purification of fungal chitosan with intact molecular weight.

    PubMed

    Naghdi, Mitra; Zamani, Akram; Karimi, Keikhosro

    2014-02-01

    The most recent method of fungal chitosan purification, i.e., two steps of dilute sulfuric acid treatment, pretreatment of cell wall at room temperature for phosphate removal and extraction of chitosan from the phosphate free cell wall at high temperature, significantly reduces the chitosan molecular weight. This study was aimed at improvement of this method. In the pretreatment step, to choose the best conditions, cell wall of Rhizopus oryzae, containing 9% phosphate, 10% glucosamine, and 21% N-acetyl glucosamine, was treated with sulfuric, lactic, acetic, nitric, or hydrochloric acid, at room temperature. Sulfuric acid showed the best performance in phosphate removal (90%) and cell wall recovery (89%). To avoid depolymerisation of chitosan, hot sulfuric acid extraction was replaced with lactic acid treatment at room temperature, and a pure fungal chitosan was obtained (0.12 g/g cell wall). Similar pretreatment and extraction processes were conducted on pure shrimp chitosan and resulted in a chitosan recovery of higher than 87% while the reduction of chitosan viscosity was less than 15%. Therefore, the sulfuric-lactic acid method purified the fungal chitosan without significant molecular weight manipulation.

  10. Implications of exercise training and distribution of protein intake on molecular processes regulating skeletal muscle plasticity.

    PubMed

    Margolis, Lee M; Rivas, Donato A

    2015-03-01

    To optimize its function, skeletal muscle exhibits exceptional plasticity and possesses the fundamental capacity to adapt its metabolic and contractile properties in response to various external stimuli (e.g., external loading, nutrient availability, and humoral factors). The adaptability of skeletal muscle, along with its relatively large mass and high metabolic rate, makes this tissue an important contributor to whole body health and mobility. This adaptational process includes changes in the number, size, and structural/functional properties of the myofibers. The adaptations of skeletal muscle to exercise are highly interrelated with dietary intake, particularly dietary protein, which has been shown to further potentiate exercise training-induced adaptations. Understanding the molecular adaptation of skeletal muscle to exercise and protein consumption is vital to elicit maximum benefit from exercise training to improve human performance and health. In this review, we will provide an overview of the molecular pathways regulating skeletal muscle adaptation to exercise and protein, and discuss the role of subsequent timing of nutrient intake following exercise.

  11. General strategy for understanding intracellular molecular interaction cascades that elicit stimulus-invoked biological processes

    PubMed Central

    OKAYAMA, Hiroto

    2016-01-01

    Recent advances in biology have been driven by chemical analyses of the substances that form living organisms. Such analyses are extremely powerful as way of learning about the static properties of molecular species, but relatively powerless for understanding their dynamic behaviors even though this dynamism is essential for organisms to perform various biological processes that perpetuate their lives. Thus, attempts to identify individual species and molecular interaction cascades that drive specific responses to external stimuli or environmental changes often fail. Here I propose a general strategy to address this problem. The strategy comprises two key elements: functional manipulation of a given protein molecule coupled with close monitoring of its biological effect, and construction of a knowledge base tailored for conjecture-driven experimentation. The original idea for this strategy co-evolved with and greatly helped a series of studies we recently performed to discover critical signal cascades and cellular components that regulate the cell cycle transition from G1 to S phase. PMID:27725475

  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.

  13. 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.

  14. 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.

  15. Basins in ARC-continental collisions

    USGS Publications Warehouse

    Draut, Amy E.; Clift, Peter D.; Busby, Cathy; Azor, Antonio

    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

  16. Oscillating collision of the granular chain on static wall

    NASA Astrophysics Data System (ADS)

    Ma, Liang; Huang, Decai; Chen, Weizhong; Jiao, Tengfei; Sun, Min; Hu, Fenglan; Su, Jiaye

    2017-02-01

    Collision of the granular chain on static wall is investigated by discrete element method. Collision time and traveling time are proposed on the basis of the characteristics of the collision of a single grain with a wall and the propagation of interaction force wave in a granular chain to explain the collision process. Simulation results show that an oscillating collision force is generated when the force waves successively arrive at the wall. For the collision of a mono-dispersed chain, the simulation data are in good agreement with the predicted relationship between the maximum chain length of nmax and the first maximum collision force FA. Rigid wall and soft wall are defined as nmax = 1 and nmax ≥ 2, respectively. Two similar processes of oscillating collisions occur when a light or a heavy impure grain is introduced. In these processes, two maximum collision forces, namely, FA and FB, are observed, respectively. The simulation results about the influence of the mass and position of light impure grain on the collision force FB further confirm our theoretical predictions.

  17. Many-body processes in atomic and molecular physics. Progress report

    SciTech Connect

    Chu, S.I.

    1981-01-01

    A proposal is presented for theoretical efforts towards the following projects: (1) carry out rotational predissociation lifetime calculations of several van der Waals molecules for which accurate potential energy surfaces were obtained recently by van der Waals molecular spectroscopic methods; (2) development and extension of the complex coordinate - coupled channel formalism to vibrational predissociation studies; (3) Floquet theory study of the quantum dynamics of multiphoton excitation of vibrational-rotational states of small molecules by laser light; (4) development and extension of the method of complex quasi-vibrational energy formalism to the study of intense field multiphoton dissociation of diatomic molecules and to photodissociation process in the presence of shape resonances; (5) investigation of the external field effects in multiphoton excitation and dissociation of small molecules. Depending on time and resources, several other projects may also be pursued. A detailed discussion covering these proposed projects is presented.

  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. 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.

  20. 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.

  1. Mapping variable ring polymer molecular dynamics: A path-integral based method for nonadiabatic processes

    NASA Astrophysics Data System (ADS)

    Ananth, Nandini

    2013-09-01

    We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral representation of the quantum Boltzmann operator using continuous Cartesian variables for both electronic states and nuclear degrees of freedom. We demonstrate the accuracy of the MV-RPMD approach in calculations of real-time, thermal correlation functions for a range of two-state single-mode model systems with different coupling strengths and asymmetries. Further, we show that the ensemble of classical trajectories employed in these simulations preserves the Boltzmann distribution and provides a direct probe into real-time coupling between electronic state transitions and nuclear dynamics.

  2. Quinacridone-based molecular donors for solution processed bulk-heterojunction organic solar cells.

    PubMed

    Chen, John Jun-An; Chen, Teresa L; Kim, BongSoo; Poulsen, Daniel A; Mynar, Justin L; Fréchet, Jean M J; Ma, Biwu

    2010-09-01

    New soluble quinacridone-based molecules have been developed as electron donor materials for solution-processed organic solar cells. By functionalizing the pristine pigment core of quinacridone with solubilizing alkyl chains and light absorbing/charge transporting thiophene units, i.e., bithiophene (BT) and thienylbenzo[c][1,2,5]thiadiazolethienyl (BTD), we prepared a series of multifunctional quinacridone-based molecules. These molecular donors show intense absorption in the visible spectral region, and the absorption range and intensity are well-tuned by the interaction between the quinacridone core and the incorporated thiophene units. The thin film absorption edge extends with the expansion of molecular conjugation, i.e., 552 nm for N,N'-di(2-ethylhexyl)quinacridone (QA), 592 nm for 2,9-Bis(5'-hexyl-2,2'-bithiophene)-N,N'-di(2-ethylhexyl)quinacridone (QA-BT), and 637 nm for 4-(5-hexylthiophen-2-yl)-7-(thiophen-2-yl)benzo[c][1,2,5]thiadiazole (QA-BTD). The change of molecular structure also influences the electrochemical properties. Observed from cyclic voltammetry measurements, the oxidation and reduction potentials (vs ferrocene) are 0.7 and -1.83 V for QA, 0.54 and -1.76 V for QA-BT, and 0.45 and -1.68 V for QA-BTD. Uniform thin films can be generated from both single component molecular solutions and blend solutions of these molecules with [6,6]-phenyl C70-butyric acid methyl ester (PC70BM). The blend films exhibit space-charge limited current (SCLC) hole mobilities on the order of 1×10(-4) cm(2) V(-1) S(-1). Bulk heterojunction (BHJ) solar cells using these soluble molecules as donors and PC70BM as the acceptor were fabricated. Power conversion efficiencies (PCEs) of up to 2.22% under AM 1.5 G simulated 1 sun solar illumination have been achieved and external quantum efficiencies (EQEs) reach as high as ∼45%.

  3. Planarization process of single crystalline silicon asperity under abrasive rolling effect studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Si, Lina; Guo, Dan; Luo, Jianbin; Xie, Guoxin

    2012-10-01

    In the chemical mechanical polishing (CMP) process, the complex behaviors of abrasive particles play important roles in the planarization of wafer surface. Particles embedded in the pad remove materials by ploughing, while particles immersed in the slurry by rolling across the wafer surface. In this paper, processes of the particle rolling across a silicon surface with an asperity under various down forces and external driving forces were studied using molecular dynamics (MD) simulation method. The simulations clarified the asperity shape evolution during the rolling process and analyzed the energy changes of the simulation system and the interaction forces acted on the silica particle. It was shown that both the down force and the driving force had important influences on the amount of the material removed. With relatively small down forces and driving forces applied on the particle, the material removal occurred mainly in the front end of the asperity; when the down forces and driving forces were large enough, e.g., 100 nN, the material removal could take place at the whole top part of the asperity. The analysis of energy changes and interaction forces provided favorable explanations to the simulation results.

  4. 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...

  5. Understanding the role of London dispersion forces in molecular surface processes

    NASA Astrophysics Data System (ADS)

    Cooper, Valentino R.

    2012-02-01

    The interactions and dynamics of molecules at surfaces and within pores are essential to many chemical processes, ranging from molecular storage to catalysis and self-assembly. A molecular level understanding of molecule-surface interactions is crucial for tuning surface/pore selectivity and reactivity. While it is clear that strong chemisorption bonds facilitate these interactions, the role of weaker van der Waals (vdW) forces, which include London dispersion and π-π stacking interactions, are often unknown or overlooked. Recent advances in density functional theory (DFT) have now made it possible to reliably account for London dispersion interactions. In this paper, I will discuss the use of one such technique, the Rutgers-Chalmers vdW non-local correlation functional,ootnotetextM. Dion, H. Rydberg, E. Schr"oder, B. I. Lundqvist and D. C. Langreth, Phys. Rev. Lett., 92, 246401 (2004)^,ootnotetextT. Thonhauser, V. R. Cooper, S. Li, A. Puzder, P. Hyldgaard, and David C. Langreth, Phys. Rev. B, 76, 125112 (2007) to demonstrate how the inclusion of London dispersion forces is critical for a truly first principles understanding of processes sensitive to molecule-surface interactions, such as the loading of H2 within porous materials and the chemisorption of organic molecules at surfaces. These works highlight the fundamental importance of London dispersion interactions in the broader context of chemical physics. This work was supported by the Department of Energy, BES, Materials Sciences and Engineering Division.ootnotetextCollaborators: Guo Li, Isaac Tamblyn, Yungok Ihm, Jun-Hyung Cho, Shixuan Du, Jeffrey B. Neaton, Hong-Jun Gao, Zhenyu Zhang, James R. Morris

  6. Heavy particle collisions in astrophysical, fusion, and other plasmas

    NASA Astrophysics Data System (ADS)

    Schultz, David

    2013-09-01

    Contemporary computational methods to treat few-body, atomic-scale interactions have opened opportunities to study them at a new level of detail to both uncover unexpected phenomena and to create data of unprecedented accuracy and scope for applications. Such interactions within gaseous, plasma, and even material environments are fundamental to such diverse phenomena as low temperature plasma processing of semiconductors, collapsing giant molecular clouds forming stars, fluorescent lighting, radiation treatment of disease, and the chemistry of earth's atmosphere. I will illustrate progress using examples from recent work treating heavy particle collision systems, for which our knowledge has been both subtly refined and significantly changed. Examples will include elastic and transport-related processes in fusion and solar-system plasmas, charge transfer leading to diagnostic light emission in planetary atmospheres and fusion plasmas, and excitation and ionization processes needed for plasma modeling and diagnostics.

  7. Reactive Molecular Dynamics Investigations of Alkoxysilane Sol-Gel and Surface Coating Processes

    NASA Astrophysics Data System (ADS)

    Deetz, Joshua David

    The ability to generate nanostructured materials with tailored morphology or chemistry is of great technological interest. One proven method of generating metal-oxide materials, and chemically modifying metal-oxide surfaces is through the reactions of molecular building blocks known as alkoxysilanes. Alkoxysilanes are a class of chemicals which contain one or more organic alkoxy groups bonded to silicon atoms. Alkoxysilane (Si-O-R) chemical groups can undergo reactions to form bridges (Si-O-M) with metal oxides. Due to their ability to "attach" to metal-oxides through condensation reactions, alkoxysilanes have a number of interesting applications, such as: the generation of synthetic siloxane materials through the sol-gel process, and the formation of functionalized surface coatings on metal-oxide surfaces. Despite widespread study of sol-gel and surface coatings processes, it is difficult to predict the morphology of the final products due to the large number of process variables involved, such as precursor molecule structure, solvent effects, solution composition, temperature, and pH. To determine the influence of these variables on the products of sol-gel and coatings processes reactive molecular dynamics simulations are used. A reactive force field was used (ReaxFF) to allow the chemical bonds in simulation to dynamically form and break. The force field parameters were optimized using a parallel optimization scheme with a combination of experimental information, and density functional theory calculations. Polycondensation of alkoxysilanes in mixtures of alcohol and water were studied. Steric effects were observed to influence the rates of hydrolysis and condensation in solutions containing different precursor monomers. By restricting the access of nucleophiles to the central silicon atom, the nucleation rate of siloxanes can be controlled. The influence of solution precursor, water, and methanol composition on reaction rates was explored. It was determined that

  8. Molecular-dynamics simulation of clustering processes in sea-ice floes.

    PubMed

    Herman, Agnieszka

    2011-11-01

    In seasonally ice-covered seas and along the margins of perennial ice pack, i.e., in regions with medium ice concentrations, the ice cover typically consists of separate floes interacting with each other by inelastic collisions. In this paper, hitherto unexplored analogies between this type of ice cover and two-dimensional granular gases are used to formulate a model of ice dynamics at the floe level. The model consists of (i) momentum equations for floe motion between collisions, formulated in the form of a Stokes-flow problem, with floe-size-dependent time constant and equilibrium velocity, and (ii) a hard-disk collision model. The numerical algorithm developed is suitable for simulating particle-laden flow of N disk-shaped floes with arbitrary size distributions. The model is applied to study clustering phenomena in sea ice with power-law floe-size distribution. In particular, the influence of the average ice concentration A on the formation and characteristics of clusters is analyzed in detail. The results show the existence of two regimes, at low and high ice concentrations, differing in terms of the exponents of the cluster-size distribution and of the size of the largest cluster.

  9. Ball Collision Experiments

    ERIC Educational Resources Information Center

    Cross, R.

    2015-01-01

    Experiments are described on collisions between two billiard balls and between a bat and a ball. The experiments are designed to extend a student's understanding of collision events and could be used either as a classroom demonstration or for a student project.

  10. Elastic and Inelastic Collisions

    ERIC Educational Resources Information Center

    Gluck, Paul

    2010-01-01

    There have been two articles in this journal that described a pair of collision carts used to demonstrate vividly the difference between elastic and inelastic collisions. One cart had a series of washers that were mounted rigidly on a rigid wooden framework, the other had washers mounted on rubber bands stretched across a framework. The rigidly…

  11. Reconsolidation and extinction are dissociable and mutually exclusive processes: behavioral and molecular evidence.

    PubMed

    Merlo, Emiliano; Milton, Amy L; Goozée, Zara Y; Theobald, David E; Everitt, Barry J

    2014-02-12

    Memory persistence is critically influenced by retrieval. In rats, a single presentation of a conditioned fear stimulus induces memory reconsolidation and fear memory persistence, while repeated fear cue presentations result in loss of fear through extinction. These two opposite behavioral outcomes are operationally linked by the number of cue presentations at memory retrieval. However, the behavioral properties and mechanistic determinants of the transition have not yet been explored; in particular, whether reconsolidation and extinction processes coexist or are mutually exclusive, depending on the exposure to non-reinforced retrieval events. We characterized both behaviorally and molecularly the transition from reconsolidation to extinction of conditioned fear and showed that an increase in calcineurin (CaN) in the basolateral amygdala (BLA) supports the shift from fear maintenance to fear inhibition. Gradually increasing the extent of retrieval induces a gradual decrease in freezing responses to the conditioned stimulus and a gradual increase in amygdala CaN level. This newly synthesized CaN is required for the extinction, but not the reconsolidation, of conditioned fear. During the transition from reconsolidation to extinction, we have revealed an insensitive state of the fear memory where NMDA-type glutamate receptor agonist and antagonist drugs are unable either to modulate CaN levels in the BLA or alter the reconsolidation or extinction processes. Together, our data indicate both that reconsolidation and extinction are mutually exclusive processes and also reveal the presence of a transitional, or "limbo," state of the original memory between these two alternative outcomes of fear memory retrieval, when neither process is engaged.

  12. Head-on collision and overtaking collision between an envelope solitary wave and a KdV solitary wave in a dusty plasma

    PubMed Central

    Zhang, Heng; Duan, Wen-Shan; Qi, Xin; Yang, Lei

    2016-01-01

    Head-on collision and overtaking collision between a KdV solitary wave and an envelope solitary wave are first studied in present paper by using Particle-in-cell (PIC) method in a dusty plasma. There are phase shifts of the KdV solitary wave in both head-on collision and the overtaking collision, while no phase shift is found for the envelop solitary wave in any cases. The remarkable difference between head-on collision and the overtaking collision is that the phase shift of KdV solitary wave increases as amplitude of KdV solitary wave increases in head-on collision, while it decreases as amplitude of the KdV solitary wave increases in the overtaking collision. It is found that the maximum amplitude during the collision process is less than sum of two amplitudes of both solitary waves, but is larger than either of the amplitude. PMID:26868526

  13. Head-on collision and overtaking collision between an envelope solitary wave and a KdV solitary wave in a dusty plasma.

    PubMed

    Zhang, Heng; Duan, Wen-Shan; Qi, Xin; Yang, Lei

    2016-02-12

    Head-on collision and overtaking collision between a KdV solitary wave and an envelope solitary wave are first studied in present paper by using Particle-in-cell (PIC) method in a dusty plasma. There are phase shifts of the KdV solitary wave in both head-on collision and the overtaking collision, while no phase shift is found for the envelop solitary wave in any cases. The remarkable difference between head-on collision and the overtaking collision is that the phase shift of KdV solitary wave increases as amplitude of KdV solitary wave increases in head-on collision, while it decreases as amplitude of the KdV solitary wave increases in the overtaking collision. It is found that the maximum amplitude during the collision process is less than sum of two amplitudes of both solitary waves, but is larger than either of the amplitude.

  14. 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.

  15. Bubble collision with gravitation

    SciTech Connect

    Hwang, Dong-il; Lee, Bum-Hoon; Lee, Wonwoo; Yeom, Dong-han E-mail: bhl@sogang.ac.kr E-mail: innocent.yeom@gmail.com

    2012-07-01

    In this paper, we study vacuum bubble collisions with various potentials including gravitation, assuming spherical, planar, and hyperbolic symmetry. We use numerical calculations from double-null formalism. Spherical symmetry can mimic the formation of a black hole via multiple bubble collisions. Planar and especially hyperbolic symmetry describes two bubble collisions. We study both cases, when two true vacuum regions have the same field value or different field values, by varying tensions. For the latter case, we also test symmetric and asymmetric bubble collisions, and see details of causal structures. If the colliding energy is sufficient, then the vacuum can be destabilized, and it is also demonstrated. This double-null formalism can be a complementary approach in the context of bubble collisions.

  16. Directly probing anisotropy in atom-molecule collisions through quantum scattering resonances

    NASA Astrophysics Data System (ADS)

    Klein, Ayelet; Shagam, Yuval; Skomorowski, Wojciech; Żuchowski, Piotr S.; Pawlak, Mariusz; Janssen, Liesbeth M. C.; Moiseyev, Nimrod; van de Meerakker, Sebastiaan Y. T.; van der Avoird, Ad; Koch, Christiane P.; Narevicius, Edvardas

    2017-01-01

    Anisotropy is a fundamental property of particle interactions. It occupies a central role in cold and ultracold molecular processes, where orientation-dependent long-range forces have been studied in ultracold polar molecule collisions. In the cold collisions regime, quantization of the intermolecular degrees of freedom leads to quantum scattering resonances. Although these states have been shown to be sensitive to details of the interaction potential, the effect of anisotropy on quantum resonances has so far eluded experimental observation. Here, we directly measure the anisotropy in atom-molecule interactions via quantum resonances by changing the quantum state of the internal molecular rotor. We observe that a quantum scattering resonance at a collision energy of kB × 270 mK appears in the Penning ionization of molecular hydrogen with metastable helium only if the molecule is rotationally excited. We use state-of-the-art ab initio theory to show that control over the rotational state effectively switches the anisotropy on or off, disentangling the isotropic and anisotropic parts of the interaction.

  17. Ultrasonic attenuation in molecular crystals

    NASA Astrophysics Data System (ADS)

    Perrin, Bernard

    1981-11-01

    It is now well established from an experimental point of view that, concerning the ultrasonic attenuation, molecular crystals exhibit a specific behavior among dielectric crystals. This fact suggests the presence of a relaxation process. Liebermann, who has introduced this field, has proposed a way to analyze this problem and in particular has given an expression for the ultrasonic absorption coefficient in terms of a relaxation time and some thermodynamic quantities. In contrast to Liebermann's approach, a solid-state viewpoint is presented here, and it is shown that this ultrasonic relaxation can be taken into account in the framework of Akhieser's theory. A general expression of the ultrasonic absorption coefficient is calculated in terms of the phonon collision operator using the Boltzmann-equation approach of Woodruff and Ehrenreich. The collision-time approximation widely used in dielectric crystals fails in molecular crystals for which the presence of slow relaxation times in the collision operator prevents the thermalization of the whole set of phonons and gives rise to an ultrasonic relaxation. Thus a more suitable approximation is suggested here, which leads to a new expression of the ultrasonic attenuation valid in molecular crystals. Different forms of this expression are discussed, and comparison with Liebermann's expression used in most of the previous papers shows that the present treatment takes better account of the anisotropy of the solid state. The fit of experimental results obtained for some ionic-molecular crystals also shows that the expression derived here gives better agreement than does Liebermann's. Finally, it is shown that in the framework of the present treatment and under rather general conditions, the anisotropy affects primarily the magnitude of the ultrasonic absorption due to the molecular relaxation, but it does not affect its frequency dependence.

  18. Distinct molecular processes associated with isometric force generation and rapid tension recovery after quick release.

    PubMed Central

    Brenner, B; Chalovich, J M; Yu, L C

    1995-01-01

    It was proposed by Huxley and Simmons (Nature 1971, 233:533-538) that force-generating cross-bridges are attached to actin in several stable positions. In this concept, isometric force is generated by the same mechanism as the quick tension recovery after an abrupt release of length; i.e., when crossbridges proceed from the first postulated stable position to the second and/or subsequent positions, resulting in straining of the elastic elements within the cross-bridges. Therefore, isometric force is generated by cross-bridges in the second or even subsequent stable positions. However, through mechanical measurements of skinned rabbit psoas muscle fibers, we found that during isometric contraction only the first stable state is significantly occupied; i.e., isometric force is generated by cross-bridges in the first of the stable states. Thus, isometric force and the quick tension recovery appear to result from two distinctly different molecular processes. We propose that isometric force results from a structural change in the actomyosin complex associated with the transition from a weakly bound configuration to a strongly bound configuration before the reaction steps in the Huxley-Simmons model, whereas a major component of quick tension recovery originates from transitions among the subsequent strongly bound states. Mechanical, biochemical, and structural evidence for the two distinct processes is summarized and reviewed. PMID:7787051

  19. 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

  20. Organic Semiconductors: A Molecular Picture of the Charge-Transport and Energy-Transport Processes.

    NASA Astrophysics Data System (ADS)

    Brédas, Jean-Luc

    2007-03-01

    Conjugated organic oligomer and polymer materials are being increasingly considered for their incorporation as the active semiconductor elements in devices such as photo-voltaic cells, light-emitting diodes, or field-effects transistors. In the operation of these devices, electron-transfer and energy-transfer processes play a key role, for instance in the form of charge transport (in the bulk or across interfaces), energy transport, charge separation, or charge recombination [1]. Here, we provide a theoretical description of electron-transfer phenomena based on electron-transfer theory, which allows us to provide a molecular, chemically-oriented understanding. In this presentation, we focus on the parameters that impact the mobility of charge carriers [2], that is the electronic coupling within chains and between adjacent chains and the reorganization energy of the chains upon ionization. Materials under study include conjugated oligomers such as oligoacenes, oligothiophene-acenes, oligothiophenes, and oligothienacenes. [1] J.L. Br'edas, D. Beljonne, V. Coropceanu, and J. Cornil, ``Charge-Transfer and Energy-Transfer Processes in pi-Conjugated Oligomers and Polymers'', Chemical Reviews, 104, 4971-5004 (2004). [2] V. Coropceanu, J. Cornil, D.A. da Silva Filho, Y. Olivier, R. Silbey, and J.L. Br'edas, ``Charge Transport in Organic Semiconductors'', Chemical Reviews, 107, xxx (2007).

  1. Distinct molecular processes associated with isometric force generation and rapid tension recovery after quick release.

    PubMed

    Brenner, B; Chalovich, J M; Yu, L C

    1995-04-01

    It was proposed by Huxley and Simmons (Nature 1971, 233:533-538) that force-generating cross-bridges are attached to actin in several stable positions. In this concept, isometric force is generated by the same mechanism as the quick tension recovery after an abrupt release of length; i.e., when crossbridges proceed from the first postulated stable position to the second and/or subsequent positions, resulting in straining of the elastic elements within the cross-bridges. Therefore, isometric force is generated by cross-bridges in the second or even subsequent stable positions. However, through mechanical measurements of skinned rabbit psoas muscle fibers, we found that during isometric contraction only the first stable state is significantly occupied; i.e., isometric force is generated by cross-bridges in the first of the stable states. Thus, isometric force and the quick tension recovery appear to result from two distinctly different molecular processes. We propose that isometric force results from a structural change in the actomyosin complex associated with the transition from a weakly bound configuration to a strongly bound configuration before the reaction steps in the Huxley-Simmons model, whereas a major component of quick tension recovery originates from transitions among the subsequent strongly bound states. Mechanical, biochemical, and structural evidence for the two distinct processes is summarized and reviewed.

  2. 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.

  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.

  4. 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

  5. Collision-spike sputtering of Au nanoparticles

    DOE PAGES

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For this specific case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31% of the impact energy remains in the nanoparticles after impact; the remaindermore » is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80% of that of free nanoparticles due to the suppression of forward sputtering.« less

  6. Collision-spike sputtering of Au nanoparticles

    SciTech Connect

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For this specific case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31% of the impact energy remains in the nanoparticles after impact; the remainder is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80% of that of free nanoparticles due to the suppression of forward sputtering.

  7. Collision-spike Sputtering of Au Nanoparticles.

    PubMed

    Sandoval, Luis; Urbassek, Herbert M

    2015-12-01

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For the particular case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31 % of the impact energy remains in the nanoparticles after impact; the remainder is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80 % of that of free nanoparticles due to the suppression of forward sputtering.

  8. The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.

    PubMed

    Cramer, R; Corless, S

    2001-01-01

    Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.

  9. Possible conformational change within the desolvated and cationized sBBI/trypsin non-covalent complex during the collision-induced dissociation process.

    PubMed

    Darii, Ekaterina; Saravanamuthu, Gunalini; Afonso, Carlos; Alves, Sandra; Gut, Ivo; Tabet, Jean-Claude

    2011-06-30

    Electrospray ionization mass spectrometry (ESI-MS) has become an analytical technique widely used for the investigation of non-covalent protein-protein and protein-ligand complexes due to the soft desolvation conditions that preserve the stoichiometry of the interacting partners. Dissociation studies of solvated or desolvated complexes (in the source and in the collision cell, respectively) allow access to information on protein conformation and localization of the metal ions involved in protein structure stabilization and biological activity. The complex of bovine trypsin and small soybean Bowman-Birk inhibitor (sBBI) was studied by ESI-MS to determine changes occurring within the complex during its transfer from droplets to the gas phase independently of the ion polarity. Under collision-induced dissociation (CID) conditions, unexpected binding of the Ca(2+) ion (cofactor of native trypsin) to the inhibitor molecule was observed within the desolvated sBBI/trypsin/Ca(2+) complex (with a 1:1:1 stoichiometry). This formal gas-phase migration of the calcium ion from trypsin to the inhibitor may be related to conformational rearrangements in the solvent-free and likely collapsed complex. However, under conditions leading to the increase in complex charge state, the appearance of the cationized trypsin molecule was detected during complex dissociation, thus reflecting different pathways of the evolution of complex conformation.

  10. Cross sections for 14-eV e-H{sub 2} resonant collisions: Dissociative electron attachment

    SciTech Connect

    Celiberto, R.; Janev, R. K.; Wadehra, J. M.; Laricchiuta, A.

    2009-07-15

    The dissociative electron attachment (DEA) process in electron-H{sub 2} molecule collisions, involving the {sup 2}{sigma}{sub g}{sup +} excited electronic Rydberg state of molecular hydrogen ion H{sub 2}{sup -}, is investigated theoretically. The DEA cross section has been calculated within the local complex potential approximation. The convoluted cross section, which presents a peak located at the incident energy of about 14 eV, compares favorably with available experimental data.

  11. 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.

  12. Coincidence studies of ion-molecule collisions

    NASA Astrophysics Data System (ADS)

    Ben-Itzhak, Itzik

    1998-05-01

    Two of the simplest collision systems one can imagine are H^+ + H(1s) and H^+ + D(1s). Electron transfer is resonant in the first and nearly resonant in the latter because of the 3.7 meV gap between the H(1s) and D(1s). Once the collision velocity becomes small enough quantum effects become more pronounced and the electron transfer rate as a function of collision energy exhibits many resonances(G. Hunter and M. Kuriyan, Proc. Roy. Soc. Lond. A 358), 321 (1977).^,(J.P. Davis and W.R. Thorson, Can. J. Phys. 56), 996 (1978).. However, most of the interesting features appear at very low energies, of a few meV, and these collision systems which are the ``theorist's dream'' become a nightmare to experimentalists. Nevertheless, we are undertaking the challenging measurement of near resonant electron transfer in the H^+ + D(1s) collision system. When a HD molecule is ionized quickly, such that the transition to the HD^+ molecular ion is vertical, about 1% of the HD^+(1sσ) is in the vibrational continuum. The transition probability falls off approximately exponentially above threshold and its width is about 200 meV. During the dissociation, the electron initially centered on the D core can make a transition to the H core when the 2pσ and 1sσ potential energy curves associated with the two dissociation limits get close to each other. It is important to note that during molecular dissociation the ``avoided crossing'' is crossed only once in contrast to twice during a full collision. Using a localized cold HD target and 3D imaging of the low energy H^+ and D^+ dissociation fragments one can experimentally determine the transition probability between these two states as a function of the dissociation energy. Clearly, a recoil energy resolution of the order of a meV is necessary, which is the primary experimental challenge.

  13. On determining continuum quantities of non-equilibrium processes via molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Fu, Yao

    In this dissertation, a high-fidelity atomistic-to-continuum link for highly non-equilibrium processes has been established by making several modifications to Hardy's theory. Although Hardy's thermomechanical quantities were derived analytically to conserve mass, momentum and energy, they have not been rigorously tested and validated numerically in the past. Hence the first task was to investigate the effectiveness of ensemble averaging in removing thermal fluctuations and compare with conventional time averaging for fcc crystals simulated using both equilibrium and non-equilibrium molecular dynamics (MD) simulations, where the non-equilibrium process was introduced by a shock impact. It has been found that the ensemble averaging has better convergence than time averaging due to the statistical independence of the thermomechanical quantities computed using ensemble averaging. The second task was to test the validity of Hardy's theory by checking if it is able to conserve mass, momentum and energy numerically. A few highly non-equilibrium processes were simulated using MD, including Gaussian wave and shock impact propagation in 1D and 3D fcc crystals. Based on the test results, a new normalization rule has been proposed so that the computed thermomechanical quantities can conserve the fundamental properties more accurately. To a large extent, Hardy's theory has been found to be valid regardless of the width of the localization function, the interatomic potential and crystal structure, and with and without ensemble averaging. To further test the validity of Hardy's theory for more complex non-equilibrium processes, where plastic deformation is accomplished through dislocation glide and slip band emission, a crack propagation problem in iron crystal with a pre-created center crack is simulated using MD. The computed Hardy's thermomechanical quantities can generally conserve mass, momentum and energy. Exceptions have been found around the crack region, where the

  14. Spintronic characteristics of self-assembled neurotransmitter acetylcholine molecular complexes enable quantum information processing in neural networks and brain

    NASA Astrophysics Data System (ADS)

    Tamulis, Arvydas; Majauskaite, Kristina; Kairys, Visvaldas; Zborowski, Krzysztof; Adhikari, Kapil; Krisciukaitis, Sarunas

    2016-09-01

    Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information processing. The necessary operating conditions for ACh molecule are formulated in self-assembled dimer and more complex systems. The main quantum mechanical research result of this paper is that the neurotransmitter ACh systems, which were proposed, include the use of quantum molecular spintronics arrays to control the neurotransmission in neural networks.

  15. 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.

  16. Variational collision integrator for polymer chains

    NASA Astrophysics Data System (ADS)

    Leyendecker, Sigrid; Hartmann, Carsten; Koch, Michael

    2012-05-01

    The numerical simulation of many-particle systems (e.g. in molecular dynamics) often involves constraints of various forms. We present a symplectic integrator for mechanical systems with holonomic (bilateral) and unilateral contact constraints, the latter being in the form of a non-penetration condition. The scheme is based on a discrete variant of Hamilton's principle in which both the discrete trajectory and the unknown collision time are varied (cf. [R. Fetecau, J. Marsden, M. Ortiz, M. West, Nonsmooth Lagrangian mechanics and variational collision integrators, SIAM J. Appl. Dyn. Syst. 2 (2003) 381-416]). As a consequence, the collision event enters the discrete equations of motion as an unknown that has to be computed on-the-fly whenever a collision is imminent. The additional bilateral constraints are efficiently dealt with employing a discrete null space reduction (including a projection and a local reparametrisation step) which considerably reduces the number of unknowns and improves the condition number during each time-step as compared to a standard treatment with Lagrange multipliers. We illustrate the numerical scheme with a simple example from polymer dynamics, a linear chain of beads, and test it against other standard numerical schemes for collision problems.

  17. Studies on the Process of Formation, Nature and Stability of Binding Sites in Molecularly Imprinted Polymers

    DTIC Science & Technology

    2002-04-05

    MIPs in dynamic applications such as in chromatography, membrane separation or in chemical sensors . 93 In non-covalent molecular imprinting this...6 8 10 Molecular Radius (rm) - - MIP DCM - NIP DCM Figure 6. Pore size distributions obtained from ISEC measurements on an ametryn imprinted polymer ...unger.chemie.uni- mainz.de) ’ Polymer Research Unit, Material Ireland, Trinity College Dublin, Ireland ABSTRACT In Molecular Imprinting the nature of the

  18. Molecular level energy and electron transfer processes at nanocrystalline titanium dioxide interfaces

    NASA Astrophysics Data System (ADS)

    Farzad, Fereshteh

    This thesis describes photo-induced molecular electron and energy transfer processes occurring at nanocrystalline semiconductor interfaces. The Introductory Chapter provides background and describes how these materials may be useful for solar energy conversion. In Chapter 2, results describing excitation of Ru(deeb)(bpy)2 2+, bis(2,2'-bipyridine)(2,2'-bipyridine-4,4 '-diethylester)ruthenium(II) hexafluorophosphate, bound to nanocrystalline TiO2 thin films, immersed in an acetonitrile bath are presented. The data indicates that light excitation forms predominately long-lived metal-to-ligand charge-transfer, MLCT, excited states under these conditions. Modeling of the data as a function of irradiance has been accomplished assuming parallel unimolecular and bimolecular excited state deactivation processes. The quantum yield for excited state formation depends on the excitation irradiance, consistent with triplet-triplet annihilation processes that occur with k > 1 x 108 s-1. Chapter 3 extends the work described in Chapter 2 to LiClO4 acetonitrile solutions. Li+ addition results in a red shift in the MLCT absorption and photoluminescence, PL, and a concentration dependent quenching of the PL intensity on TiO2. The Li+ induced spectroscopic changes were found to be reversible by varying the electrolyte composition. A second-order kinetic model quantified charge recombination transients. A model is proposed wherein Li+ ion adsorption stabilizes TiO2 acceptor states resulting in energetically more favorable interfacial electron transfer. The photophysical and photoelectrochemical properties of porous nanocrystalline anatase TiO2 electrodes modified with Ru(deeb)(bpy)2 2+, Os(deeb)(bpy)22+, and mixtures of both are described in Chapters 4 and 5. In regenerative solar cells with 0.5 M LiI/0.05 M I2 acetonitrile electrolyte, both compounds efficiently inject electrons into TiO2 producing monochromatic incident photon-to-current efficiencies (IPCE), IPCE (460 nm) = 0.70 + 0

  19. Rovibrational transitions of H2 by collision with H+ at high temperature

    NASA Astrophysics Data System (ADS)

    González-Lezana, T.; Honvault, P.

    2017-01-01

    The H+ +H2 reaction is studied by means of both exact and statistical quantum methods. Integral cross sections for processes initiated with rotationally excited H2(v, j = 1) to produce molecular hydrogen in its rotational ground state are reported up to a value of the collision energy of 3 eV. Rate constants for state-to-state transitions between different H2 rovibrational states are calculated up to 3000 K. Special emphasis is made on ortho/para conversion processes in which the parity j of the H2(j) states changes.

  20. Uncovering Molecular Relaxation Processes with Nonlinear Spectroscopies in the Deep UV

    NASA Astrophysics Data System (ADS)

    West, Brantley Andrew

    Conical intersections mediate internal conversion dynamics that compete with even the fastest nuclear motions in molecular systems. Traditional kinetic models do not apply in this regime of commensurate electronic and nuclear motion because the surroundings do not maintain equilibrium throughout the relaxation process. This dissertation focuses on uncovering the physics associated with vibronic interactions at conical intersections. Of particular interest are coherent nuclear motions driven by steep excited state potential energy gradients. Technical advances have only recently made these dynamics accessible in many systems including DNA nucleobases and cyclic polyene molecules. Optical analogues of multidimensional NMR spectroscopies have recently yielded transformative insight in relaxation processes ranging from energy transfer in photosynthesis to bond making and breaking in liquids. Prior to the start of this research, such experiments had only been conducted at infrared and visible wavelengths. Applications in the ultraviolet were motivated by studies of numerous biological systems (e.g., DNA, proteins), but had been challenged by technical issues. The work presented in this dissertation combines pulse generation techniques developed in the optical physics community with spectroscopic techniques largely pioneered by physical chemists to implement two-dimensional ultraviolet spectroscopy (2DUV). This technique is applied at the shortest wavelengths and with the best signal-to-noise ratios reported to date. Sub-picosecond excited state deactivation processes provide photo stability to the DNA double helix. Vibrational energy transfer from the solute to surrounding solvent enables relaxation of the highly non-equilibrium ground state produced by fast internal conversion. In this dissertation, nonlinear spectroscopies carried out at cryogenic temperatures are used to uncover the particular nuclear modes in the solvent that primarily accept vibrational energy from

  1. A molecular dynamics simulation study of dynamic process and mesoscopic structure in liquid mixture systems

    NASA Astrophysics Data System (ADS)

    Yang, Peng

    The focus of this dissertation is the Molecular Dynamics (MD) simulation study of two different systems. In thefirst system, we study the dynamic process of graphene exfoliation, particularly graphene dispersion using ionic surfactants (Chapter 2). In the second system, we investigate the mesoscopic structure of binary solute/ionic liquid (IL) mixtures through the comparison between simulations and corresponding experiments (Chapter 3 and 4). In the graphene exfoliation study, we consider two separation mechanisms: changing the interlayer distance and sliding away the relative distance of two single-layer graphene sheets. By calculating the energy barrier as a function of separation (interlayer or sliding-away) distance and performing sodium dodecyl sulfate (SDS) structure analysis around graphene surface in SDS surfactant/water + bilayer graphene mixture systems, we find that the sliding-away mechanism is the dominant, feasible separation process. In this process, the SDS-graphene interaction gradually replaces the graphene-graphene Van der Waals (VdW) interaction, and decreases the energy barrier until almost zero at critical SDS concentration. In solute/IL study, we investigate nonpolar (CS2) and dipolar (CH 3CN) solute/IL mixture systems. MD simulation shows that at low concentrations, IL is nanosegregated into an ionic network and nonpolar domain. It is also found that CS2 molecules tend to be localized into the nonpolar domain, while CH3CN interacts with nonpolar domain as well as with the charged head groups in the ionic network because of its amphiphilicity. At high concentrations, CH3CN molecules eventually disrupt the nanostructural organization. This dissertation is organized in four chapters: (1) introduction to graphene, ionic liquids and the methodology of MD; (2) MD simulation of graphene exfoliation; (3) Nanostructural organization in acetonitrile/IL mixtures; (4) Nanostructural organization in carbon disulfide/IL mixtures; (5) Conclusions. Results

  2. Beyond Fullerenes: Designing Alternative Molecular Electron Acceptors for Solution-Processable Bulk Heterojunction Organic Photovoltaics.

    PubMed

    Sauvé, Geneviève; Fernando, Roshan

    2015-09-17

    Organic photovoltaics (OPVs) are promising candidates for providing a low cost, widespread energy source by converting sunlight into electricity. Solution-processable active layers have predominantly consisted of a conjugated polymer donor blended with a fullerene derivative as the acceptor. Although fullerene derivatives have been the acceptor of choice, they have drawbacks such as weak visible light absorption and poor energy tuning that limit overall efficiencies. This has recently fueled new research to explore alternative acceptors that would overcome those limitations. During this exploration, one question arises: what are the important design principles for developing nonfullerene acceptors? It is generally accepted that acceptors should have high electron affinity, electron mobility, and absorption coefficient in the visible and near-IR region of the spectra. In this Perspective, we argue that alternative molecular acceptors, when blended with a conjugated polymer donor, should also have large nonplanar structures to promote nanoscale phase separation, charge separation and charge transport in blend films. Additionally, new material design should address the low dielectric constant of organic semiconductors that have so far limited their widespread application.

  3. Folic acid: nutritional biochemistry, molecular biology, and role in disease processes.

    PubMed

    Lucock, M

    2000-01-01

    This paper reviews the chemistry, metabolism, and molecular biology of folic acid, with a particular emphasis on how it is, or may be, involved in many disease processes. Folic acid prevents neural tube defects like spina bifida, while its ability to lower homocysteine suggests it might have a positive influence on cardiovascular disease. A role for this B vitamin in maintaining good health may, in fact, extend beyond these clinical conditions to encompass other birth defects, several types of cancer, dementia, affective disorders, Down's syndrome, and serious conditions affecting pregnancy outcome. The effect of folate in these conditions can be explained largely within the context of folate-dependent pathways leading to methionine and nucleotide biosynthesis, and genetic variability resulting from a number of common polymorphisms of folate-dependent enzymes involved in the homocysteine remethylation cycle. Allelic variants of folate genes that have a high frequency in the population, and that may play a role in disease formation include 677C --> T-MTHFR, 1298A --> C-MTHFR, 2756A --> G-MetSyn, and 66A --> G-MSR. Future work will probably uncover further polymorphisms of folate metabolism, and lead to a wider understanding of the interaction between this essential nutrient and the many genes which underpin its enzymatic utilization in a plethora of critical biosynthetic reactions, and which, under adverse nutritional conditions, may promote disease.

  4. Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

    PubMed

    Quesne, Matthew G; Borowski, Tomasz; de Visser, Sam P

    2016-02-18

    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.

  5. 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

  6. 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.

  7. 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.

  8. Electron loss of fast projectiles in collisions with molecules

    SciTech Connect

    Matveev, V. I.; Makarov, D. N.; Rakhimov, Kh. Yu.

    2011-07-15

    The single- and multiple-electron loss of fast highly charged projectiles in collisions with neutral molecules is studied within the framework of a nonperturbative approach. The cross sections for single-, double-, and triple-electron losses are calculated for the collision system Fe{sup q+}{yields}N{sub 2} (q=24, 25, 26) at the collision energies 10, 100, and 1000 MeV/nucleon. The effects caused by the collision multiplicity and the orientation of the axis of the target molecule are treated. It is shown that the collision multiplicity effect leads to considerable differences for the cases of perpendicular and parallel orientations of the molecular axes with respect to the direction of the projectile motion, while for chaotic orientation such an effect is negligible.

  9. Icy Collisions - Planet Building beyond the snowline

    NASA Astrophysics Data System (ADS)

    Gaertner, Sabrina; Hill, Catherine; Heisselmann, Daniel; Blum, Juergen; Fraser, Helen

    2015-11-01

    Collisions of small icy and dust particles beyond the “snow-line” are a key step in planet formation. Whilst the physical forces that underpin the aggregation of the smallest grains (van der Waals) and the largest planetessimals (gravity) are well understood, the processes involving mm - cm sized particles remain a mystery.In a unique set of experiments, we investigated low velocity collisions of dust and icy particles in this size range under microgravity conditions - utilizing parabolic flight (e.g. Salter 2009, Hill 2015 (a) & (b)). Experiments were performed at cryogenic temperatures (below 140 K) for icy aggregates and ambient as well as cryogenic temperatures (80 - 220 K) for dust aggregates.The kinetic analysis of the observed collisions of different aggregate types in different shapes and sizes revealed astonishing results - as the collisional properties of all investigated particles differ strongly from the usual assumptions in models of planet formation.Here, we present a summary of the results on the collisions of icy particles as well as first results on the collisions of dust aggregates. Focus will be on the coefficient of restitution, which measures the loss of translational energy in bouncing collisions and is a key parameter in models of planet formation.

  10. Real-time investigation of nucleic acids phosphorylation process using molecular beacons

    PubMed Central

    Tang, Zhiwen; Wang, Kemin; Tan, Weihong; Ma, Changbei; Li, Jun; Liu, Lingfeng; Guo, Qiuping; Meng, Xiangxian

    2005-01-01

    Phosphorylation of nucleic acids is an indispensable process to repair strand interruption of nucleic acids. We have studied the process of phosphorylation using molecular beacon (MB) DNA probes in real-time and with high selectivity. The MB employed in this method is devised to sense the product of a ‘phosphorylation–ligation’ coupled enzyme reaction. Compared with the current assays, this novel method is convenient, fast, selective, highly sensitive and capable of real-time monitoring in a homogenous solution. The preference of T4 polynucleotide kinase (T4 PNK) has been investigated using this approach. The results revealed that a single-stranded oligonucleotide containing guanine at the 5′ termini is most preferred, while those utilizing cytosine in this location are least preferred. The preference of (T)9 was reduced greatly when phosphoryl was modified at the 5′ end, implying that T4 PNK could discern the phosphorylated/unphosphorylated oligonucleotides. The increase of oligonucleotide DNA length leads to an enhancement in preference. A fast and accurate method for assaying the kinase activity of T4 PNK has been developed with a wide linear detection range from 0.002 to 4.0 U/ml in 3 min. The effects of certain factors, such as NTP, ADP, (NH4)2SO4 and Na2HPO4, on phosphorylation have been investigated. This novel approach enables us to investigate the interactions between proteins and nucleic acids in a homogenous solution, such as those found in DNA repair or in drug development. PMID:15961728

  11. Stochastic dynamics of small ensembles of non-processive molecular motors: the parallel cluster model.

    PubMed

    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.

  12. 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.

  13. Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface

    NASA Astrophysics Data System (ADS)

    Tian, Ziqi; Wen, Jin; Ma, Jing

    2013-07-01

    It is a challenge to simulate the switching process of functional self-assembled monolayers (SAMs) on metal surfaces, since the systems consist of thousands of atoms and the switching is triggered by quantum-mechanical events. Herein a molecular dynamics simulation with a reactive rotation potential of N=N bond is implemented to investigate the dynamic conformational changes and packing effects on the stimuli-responsive isomerization of the terminally thiol functionalized azobiphenyls (AZOs), which are bound on the Au(111) surface. To, respectively, distinguish the time evolutions that start from cis and trans initial configurations, two different functions are established to model the potential energy curves for cis-to-trans and trans-to-cis transitions, instead of the only one cosine function used in the conventional non-reactive force fields. In order to simulate the conformation transitions of the AZO film on surface, a random switching function, depending on the N=N twisting angle, is constructed to consider both forward and backward cis/trans isomerization events and to trigger the reaction by changing the N atom types automatically. The factors that will influence the isomerization process, including the choice of ensembles and thermostat algorithms, the time intervals separating each switching, and the forms of the switching function, are systematically tested. Most AZO molecules switch from the cis to trans configuration with a coverage of 5.76 × 10-6 mol/m2 on a picosecond time scale, and a low coverage might make the switching irreversible, which is in agreement with the experiments.

  14. Collision avoidance in computer optimized treatment planning.

    PubMed

    Humm, J L

    1994-07-01

    Of major concern in fully automated computerized treatment delivery is the possibility of gantry/couch or gantry/patient collisions. In this work, software has been developed to detect collisions between gantry and couch or patient for both transaxial and noncoplanar treatment fields during the treatment planning process. The code uses the gantry angles, turntable angles, and position of the couch surface relative to the isocenter supplied by the planner for the prescribed radiation fields. In addition, the maximum patient anterior-posterior and lateral separations are entered in order to model the patient outline by a conservative cylindrical ellipse. By accessing a database containing the precise mechanical dimensions of the therapy equipment, 3D analytical geometry is used to test for collisions between gantry/patient and gantry/couch for each treatment field. When collisions are detected, the software inspects the use of an extended distance treatment, by recalculating and testing for collisions, with the couch at a greater distance from the collimator along the direction of the central axis. If a collision is avoided at extended distance, the lateral, longitudinal, and vertical motions of the couch are recorded for entry into the treatment plan, or else a warning message is printed, together with the nearest permissible collision-free gantry angle. Upon inspection, the planner can either elect to use the calculated closest permissible gantry angle or reject the plan. The software verifies that each proposed treatment field is safe, but also that the transition between fields is collision-free. This requires that the sequence of the treatment fields be ordered, preferably into a sequence which minimizes the delivery time compatible with patient safety.(ABSTRACT TRUNCATED AT 250 WORDS)

  15. Chemical activation through super energy transfer collisions.

    PubMed

    Smith, Jonathan M; Nikow, Matthew; Ma, Jianqiang; Wilhelm, Michael J; Han, Yong-Chang; Sharma, Amit R; Bowman, Joel M; Dai, Hai-Lung

    2014-02-05

    Can a molecule be efficiently activated with a large amount of energy in a single collision with a fast atom? If so, this type of collision will greatly affect molecular reactivity and equilibrium in systems where abundant hot atoms exist. Conventional expectation of molecular energy transfer (ET) is that the probability decreases exponentially with the amount of energy transferred, hence the probability of what we label "super energy transfer" is negligible. We show, however, that in collisions between an atom and a molecule for which chemical reactions may occur, such as those between a translationally hot H atom and an ambient acetylene (HCCH) or sulfur dioxide, ET of chemically significant amounts of energy commences with surprisingly high efficiency through chemical complex formation. Time-resolved infrared emission observations are supported by quasi-classical trajectory calculations on a global ab initio potential energy surface. Results show that ∼10% of collisions between H atoms moving with ∼60 kcal/mol energy and HCCH result in transfer of up to 70% of this energy to activate internal degrees of freedom.

  16. Ultrafast in cellulo photoinduced dynamics processes of the paradigm molecular light switch [Ru(bpy)2dppz]2+

    NASA Astrophysics Data System (ADS)

    de La Cadena, Alejandro; Davydova, Dar’Ya; Tolstik, Tatiana; Reichardt, Christian; Shukla, Sapna; Akimov, Denis; Heintzmann, Rainer; Popp, Jürgen; Dietzek, Benjamin

    2016-09-01

    An in cellulo study of the ultrafast excited state processes in the paradigm molecular light switch [Ru(bpy)2dppz]2+ by localized pump-probe spectroscopy is reported for the first time. The localization of [Ru(bpy)2dppz]2+ in HepG2 cells is verified by emission microscopy and the characteristic photoinduced picosecond dynamics of the molecular light switch is observed in cellulo. The observation of the typical phosphorescence stemming from a 3MLCT state suggests that the [Ru(bpy)2dppz]2+ complex intercalates with the DNA in the nucleus. The results presented for this benchmark coordination compound reveal the necessity to study the photoinduced processes in coordination compounds for intracellular use, e.g. as sensors or as photodrugs, in the actual biological target environment in order to derive a detailed molecular mechanistic understanding of the excited-state properties of the systems in the actual biological target environment.

  17. Towards better modelling of drug-loading in solid lipid nanoparticles: Molecular dynamics, docking experiments and Gaussian Processes machine learning.

    PubMed

    Hathout, Rania M; Metwally, Abdelkader A

    2016-11-01

    This study represents one of the series applying computer-oriented processes and tools in digging for information, analysing data and finally extracting correlations and meaningful outcomes. In this context, binding energies could be used to model and predict the mass of loaded drugs in solid lipid nanoparticles after molecular docking of literature-gathered drugs using MOE® software package on molecularly simulated tripalmitin matrices using GROMACS®. Consequently, Gaussian processes as a supervised machine learning artificial intelligence technique were used to correlate the drugs' descriptors (e.g. M.W., xLogP, TPSA and fragment complexity) with their molecular docking binding energies. Lower percentage bias was obtained compared to previous studies which allows the accurate estimation of the loaded mass of any drug in the investigated solid lipid nanoparticles by just projecting its chemical structure to its main features (descriptors).

  18. Ultrafast in cellulo photoinduced dynamics processes of the paradigm molecular light switch [Ru(bpy)2dppz]2+

    PubMed Central

    De la Cadena, Alejandro; Davydova, Dar’ya; Tolstik, Tatiana; Reichardt, Christian; Shukla, Sapna; Akimov, Denis; Heintzmann, Rainer; Popp, Jürgen; Dietzek, Benjamin

    2016-01-01

    An in cellulo study of the ultrafast excited state processes in the paradigm molecular light switch [Ru(bpy)2dppz]2+ by localized pump-probe spectroscopy is reported for the first time. The localization of [Ru(bpy)2dppz]2+ in HepG2 cells is verified by emission microscopy and the characteristic photoinduced picosecond dynamics of the molecular light switch is observed in cellulo. The observation of the typical phosphorescence stemming from a 3MLCT state suggests that the [Ru(bpy)2dppz]2+ complex intercalates with the DNA in the nucleus. The results presented for this benchmark coordination compound reveal the necessity to study the photoinduced processes in coordination compounds for intracellular use, e.g. as sensors or as photodrugs, in the actual biological target environment in order to derive a detailed molecular mechanistic understanding of the excited-state properties of the systems in the actual biological target environment. PMID:27644587

  19. Contributions of collision rate and collision efficiency to erythrocyte aggregation in postcapillary venules at low flow rates.

    PubMed

    Kim, Sangho; Zhen, Janet; Popel, Aleksander S; Intaglietta, Marcos; Johnson, Paul C

    2007-09-01

    Red blood cell aggregation at low flow rates increases venous vascular resistance, but the process of aggregate formation in these vessels is not well understood. We previously reported that aggregate formation in postcapillary venules of the rat spinotrapezius muscle mainly occurs in a middle region between 15 and 30 microm downstream from the entrance. In light of the findings in that study, the main purpose of this study was to test two hypotheses by measuring collision frequency along the length of the venules during low flow. We tested the hypothesis that aggregation rarely occurs in the initial 15-microm region of the venule because collision frequency is very low. We found that collision frequency was lower than in other regions, but collision efficiency (the ratio of aggregate formation to collisions) was almost nil in this region, most likely because of entrance effects and time required for aggregation. Radial migration of red blood cells and Dextran 500 had no effect on collision frequency. We also tested the hypothesis that aggregation was reduced in the distal venule region because of the low aggregability of remaining nonaggregated cells. Our findings support this hypothesis, since a simple model based on the ratio of aggregatable to nonaggregatable red blood cells predicts the time course of collision efficiency in this region. Collision efficiency averaged 18% overall but varied from 0 to 52% and was highest in the middle region. We conclude that while collision frequency influences red blood cell aggregate formation in postcapillary venules, collision efficiency is more important.

  20. Electronic excitation of ground state atoms by collision with heavy gas particles

    NASA Technical Reports Server (NTRS)

    Hansen, C. Frederick

    1993-01-01

    Most of the important chemical reactions which occur in the very high temperature air produced around space vehicles as they enter the atmosphere were investigated both experimentally and theoretically, to some extent at least. One remaining reaction about which little is known, and which could be quite important at the extremely high temperatures that will be produced by the class of space vehicles now contemplated - such as the AOTV - is the excitation of bound electron states due to collisions between heavy gas particles. Rates of electronic excitation due to free electron collisions are known to be very rapid, but because these collisions quickly equilibrate the free and bound electron energy, the approach to full equilibrium with the heavy particle kinetic energy will depend primarily on the much slower process of bound electron excitation in heavy particle collisions and the subsequent rapid transfer to free electron energy. This may be the dominant mechanism leading to full equilibrium in the gas once the dissociation process has depleted the molecular states so the transfer between molecular vibrational energy and free electron energy is no longer available as a channel for equilibration of free electron and heavy particle kinetic energies. Two mechanisms seem probable in electronic excitation by heavy particle impact. One of these is the collision excitation and deexcitation of higher electronic states which are Rydberg like. A report, entitled 'Semi-Classical Theory of Electronic Excitation Rates', was submitted previously. This presented analytic expressions for the transition probabilities, assuming that the interaction potential is an exponential repulsion with a perturbation ripple due to the dipole-induced dipole effect in the case of neutral-neutral collisions, and to the ion-dipole interaction in the case of ion-neutral collisions. However the above may be, there is little doubt that excitation of ground state species by collision occurs at the

  1. Squeezed States and Particle Production in High Energy Collisions

    NASA Technical Reports Server (NTRS)

    Bambah, Bindu A.

    1996-01-01

    Using the 'quantum optical approach' we propose a model of multiplicity distributions in high energy collisions based on squeezed coherent states. We show that the k-mode squeezed coherent state is the most general one in describing hadronic multiplicity distributions in particle collision processes, describing not only p(bar-p) collisions but e(+)e(-), vp and diffractive collisions as well. The reason for this phenomenological fit has been gained by working out a microscopic theory in which the squeezed coherent sources arise naturally if one considers the Lorentz squeezing of hadrons and works in the covariant phase space formalism.

  2. A new technique for predicting geosynchronous satellite collision probability

    NASA Technical Reports Server (NTRS)

    Mccormick, B.

    1986-01-01

    A new technique has been developed to predict the probability of an expired geosynchronous satellite colliding with an active satellite. This new technique employs deterministic methods for modeling the motion of satellites and applies statistical techniques to estimate the collision probability. The collision probability is used to estimate the expected time between collisions based on realistic distributions of expired and active satellites. The primary advantage of this new technique is that realistic distributions can be used in the prediction process instead of uniform distributions as has been used in previous techniques. The expected time between collisions based on a current NORAD database is estimated to be in the hundreds of years.

  3. A New Aloha Anti-Collision Algorithm Based on CDMA

    NASA Astrophysics Data System (ADS)

    Bai, Enjian; Feng, Zhu

    The tags' collision is a common problem in RFID (radio frequency identification) system. The problem has affected the integrity of the data transmission during the process of communication in the RFID system. Based on analysis of the existing anti-collision algorithm, a novel anti-collision algorithm is presented. The new algorithm combines the group dynamic frame slotted Aloha algorithm with code division multiple access technology. The algorithm can effectively reduce the collision probability between tags. Under the same number of tags, the algorithm is effective in reducing the reader recognition time and improve overall system throughput rate.

  4. Molecular Processes Underlying the Structure and Assembly of Thin Films and Nanoparticles at Complex interfaces

    SciTech Connect

    Richmond, Geraldine

    2016-06-03

    Since 1995 we have pursued a number of different studies that are quite diverse in nature but with the common theme of using novel laser based methods to study important processes at buried interfaces. Studies of Corrosion, Passivation on n-GaAs(100)Methanol Photoelectrochemical Cell In these studies we have used picosecond photoluminescence and electrochemical studies to understand the GaAs/methanol interface. In our most extensive set of studies we conducted photo-illumination and XPS experiments to understand the chemistry occurring in the GaAs/methanol photoelectrochemical during photoexcitation. An important distinction between photocorrosion and photoetching of GaAs is elucidated by these studies. The dependence of GaAs photocorrosion on light intensity has been explored to better understand intrinsic differences between the lamplight studies and the picosecond photoluminescence studies. The effect of coating the GaAs with a sulfide layer prior to immersion in the cell has also been explored. This last result has led us to examine n-GaAs as a function of crystallographic orientation after exposure to aqueous Na2S containing solutions has been studied as a function of crystallographic orientation of the GaAs surface. The (100) and (110) surfaces are relatively similar, with significant amounts of As-S species present at the interface. The (111)B surface lacks this constituent, but shows significant amounts of metallic As. The XPS results have been correlated with the results of previous photocorrosion and passivation studies conducted in a photoelectrochemical cell. The studies indicate that the metallic As present at (111)B surface contributes strongly to the large surface recombination velocity found there, and to the inability of Na2S to passivate the (111)B surface. SAMS Under Water: Water Molecular Structure and Bonding at Hydrophobic Surfaces In these DOE sponsored studies we have been interested in learning the similarities and

  5. 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...

  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…

  7. Recent research in flaxseed (oil seed) on molecular structure and metabolic characteristics of protein, heat processing-induced effect and nutrition with advanced synchrotron-based molecular techniques.

    PubMed

    Doiron, Kevin J; Yu, Peiqiang

    2017-01-02

    Advanced synchrotron radiation-based infrared microspectroscopy is able to reveal feed and food structure feature at cellular and molecular levels and simultaneously provides composition, structure, environment, and chemistry within intact tissue. However, to date, this advanced synchrotron-based technique is still seldom known to food and feed scientists. This article aims to provide detailed background for flaxseed (oil seed) protein research and then review recent progress and development in flaxseed research in ruminant nutrition in the areas of (1) dietary inclusion of flaxseed in rations; (2) heat processing effect; (3) assessing dietary protein; (4) synchrotron-based Fourier transform infrared microspectroscopy as a tool of nutritive evaluation within cellular and subcellular dimensions; (5) recent synchrotron applications in flaxseed research on a molecular basis. The information described in this paper gives better insight in flaxseed research progress and update.

  8. Asteroidal collision probabilities

    NASA Astrophysics Data System (ADS)

    Bottke, W. F.; Greenberg, R.

    1993-05-01

    Several past calculations of collision probabilities between pairs of bodies on independent orbits have yielded inconsistent results. We review the methodologies and identify their various problems. Greenberg's (1982) collision probability formalism (now with a corrected symmetry assumption) is equivalent to Wetherill's (1967) approach, except that it includes a way to avoid singularities near apsides. That method shows that the procedure by Namiki and Binzel (1991) was accurate for those cases where singularities did not arise.

  9. Photon-photon collisions

    SciTech Connect

    Burke, D.L.

    1982-10-01

    Studies of photon-photon collisions are reviewed with particular emphasis on new results reported to this conference. These include results on light meson spectroscopy and deep inelastic e..gamma.. scattering. Considerable work has now been accumulated on resonance production by ..gamma gamma.. collisions. Preliminary high statistics studies of the photon structure function F/sub 2//sup ..gamma../(x,Q/sup 2/) are given and comments are made on the problems that remain to be solved.

  10. Visualization of complex processes in lipid systems using computer simulations and molecular graphics.

    PubMed

    Telenius, Jelena; Vattulainen, Ilpo; Monticelli, Luca

    2009-01-01

    Computer simulation has become an increasingly popular tool in the study of lipid membranes, complementing experimental techniques by providing information on structure and dynamics at high spatial and temporal resolution. Molecular visualization is the most powerful way to represent the results of molecular simulations, and can be used to illustrate complex transformations of lipid aggregates more easily and more effectively than written text. In this chapter, we review some basic aspects of simulation methodologies commonly employed in the study of lipid membranes and we describe a few examples of complex phenomena that have been recently investigated using molecular simulations. We then explain how molecular visualization provides added value to computational work in the field of biological membranes, and we conclude by listing a few molecular graphics packages widely used in scientific publications.

  11. New Caledonia a classic example of an arc continent collision

    NASA Astrophysics Data System (ADS)

    Aitchison, J.

    2011-12-01

    The SW Pacific island of New Caledonia presents a classic example of an arc-continent collision. This event occurred in the Late Eocene when elements of an intra-oceanic island arc system, the Loyalty-D'Entrecasteaux arc, which stretched SSE from near Papua New Guinea east of New Caledonia to offshore New Zealand, collided with micro-continental fragments that had rifted off eastern Gondwana (Australia) in the late Cretaceous. Intervening Late Cretaceous to Paleogene oceanic crust of the South Loyalty Basin was eliminated through eastward subduction beneath this west-facing intra-oceanic island arc. As with many arc-continent collisions elsewhere collision was accompanied by ophiolite emplacement. The erosional remnants of which are extensive in New Caledonia. Collision led to subduction flip, followed by extensive rollback in front of the newly established east-facing Vitiaz arc. Post-collisional magmatism occurred after slab break-off and is represented by small-scale granitoid intrusions. Additional important features of New Caledonia include the presence of a regionally extensive UHP metamorphic terrain consisting of blueschists and eclogites that formed during the subduction process and were rapidly exhumed as a result of the collision Not only was collision and associated orogeny short-lived this collision system has not been overprinted by any major subsequent collision. New Caledonia thus provides an exceptional location for the study of processes related to arc-continent collision in general.

  12. Radiative and nonradiative charge transfer in collisions of Be{sup 2+} and B{sup 3+} ions with H atoms

    SciTech Connect

    Liu, C. H.; Wang, J. G.; Liu, L.; Qu, Y. Z.; Janev, R. K.

    2010-08-15

    The nonradiative charge-transfer processes in Be{sup 2+}(1s{sup 2})+H(1s) and B{sup 3+}(1s{sup 2})+H(1s) collisions are investigated by the quantal molecular orbital close-coupling method in the energy range of 10{sup -5}eV/u-10 keV/u and by the two-center atomic-orbital close-coupling method in the energy range of 0.1-100 keV/u. The radiative charge-transfer cross sections are calculated by using the optical potential and semiclassical methods in the energy range 10{sup -5}-100 eV/u. For both collision systems, the nonradiative charge-transfer cross sections in the low-energy region show an increasing behavior with decreasing energy. The nonradiative process is the dominant charge-transfer process in the Be{sup 2+}(1s{sup 2})+H(1s) collision in the entire eV and sub-eV energy region. In the B{sup 3+}(1s{sup 2})+H(1s) collision case, however, the cross section for radiative decay to 1 {sup 2{Sigma}+} and 2 {sup 2{Sigma}+} molecular states significantly exceeds that for the nonradiative process for energies below 30 eV/u.

  13. Launch Collision Probability

    NASA Technical Reports Server (NTRS)

    Bollenbacher, Gary; Guptill, James D.

    1999-01-01

    This report analyzes the probability of a launch vehicle colliding with one of the nearly 10,000 tracked objects orbiting the Earth, given that an object on a near-collision course with the launch vehicle has been identified. Knowledge of the probability of collision throughout the launch window can be used to avoid launching at times when the probability of collision is unacceptably high. The analysis in this report assumes that the positions of the orbiting objects and the launch vehicle can be predicted as a function of time and therefore that any tracked object which comes close to the launch vehicle can be identified. The analysis further assumes that the position uncertainty of the launch vehicle and the approaching space object can be described with position covariance matrices. With these and some additional simplifying assumptions, a closed-form solution is developed using two approaches. The solution shows that the probability of collision is a function of position uncertainties, the size of the two potentially colliding objects, and the nominal separation distance at the point of closest approach. ne impact of the simplifying assumptions on the accuracy of the final result is assessed and the application of the results to the Cassini mission, launched in October 1997, is described. Other factors that affect the probability of collision are also discussed. Finally, the report offers alternative approaches that can be used to evaluate the probability of collision.

  14. Control of Ultracold Collisions with Frequency-Chirped Light

    SciTech Connect

    Wright, M.J.; Gould, P.L.; Gensemer, S.D.; Vala, J.; Kosloff, R.

    2005-08-05

    We report on ultracold atomic collision experiments utilizing frequency-chirped laser light. A rapid chirp below the atomic resonance results in adiabatic excitation to an attractive molecular potential over a wide range of internuclear separation. This leads to a transient inelastic collision rate which is large compared to that obtained with fixed-frequency excitation. The combination of high efficiency and temporal control demonstrates the benefit of applying the techniques of coherent control to the ultracold domain.

  15. Vibrational energy transfer in shocked molecular crystals.

    PubMed

    Hooper, Joe

    2010-01-07

    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.

  16. Bose condensation of nuclei in heavy ion collisions

    NASA Technical Reports Server (NTRS)

    Tripathi, Ram K.; Townsend, Lawrence W.

    1994-01-01

    Using a fully self-consistent quantum statistical model, we demonstrate the possibility of Bose condensation of nuclei in heavy ion collisions. The most favorable conditions of high densities and low temperatures are usually associated with astrophysical processes and may be difficult to achieve in heavy ion collisions. Nonetheless, some suggestions for the possible experimental verification of the existence of this phenomenon are made.

  17. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.

    PubMed

    Jung, Jaewoon; Naurse, Akira; Kobayashi, Chigusa; Sugita, Yuji

    2016-10-11

    The graphics processing unit (GPU) has become a popular computational platform for molecular dynamics (MD) simulations of biomolecules. A significant speedup in the simulations of small- or medium-size systems using only a few computer nodes with a single or multiple GPUs has been reported. Because of GPU memory limitation and slow communication between GPUs on different computer nodes, it is not straightforward to accelerate MD simulations of large biological systems that contain a few million or more atoms on massively parallel supercomputers with GPUs. In this study, we develop a new scheme in our MD software, GENESIS, to reduce the total computational time on such computers. Computationally intensive real-space nonbonded interactions are computed mainly on GPUs in the scheme, while less intensive bonded interactions and communication-intensive reciprocal-space interactions are performed on CPUs. On the basis of the midpoint cell method as a domain decomposition scheme, we invent the single particle interaction list for reducing the GPU memory usage. Since total computational time is limited by the reciprocal-space computation, we utilize the RESPA multiple time-step integration and reduce the CPU resting time by assigning a subset of nonbonded interactions on CPUs as well as on GPUs when the reciprocal-space computation is skipped. We validated our GPU implementations in GENESIS on BPTI and a membrane protein, porin, by MD simulations and an alanine-tripeptide by REMD simulations. Benchmark calculations on TSUBAME supercomputer showed that an MD simulation of a million atoms system was scalable up to 256 computer nodes with GPUs.

  18. First-principles-based multiscale, multiparadigm molecular mechanics and dynamics methods for describing complex chemical processes.

    PubMed

    Jaramillo-Botero, Andres; Nielsen, Robert; Abrol, Ravi; Su, Julius; Pascal, Tod; Mueller, Jonathan; Goddard, William A

    2012-01-01

    We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industries. However, despite truly dramatic progress in methods, software, and hardware, this goal remains elusive, particularly for systems that exhibit inherently complex chemistry under normal or extreme conditions of temperature, pressure, radiation, and others. We describe here some of the significant progress towards solving these problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics (QM), and the development of breakthrough methods for treating reaction processes, excited electronic states, and weak bonding effects on the conformational dynamics of large-scale molecular systems. These methods have resulted directly from filling in the physical and chemical gaps in existing theoretical and computational models, within the multiscale, multiparadigm strategy. To illustrate the procedure we demonstrate the application and transferability of such methods on an ample set of challenging problems that span multiple fields, system length- and timescales, and that lay beyond the realm of existing computational or, in some case, experimental approaches, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth, understanding the effects of electronic excitations in materials subjected to extreme conditions of temperature and pressure, following the dynamics and energetics of long-term conformational evolution of DNA macromolecules, and predicting the long-term mechanisms involved in enhancing the mechanical response of polymer-based hydrogels.

  19. Predicting the Knudsen paradox in long capillaries by decomposing the flow into ballistic and collision parts.

    PubMed

    Tatsios, Giorgos; Stefanov, Stefan K; Valougeorgis, Dimitris

    2015-06-01

    The well-known Knudsen paradox observed in pressure driven rarefied gas flows through long capillaries is quantitatively explored by decomposing the particle distribution function into its ballistic and collision parts. The classical channel, tube, and duct Poiseuille flows are considered. The solution is obtained by a typical direct simulation Monte Carlo algorithm supplemented by a suitable particle decomposition indexation process. It is computationally confirmed that in the free-molecular and early transition regimes the reduction rate of the ballistic flow is larger than the increase rate of the collision flow deducing the Knudsen minimum of the overall flow. This description interprets in a precise, quantitative manner the appearance of the Knudsen minimum and verifies previously reported qualitative physical arguments.

  20. Predicting the Knudsen paradox in long capillaries by decomposing the flow into ballistic and collision parts

    NASA Astrophysics Data System (ADS)

    Tatsios, Giorgos; Stefanov, Stefan K.; Valougeorgis, Dimitris

    2015-06-01

    The well-known Knudsen paradox observed in pressure driven rarefied gas flows through long capillaries is quantitatively explored by decomposing the particle distribution function into its ballistic and collision parts. The classical channel, tube, and duct Poiseuille flows are considered. The solution is obtained by a typical direct simulation Monte Carlo algorithm supplemented by a suitable particle decomposition indexation process. It is computationally confirmed that in the free-molecular and early transition regimes the reduction rate of the ballistic flow is larger than the increase rate of the collision flow deducing the Knudsen minimum of the overall flow. This description interprets in a precise, quantitative manner the appearance of the Knudsen minimum and verifies previously reported qualitative physical arguments.