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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. PMID:25527935

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

    SciTech Connect

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

    2014-12-21

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

  7. 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. PMID:24967721

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  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. Atomic and Molecular Collisions at Liquid Surfaces.

    PubMed

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

    2016-05-27

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

  12. Atomic and Molecular Collisions at Liquid Surfaces

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  13. 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^+).

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

    SciTech Connect

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

    1993-04-01

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

  15. 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

  16. On rainbow scattering in inelastic molecular collisions

    SciTech Connect

    Thomas, Lowell D.

    1980-01-01

    The purpose of this letter is to call attention to a growing misinterpretation in the literature on rainbow scattering in inelastic molecular collisions. The importance of rainbow structures in the angular distributions of elastic scattering cross sections is well established. However, use of approximate cross section formulas has led to an incorrect classification of the types of rainbows which are possible. Actually, however, it is possible to identify two classes of rainbows. If the relevant distributions and classifications are clearly stated, there should be little chance of confusion,

  17. 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.

  18. 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.

  19. Giant Molecular Cloud Collisions as Triggers of Star Formation

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  20. Numerical analysis of nanograin collision by classical molecular dynamics

    SciTech Connect

    Ohnishi, N; Bringa, E M; Remington, B A; Gilmer, G; Minich, R; Yamaguchi, Y; Tielens, A G M M

    2007-08-29

    Interstellar dust grains [1] comprise only 1% of the mass in the molecular clouds of galaxies and yet catalyze the formation of many gas phase molecules, in particular H2 [2], which allows for the cooling and collapse of these clouds and the formation of stars and planets. High-energy radiation and particles from hot stars, supernovae, or active black holes can alter the physical properties of dust grains and thereby affect their role in these processes. There is no experimental study on grain-grain collisions, for grain smaller than tens of microns, except for clusters with less than 100 atoms. Studies at the mm/cm scale can be roughly understood by continuum models, but these models might break down at the nanometer scale. There are many atomistic molecular dynamics (MD) simulations on the destruction of 3D droplets due to large temperature input [3], 2D solids [4, 5], or collision of disks [6], but there are very few simulations on grain-grain collisions, never going beyond tens of atoms [7, 8]. Here we demonstrate how MD simulations of grain-grain collisions for grain with more than 100 atoms can be used to understand what happens for nanometer-sized grains, colliding at relatively low velocities.

  1. Description of ionization in the molecular approach to atomic collisions

    SciTech Connect

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

    1997-01-01

    Molecular treatments of atomic collisions have traditionally been restricted to low nuclear velocities because of their failure to reproduce the fall of the capture cross sections at higher velocities. The limitation has recently been seen to be due to their description of ionizing processes. This feature is shown here to be a general one for multicharged ion-atom collisions. Its origin and characteristics are described and illustrated for the prototypical Li{sup 3+}+H(1s) reaction. Ionization appears as a result of the inertia of the electron cloud to adiabatically follow the nuclear motion. This gives rise to nonadiabatic transitions, which represent an ionizing flux whenever the nuclear velocity is high enough that the energy of the traveling molecular orbitals involved is positive in both moving atomic reference frames. Two strongly connected mechanisms appear, corresponding to the relative translational and rotational nuclear motions. Because of the finiteness of the basis, these mechanisms terminate with unphysical trapping effects. While interesting {ital per se}, knowledge of these features is also useful with respect to improving molecular treatments of atomic collisions with the addition of pseudostates. {copyright} {ital 1996} {ital The American Physical Society}

  2. A wide-open molecular magnetic trap for collision studies

    NASA Astrophysics Data System (ADS)

    Stuhl, Benjamin; Sawyer, Brian; Yeo, Mark; Wang, Dajun; Lev, Benjamin; Ye, Jun

    2008-05-01

    Cold molecular collision studies hold the potential of revolutionizing our understanding of chemical and molecular dynamics, both on Earth and astrophysically. Toward this end, we have developed and implemented a magneto-electrostatic trap with near-360 circumferential access for optical or molecular beam probes. The trap has demonstrated almost optimal loading efficiency, yielding a trapped density of 10^6 cm-3 at a temperature of 70 mK. We also report further progress towards the goal of cold molecular collisions.

  3. Continuum and molecular-dynamics simulation of nanodroplet collisions

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  5. 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.

  6. 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.

  7. Electron-atom /molecule/ collision processes

    NASA Technical Reports Server (NTRS)

    Trajmar, S.

    1980-01-01

    Electron-atom (molecule) collision processes at low and intermediate energies, from near threshold to a few hundred electron volts, are discussed. Attention is given to experimental techniques and procedures, electron impact cross sections, impact excitation and electron-atom scattering in laser fields. Specific examples are presented that illustrate various experimental techniques and interpretations of observations.

  8. Universal reaction rates for ultracold molecular collisions

    NASA Astrophysics Data System (ADS)

    Julienne, Paul; Idziaszek, Zbigniew

    2010-03-01

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

  9. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

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

  10. Electromagnetic processes in relativistic heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Bertulani, C. A.; Baur, G.

    1986-10-01

    Electromagnetic effects in relativistic heavy ion collisions with impact parameter larger than the sum of the nuclear radii are studied using the virtual photon method. With increasing value of the relativistic parameter γ the hardness of the virtual photon spectrum increases. This leads to interesting new effects which will also have to be considered in the design of future relativistic heavy ion machines and experiments. The excitation of high-lying giant E1 and E2 multipole resonances is calculated as well as electromagnetic pion production. Coulomb bremsstrahlung is calculated and compared to the bremsstrahlung emitted in the more violent central nuclear collisions. K-shell ionization and electron-positron pair production is studied. The latter process has a very large cross section for heavy ions and contributes significantly to the stopping power of relativistic heavy ions in a dense medium.

  11. Gaussian Process Model for Collision Dynamics of Complex Molecules

    NASA Astrophysics Data System (ADS)

    Cui, Jie; Krems, Roman V.

    2015-08-01

    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 -C6H6 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.

  12. Molecular collisions in a laser field - Effect of the laser linewidth

    NASA Technical Reports Server (NTRS)

    Lee, H. W.; Devries, P. L.; George, T. F.

    1978-01-01

    The effect of the laser linewidth on molecular collision processes taking place in a laser field is studied, using an approximation scheme that replaces the actual frequency distribution of the field by a finite number of frequencies and weights. The choice of the frequencies and weights is conveniently accomplished by the method of Gaussian quadrature. Close-coupling calculations are performed on model systems, and the results indicate that the neglect of the laser linewidth may be justified in most collision processes in a laser field.

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

    SciTech Connect

    Marlow, W.H.

    1988-12-31

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

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

    SciTech Connect

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

    1986-05-15

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

  15. Electron capture processes in Li2+ + H collisions

    NASA Astrophysics Data System (ADS)

    Yan, Ling Ling; Liu, Ling; Wang, Jian Guo; Janev, Ratko K.; Buenker, Robert J.

    2015-01-01

    The electron capture processes in Li2 + + H collisions have been investigated by using the quantum-mechanical molecular-orbital close-coupling method and the two-center atomic-orbital close-coupling method in the energy ranges of 10-8-10 keV/u and 0.1-300 keV/u, respectively. The capture to singlet and triplet systems of states of Li+(1 s,n l 2S + 1L) is considered separately. Total, n,S-resolved and n,l,S-resolved electron capture cross sections are calculated and compared with the results of available experimental and theoretical studies. The present calculations show that the n = 2 shell of Li+ is the main capture channel for all energies considered in both the singlet and triplet case. While for collision energies E> 5 keV/u, the cross sections for capture to the n = 2 manifold are of the same order of magnitude for both the singlet and triplet states (with the 2 p capture cross section being dominant), for energies below ~5 keV/u the cross sections for capture to the n = 2 triplet manifold is significantly (more than three orders of magnitude at 0.1 keV/u) larger than that for capture to the n = 2 singlet manifold of states (with the 2 s capture cross section being dominant). The capture dynamics at low collision energies is discussed in considerable detail, revealing the important role of rotational couplings in population of l> 0 capture states. The elastic scattering processes have been studied as well in the energy range of 10-8-1 keV/u. The calculated elastic scattering cross section is much larger than the electron capture cross section in both the singlet and triplet case. However, as the collision energy increases, the difference between the elastic and electron capture cross sections decreases rapidly.

  16. Single-parameter quantification of the sensitivity of a molecular collision to molecular polarization.

    PubMed

    de Miranda, Marcelo P; Kendrick, Brian K

    2009-12-31

    This article introduces the concept of intrinsic entropy, S, of a molecular collision. Defined in rigorously quantum mechanical terms as the von Neumann entropy of the intrinsic density matrices of reagents and products, the intrinsic entropy is a dimensionless number in the 0 < or = S < or = 1 range. Its limits are associated with situations where the collision cross section is due to a single combination of reagent and product polarizations (S = 0) or where there is absolutely no selectivity with respect to the molecular polarizations (S = 1). The usefulness of the intrinsic entropy as a quantifier of the sensitivity of a molecular collision to molecular polarizations is demonstrated with examples for the benchmark H + D(2) reaction. PMID:20028174

  17. Optimal separable bases and molecular collisions

    SciTech Connect

    Poirier, L W

    1997-12-01

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

  18. 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.

  19. 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.

  20. 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

  1. Elementary processes during collisions of ions with tryptophan molecules

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

    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 (88)SrF 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

  3. 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

  4. 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.

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

    PubMed

    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. PMID:27394110

  6. 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.

  7. 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.

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

    PubMed

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

    2013-01-28

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

  9. Laser-enhanced dynamics in molecular rate processes

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

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

    SciTech Connect

    Hu, S. X.

    2011-04-15

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

  11. Molecular collision studies with Stark-decelerated beams

    NASA Astrophysics Data System (ADS)

    Meijer, Gerard

    2008-03-01

    Molecular scattering behaviour has generally proven difficult to study at low collision energies. We formed a molecular beam of OH radicals with a narrow velocity distribution and a tunable velocity by passing the beam through a Stark decelerator [1]. The transition probabilities for inelastic scattering of the OH radicals with Xe atoms were measured as a function of the collision energy in the range of 50 to 400 wavenumbers. The behaviour of the cross-sections for inelastic scattering near the energetic thresholds was accurately measured, and excellent agreement was obtained with cross-sections derived from coupled- channel calculations on ab initio computed potential energy surfaces [2]. For collision studies at lower energies, the decelerated beams of molecules can be loaded into a variety of traps. In these traps, electric fields are used to keep the molecules confined in a region of space where they can be studied in complete isolation from the (hot) environment. Typically, 10^5 state- selected molecules can be trapped for times up to several seconds at a density of 10^7 mol/cm^3 and at a temperature of several tens of mK [3]. The long interaction time afforded by the trap has been exploited to measure the infrared radiative lifetime of vibrationally excited OH radicals, for instance, as well as to study the far-infrared optical pumping of these polar molecules due to blackbody radiation [4]. As an alternative to these traps, we have demonstrated an electrostatic storage ring for neutral molecules. In its simplest form, a storage ring is a trap in which the molecules - rather than having a minimum potential energy at a single location in space - have a minimum potential energy on a circle. To fully exploit the possibilities offered by a ring structure, it is imperative that the molecules remain in a bunch as they revolve around the ring. This ensures a high density of stored molecules, moreover, this makes it possible to inject multiple - either co-linear or

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

    NASA Technical Reports Server (NTRS)

    Stebbings, R. F.; Smith, K.

    1984-01-01

    Progress in the following research supported under NSG 7386 is reported: (1) measurement of differential cross sections for atomic and molecular collisions relevant to analysis and modeling of data from Pioneer 11, Pioneer 12, Voyager 1, and Voyager 2; (2) analysis of measured differential cross section results to provide scattering data in forms that are easy to apply to atmospheric modeling work; (3) analysis of the data to give basic information on the molecular potentials involved in the scattering process; and (4) development and initial use of apparatus to study dissociative processes in neutral molecules.

  13. 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.

  14. Molecular Processes in Biological Thermosensation

    PubMed Central

    Digel, I.; Kayser, P.; Artmann, G. M.

    2008-01-01

    Since thermal gradients are almost everywhere, thermosensation could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins) can present a target of the temperature-related stimuli. This review discusses some features of different classes of temperature-sensing molecules as well as molecular and biological processes that involve thermosensation. Biochemical, structural, and thermodynamic approaches are applied in the paper to organize the existing knowledge on molecular mechanisms of thermosensation. Special attention is paid to the fact that thermosensitive function cannot be assigned to any particular functional group or spatial structure but is rather of universal nature. For instance, the complex of thermodynamic, structural, and functional features of hemoglobin family proteins suggests their possible accessory role as “molecular thermometers”. PMID:20130806

  15. Electron-Nitrogen Collision Processes Relevant to Planetary Atmospheres

    NASA Astrophysics Data System (ADS)

    Johnson, Paul

    2011-06-01

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

  16. Spin effects in hard collision processes

    SciTech Connect

    Ranft, G.; Ranft, J.

    1984-05-01

    Questions of conservation and nonconservation of parity in phenomena associated with particle spin are reviewed. The main attention is concentrated on the production of hadrons, jets, and photons with large momentum transfer and the production of lepton pairs. The mechanisms of the hard-scattering subprocess include exchange of W/sup + -/ and Z/sup 0/ mesons, QCD and QED, and also interference between QCD and the weak interactions and between QED and the weak interactions. Effective cross sections of hard scattering processes are calculated, a factorization of the hadron--hadron scattering cross section is proposed, and the possible types of spin effects manifested in the hadronic subprocesses are classified and discussed. The properties of the polarized proton distributions and polarized structure functions are given in two appendices.

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

    NASA Astrophysics Data System (ADS)

    Oh, Chang-Whan

    2015-04-01

    east indicating propagation of collision towards east. The following collision model of the Himalayan collision belt is proposed based on data published in previous studies. Collision between the Indian and Asian blocks started in the west before ca. 55 Ma. In the western part, the amount of oceanic slab subducted prior to continent collision was enough to pull the continental crust down to the depths of UHP metamorphism, as a wide ocean existed between the Asian and Indian blocks prior to collision. Following UHP metamorphism, oceanic slab break-off started at ca. 55~46 Ma in the west due to the very strong buoyancy of the deeply subducted continental block. In contrast, the subduction of continental crust continued at this time in the middle and eastern parts of the belt. The zone of break-off migrated eastward, initiating a change from steep- to low-angle subduction. Final break-off may have occurred in the easternmost part of the belt at ca. 22-25 Ma. The depth of slab break-off decreased toward the east due to the westward decrease of the amount of subducted oceanic crust along the Himalayan collision belt, resulting eastwards decrease of an uplifting rate due to a decrease in buoyancy of the continental slab. The slower uplift resulted in a longer period of thermal relaxation and a higher geothermal gradient. In the west, the high rate of uplift resulted the epidote amphibolite facies (580-610°C) retrograde metamorphic overprint on the UHP eclogites, whereas the relatively slow uplift in the mid-eastern part caused high-grade granulites (850°C) retrograde metamorphic overprint on the HP eclogites. The study indicates that the metamorphic pattern along the collision belt is strongly related to the amount of subducted oceanic crust between continents before collision and the depth of slab break-off. Therefore metamorphic pattern can be used to interpret both the disappeared and ongoing tectonic process during continental collision.

  18. 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.

  19. 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.

  20. Electron-exchange collisions with molecular open-shell targets

    NASA Astrophysics Data System (ADS)

    Holtkötter, I.; Hanne, G. F.

    2009-08-01

    Low-energy electron-exchange collisions with the simple open-shell molecules O2 , NO, and NO2 have been investigated by measuring the change in electron-spin polarization after scattering polarized electrons from unpolarized molecules with energies between 8 and 20 eV and scattering angles up to 130° . Results for elastic collisions with O2 and NO are compared with existing theories where the agreement is fair. Direct observation of spin-exchange collisions is obtained for elastic scattering from NO2 and for electron-impact excitation of O2 (6.1 eV energy loss). It is also shown that the results may be influenced by spin-orbit interaction, which was assumed to be negligible in previous studies.

  1. 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

  2. The rate coefficients of the chemi-ionization processes in slow Li*(n) + Na collisions

    NASA Astrophysics Data System (ADS)

    Ignjatović, Lj M.; Mihajlov, A. A.; Klyucharev, A. N.

    2008-01-01

    The semi-classical method for determining the rate coefficients of the chemi-ionization processes in slow non-symmetric atom-Rydberg atom collisions is applied to the Li*(n) + Na case. Calculated rate coefficients are compared with the existing experimental data from the literature. Obtained results have confirmed that resonant mechanism of non-elastic processes in atom-Rydberg atom collisions are fully applicable to non-symmetric chemi-ionization processes. The rate coefficients of such processes in Li*(n) + Na collisions are determined in the regions of principal quantum number and temperature 4 <= n <= 20 and 700 K <= T <= 1100 K which can be of interest for possible further experiments. Also, the potential curves of several lowest Σ states of the molecular ion LiNa+, as well as the values of the square of dipole matrix element for the transition between X2Σ+- and A2Σ+-states, are presented in this paper.

  3. 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.

  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. Molecular dynamics simulation of rotational relaxation in nitrogen: Implications for rotational collision number models

    NASA Astrophysics Data System (ADS)

    Valentini, Paolo; Zhang, Chonglin; Schwartzentruber, Thomas E.

    2012-10-01

    We study the rotational relaxation process in nitrogen using all-atom molecular dynamics (MD) simulations and direct simulation Monte Carlo (DSMC). The intermolecular model used in the MD simulations is shown to (i) reproduce very well the shear viscosity of nitrogen over a wide range of temperatures, (ii) predict the near-equilibrium rotational collision number in good agreement with published trajectory calculations done on ab initio potential energy surfaces, and (iii) produce shock wave profiles in excellent accordance with the experimental measurements. We find that the rotational relaxation process is dependent not only on the near-equilibrium temperature (i.e., when systems relax to equilibrium after a small perturbation), but more importantly on both the magnitude and direction of the initial deviation from the equilibrium state. The comparison between MD and DSMC, based on the Borgnakke-Larsen model, for shock waves (both at low and high temperatures) and one-dimensional expansions shows that a judicious choice of a constant Zrot can produce DSMC results which are in relatively good agreement with MD. However, the selection of the rotational collision number is case-specific, depending not only on the temperature range, but more importantly on the type of flow (compression or expansion), with significant limitations for more complex simulations characterized both by expansion and compression zones. Parker's model, parametrized for nitrogen, overpredicts Zrot for temperatures above about 300 K. It is also unable to describe the dependence of the relaxation process on the direction to equilibrium. Finally, we present a demonstrative cell-based formulation of a rotational relaxation model to illustrate how, by including the key physics obtained from the MD data (dependence of the relaxation process on both the rotational and the translational state of the gas), the agreement between MD and DSMC solutions is drastically improved.

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

    SciTech Connect

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

    1989-04-01

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

  7. Two-dimensional model of resonant electron collisions with diatomic molecules and molecular cations

    NASA Astrophysics Data System (ADS)

    Vana, Martin; Hvizdos, David; Houfek, Karel; Curik, Roman; Greene, Chris H.; Rescigno, Thomas N.; McCurdy, C. William

    2016-05-01

    A simple model for resonant collisions of electrons with diatomic molecules with one electronic and one nuclear degree of freedom (2D model) which was solved numerically exactly within the time-independent approach was used to probe the local complex potential approximation and nonlocal approximation to nuclear dynamics of these collisions. This model was reformulated in the time-dependent picture and extended to model also electron collisions with molecular cations, especially with H2+.This model enables an assessment of approximate methods, such as the boomerang model or the frame transformation theory. We will present both time-dependent and time-independent results and show how we can use the model to extract deeper insight into the dynamics of the resonant collisions.

  8. Calculations of fast ion collisions with multi-center molecular targets

    NASA Astrophysics Data System (ADS)

    Kirchner, Tom

    2011-05-01

    The theoretical treatment of ion-molecule collisions is challenging for several reasons: the systems have many degrees of freedom, a rather complex geometry, and the electron dynamics might be nonperturbative and involve electron-electron interaction effects. However, the interest in accurate calculations has been growing recently. An important reason for this development is the relevance of ion-molecule collisions for a number of fields, such as atmospheric science, and the understanding of radiation damage of biological tissue. We have developed a new approach to meet these challenges. It disregards rovibrational motion, but it does address the multi-center geometry of the system and the generally nonperturbative nature of the electron dynamics. The key ingredients are an expansion of the initially populated molecular orbitals in terms of a single-center basis and a spectral representation of the molecular Hamiltonian. This facilitates a separation of molecular geometry and collision dynamics and makes it possible to use well-established ion-atom methods with relatively minor modifications. We have extended our basis generator method to deal with the collision dynamics and report on results for ionization and fragmentation of water molecules by proton and He+ ion impact over wide ranges of collision energies. For the case of He+ impact this will include a discussion of effects due to the presence of the projectile electron. This work has been supported by the Natural Sciences and Engineering Research Council of Canada.

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

    PubMed

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

    2016-05-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  11. Spectroscopy of quasibound states formed by molecular collisions in the presence of a laser

    NASA Technical Reports Server (NTRS)

    Hutchinson, M.; George, T. F.

    1981-01-01

    A theory is reported which describes spectroscopic transitions between quasibound states formed during molecular collisions in a laser field. A preliminary calculation suggests that the shapes of absorption lines are sensitive to the shapes of the potentials; hence a method for determining the latter. The calculation also shows that respectable cross-sections for scattering can be obtained at low laser powers.

  12. Reply to comment by Thomas on ''On rainbow scattering in inelastic molecular collisions''

    SciTech Connect

    Bowman, J.M.; Lee, K.T.

    1981-02-15

    The comments of Thomas/sup 1/ on the location of rainbows in inelastic molecular scattering of Ref. 2 are discussed and evaluated. It is contended that more insight into the nature of reainbows in rotatinally inelstic collisions is obtained by using the arguments in ref. 2. (AIP)

  13. Theoretical studies of molecular processes

    NASA Astrophysics Data System (ADS)

    Cui, Qiang

    1997-09-01

    The current thesis concerns with theoretical studies of molecular processes and consists of two parts. The first part includes theoretical studies of dynamics of unimolecular and bimolecular reactions, in particular those involving non-adiabatic processes. In chapter 2 and 3, we have presented our studies of detailed mechanisms for the photodissociation of C2H2 and C2H, and the ion-molecule reactions of C2H2+ + CH4 or NH3, respectively. In chapter 4, we have presented our study that extends TST to non-adiabatic reactions, and an application of the theory of the spin-forbidden reaction of CH(2/Pi)+N2. In chapter 5, we have included our analyses on the photodissociation of triplet ketene, where an extensive seam has been found all along the reaction coordinate. Finally, in Chapter 6, we have presented our study on the photodissociation of O3/sp-, which includes qualitative electronic structure calculations and construction of global potential energy functions for coupled electronic states. The second part of the thesis deals with theoretical studies of organometallic reactions, metal clusters, and gas-surface interactions. With theoretical calculations, one can study the reactivities of transition metal compounds systematically, which allows one to understand the key parameters that control the reactivities of those compounds. In chapter 2, we have presented our implementation of analytical hessian for effective core potential, which makes normal mode analysis possible for large organometallic systems and has proven to be very useful in the study of systems containing transition metals. In chapter 3-5, we have included our studies on the detailed mechanisms of several interesting reactions including platinum/palladium(0) catalyzed diboration and thioboration reactions of acetylene and olefin, and H- H/C-H bond activation on small metal clusters Pt/Pdn(n = 1[-]3). For truly large systems such as surfaces or proteins, full quantum mechanical treatments are

  14. Thermodynamic model for electron emission and negative- and positive-ion formation in keV molecular collisions

    NASA Astrophysics Data System (ADS)

    Juhász, Z.

    2016-08-01

    A statistical-type model is developed to describe the ion production and electron emission in collisions of (molecular) ions with atoms. The model is based on the Boltzmann population of the bound electronic energy levels of the quasimolecule formed in the collision and the discretized continuum. The discretization of the continuum is implemented by a free-electron gas in a box model assuming an effective square potential of the quasimolecule. The temperature of the electron gas is calculated by taking into account a thermodynamically adiabatic process due to the change of the effective volume of the quasimolecule as the system evolves. The system may undergo a transition with a small probability from the discretized continuum to the states of the complementary continuum. It is assumed that these states are decoupled from the thermodynamic time development. The decoupled states overwhelmingly determine the yield of the asymptotically observed fragment ions. The main motivation of this work is to describe the recently observed H- ion production in O H++Ar collisions. The obtained differential cross sections for H- formation, cation production, and electron emission are close to the experimental ones. Calculations for the atomic systems O++Ar and H++Ar are also in reasonable agreement with the experiments indicating that the model can be applied to a wide class of collisions.

  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. 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

  17. Analysis of angular distribution of fragments in relativistic heavy-ion collisions by quantum molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

    2016-05-01

    To predict angular distribution of fragments produced in nucleusnucleus collisions, JAERI quantum molecular dynamics model (JQMD) was improved. Because JQMD underestimated fragments in the forward angle, which were mainly produced by peripheral collisions, JQMD was revised so as to simulate peripheral collisions accurately. Density-dependent in-medium effect and relativistic effect on nucleonnucleon interactions were incorporated for this purpose. The revised version of JQMD coupled with a statistical decay model was used to calculate differential fragment production cross sections measured in earlier studies. Comparison of the measured data and calculation by the revised and old JQMD showed that the revised JQMD can predict fragment angular distribution better than old JQMD. Particularly, agreement of fragment yield in the forward angle is substantially improved.

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

    NASA Astrophysics Data System (ADS)

    Schweigert, Igor V.; Dunlap, Brett I.

    2011-09-01

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

  19. 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.

  20. 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.

  1. Collisions of Molecular Clouds as a Trigger of Enhanced Accretion onto the Supermassive Black Hole in Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Tscharnuter, W. M.

    2004-02-01

    On the basis of numerical calculations I will discuss to which extent direct hydrodynamical interactions of molecular clouds in the vicinity of galactic centers (within a few 100 pc) can give rise to a temporarily enhanced mass flux toward the central black hole, thus triggering or at least modulating an AGN. The models take into account (i) the mutual gravitational interaction of the clouds considered as point masses, (ii) isothermal collisions of the clouds assumed to be initially of spherical shape, (iii) tidal interactions of the clouds with the central black hole (loss of cloud material outside the cloud Hill sphere), (iv) the influence of the (linearized) tidal forces on the outcome of the hydrodynamical cloud-cloud collision process. In addition, a global bookkeeping for the most mass and the respective angular momentum gives a rough idea of the size an mass content of the accretion disk that will form out of the dispersed cloud material. If, due to the collision event, star formation is indicated (Jeans instability, appearance of collapse flow patterns), part of the cloud mass is assumed to be compactified into stars, according a given IMF.

  2. Effect of molecular weight on polymer processability

    SciTech Connect

    Karg, R.F.

    1983-01-01

    Differences in rheological behavior due to the polymer molecular weight and molecular weight distribution have been shown with the MPT. SBR polymers having high molecular weight fractions develop higher stress relaxation time values due to the higher degree of polymer entanglements. Tests conducted at increasing temperatures show the diminishing influence of the polymer entanglements upon stress relaxation time. EPDM polymers show stress relaxation time and head pressure behavior which correlates with mill processability. As anticipated, compounded stock of EPDM have broad molecular weight distribution has higher stress relaxation time values than EPDM compounds with narrow molecular weight distribution.

  3. 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.

  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. PMID:22082054

  5. Application of JAERI quantum molecular dynamics model for collisions of heavy nuclei

    NASA Astrophysics Data System (ADS)

    Ogawa, Tatsuhiko; Hashimoto, Shintaro; Sato, Tatsuhiko; Niita, Koji

    2016-06-01

    The quantum molecular dynamics (QMD) model incorporated into the general-purpose radiation transport code PHITS was revised for accurate prediction of fragment yields in peripheral collisions. For more accurate simulation of peripheral collisions, stability of the nuclei at their ground state was improved and the algorithm to reject invalid events was modified. In-medium correction on nucleon-nucleon cross sections was also considered. To clarify the effect of this improvement on fragmentation of heavy nuclei, the new QMD model coupled with a statistical decay model was used to calculate fragment production cross sections of Ag and Au targets and compared with the data of earlier measurement. It is shown that the revised version can predict cross section more accurately.

  6. H+-H2O collisions studied by time-dependent density-functional theory combined with the molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Hong, Xuhai; Wang, Feng; Wu, Yong; Gou, Bingcong; Wang, Jianguo

    2016-06-01

    H+-H2O collisions are investigated using the time-dependent density-functional theory combined with the molecular dynamics method, in which the electrons are described quantum mechanically within the framework of time-dependent density-functional theory and the ionic cores are described classically by Newton's equations. The feedback between quantum electrons and classical ions is self-consistently coupled by Ehrenfest's method. The electron capture, electron loss, and ionization cross sections are obtained in the energy range of 1-1000 keV and excellent agreements are achieved with available experimental and theoretical data. The orientation effects of the H2O target are found to be significant in the collision processes, especially in low-energy collisions.

  7. Gas phase atomic and molecular processes

    NASA Astrophysics Data System (ADS)

    Zhu, Cheng

    We perform fully quantum mechanical calculations of the lithium 2 p -2 s and sodium 3 p -3 s resonance lines pressure broadened by collisions with helium atoms. Using carefully constructed potential energy surfaces and transition dipole moments, we have obtained the emission and absorption coefficients at temperatures from 200 to 3000 K at wavelengths between 500 and 1000 nm for lithium and at temperatures from 158 to 3000 K at wavelengths between 500 and 760 nm for sodium. Contributions from quasi-bound levels are included. Our results are in good agreement with experiment. These broadened line profiles are important in developing effective diagnostics on the temperatures, densities, albedos and composition of the atmospheres of brown dwarfs and extrasolar giant planets. We compute the diffusion coefficients of ground and excited-state lithium and sodium atoms in a helium gas. They are valuable in predicting the sign and magnitude of the light-induced drift for the gas mixture. We calculate the dispersion coefficients of the long range interactions of alkali-metal atoms with molecular hydrogen and helium atoms. The uncertainties in our results are less than 2%. We study the relaxation of the v = 1 vibrational level of carbon monoxide induced by collisions with helium three atoms in ultracold temperatures. We confirm the Wigner's threshold law which states that in the zero temperature limit the inelastic quenching cross sections are inversely proportional to the velocity of the incident atom. Our calculations agree well with experiment and we find enhanced rate coefficients as compared to those for 4 He-CO. We study the chemistry of hydrogen fluoride in the interstellar medium. We consider fine-structure collisions and find that most fluorine atoms reside in the ground 2 P 3/ 2 state. We calculate the rate coefficients for the reaction of F( 2 P 3/2 ) atoms in collisions with H 2 . Our results agree well with experiment. We confirm the conclusions of Neufeld et al

  8. 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.

  9. Analyzing collision processes with the smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2014-02-01

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

  10. 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.

  11. 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.

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

    SciTech Connect

    Janev, R.K.

    1983-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Arora, Sanjeev

    1992-01-01

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Geller, Michael

    2013-05-01

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

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

    PubMed

    Zhang, Dali; Ke, Jiajun; Lu, Lizhu

    2015-10-01

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

  17. Bulk atomic relocation in low-energy collision cascades in silicon: Molecular Dynamics versus Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Konoplev, V.; Caturla, M. J.; Abril, I.; Gras-Marti, A.

    1994-05-01

    We investigate the atomic mixing produced in the bulk of a zero-temperature silicon target by internally-starting low-energy (100 eV) self-recoils. Molecular Dynamics (MD) and Monte Carlo (MC) simulations are applied. The many-body Tersoff potential connected smoothly with the pairlike Ziegler-Biersack potential is used in the MD simulation. The collisional model of the MC code is based on the Ziegler-Biersack potential and includes a calculation of the mean free-flight path and the random impact parameter by using the energy-dependent total cross-section for elastic collisions. For a quantitative description of the process of ion-induced atomic mixing we calculate the depth dependence of the number of displaced atoms, and the first and second moments of the relocation cross-section. We analyse the discrepancies between the two computer simulations, and suggest an adjustment of the pertinent parameters in the MC model.

  18. Cumulant moments in hadron-nucleus collisions and stochastic processes

    NASA Astrophysics Data System (ADS)

    Suzuki, N.; Biyajima, M.; Wilk, G.; Wlodarczyk, Z.

    1998-09-01

    Cumulant moments of negatively charged particles observed in hadron-nulceus collisions are analyzed by a leading particle cascade model. A modified negative binomial distribution (MNBD) or a negative binomial distribution (NBD) is used for multiplicity distribution from each participant hadron. If multiplicity distributions are truncated, both calculated results with the MNBD and the NBD can explain the oscillation of cumulant moments obtained from the data.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K.; Brinker, Charles Jeffrey

    1999-01-01

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

  6. 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.

  7. Resource Paper: Molecular Excited State Relaxation Processes.

    ERIC Educational Resources Information Center

    Rhodes, William

    1979-01-01

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

  8. 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...

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Swaminathan-Gopalan, Krishnan; Stephani, Kelly A.

    2016-02-01

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

  11. 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. PMID:22979854

  12. 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.

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

    SciTech Connect

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

    1980-09-01

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

  14. 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.

  15. 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.

  16. 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.

  17. Hybrid BEEQ tandem mass spectrometer for the study of ion/surface collision processes

    NASA Astrophysics Data System (ADS)

    Winger, B. E.; Laue, H.-J.; Horning, S. R.; Julian, R. K., Jr.; Lammert, S. A.; Riederer, D. E., Jr.; Cooks, R. G.

    1992-12-01

    A hybrid mass spectrometer consisting of a magnetic sector, two electric sectors, and a quadrupole mass filter (BEEQ) has been built for the study of polyatomic ion/surface collision phenomena over the energy range of a few electron volts to several keV. Primary ions are generated by electron ionization or by chemical ionization, and the first two sectors are used to deliver a monoenergetic beam of ions, of a selected mass-to-charge m/z ratio, to a decelerator which sets the desired collision energy. The target, which can be introduced into the system without breaking vacuum, is mounted on a goniometer and situated in an electrically shielded region in the center of a large scattering chamber which contains an electric sector and a quadrupole mass analyzer used for kinetic energy and mass measurements on the ejected ions. These analyzers rotate around the scattering center to allow selection of the scattering angle of ions leaving the surface. Ultimate pressures attainable in the main scattering chamber are below 10-9 Torr allowing molecular targets, such as self-assembled monolayers of alkyl thiols on gold, to be examined without surface contamination. Low-energy (20-100 eV) collisions of polyatomic ions are reported, and examples are given of the effects of collision energy and scattering angle on surface induced dissociation mass spectra. The kinetic energy of the inelastically scattered ions is also measured, and in some cases, the internal energy can be estimated, the two measurements together providing information on energy partitioning associated with surface collisions. For example, it is shown that n-butylbenzene molecular ions of 25 eV colliding with ferrocenyl-terminated self-assembled monolayer surfaces, rebound with 10 eV of recoil energy and 3 eV of internal energy. The remainder of the energy goes into the surface. The capability of the BEEQ instrument to provide data on ion/surface reactive collisions is also illustrated with reactions such as alkyl

  18. 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

  19. 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.

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

    NASA Technical Reports Server (NTRS)

    Stebbings, R. F.; Smith, K.

    1985-01-01

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

  1. 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.

  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. 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.

  4. 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.

  5. Optimizing rotary processes in synthetic molecular motors

    PubMed Central

    Geertsema, Edzard M.; van der Molen, Sense Jan; Martens, Marco; Feringa, Ben L.

    2009-01-01

    We deal with the issue of quantifying and optimizing the rotation dynamics of synthetic molecular motors. For this purpose, the continuous four-stage rotation behavior of a typical light-activated molecular motor was measured in detail. All reaction constants were determined empirically. Next, we developed a Markov model that describes the full motor dynamics mathematically. We derived expressions for a set of characteristic quantities, i.e., the average rate of quarter rotations or “velocity,” V, the spread in the average number of quarter rotations, D, and the dimensionless Péclet number, Pe = V/D. Furthermore, we determined the rate of full, four-step rotations (Ωeff), from which we derived another dimensionless quantity, the “rotational excess,” r.e. This quantity, defined as the relative difference between total forward (Ω+) and backward (Ω−) full rotations, is a good measure of the unidirectionality of the rotation process. Our model provides a pragmatic tool to optimize motor performance. We demonstrate this by calculating V, D, Pe, Ωeff, and r.e. for different rates of thermal versus photochemical energy input. We find that for a given light intensity, an optimal temperature range exists in which the motor exhibits excellent efficiency and unidirectional behavior, above or below which motor performance decreases. PMID:19805100

  6. Optimizing rotary processes in synthetic molecular motors.

    PubMed

    Geertsema, Edzard M; van der Molen, Sense Jan; Martens, Marco; Feringa, Ben L

    2009-10-01

    We deal with the issue of quantifying and optimizing the rotation dynamics of synthetic molecular motors. For this purpose, the continuous four-stage rotation behavior of a typical light-activated molecular motor was measured in detail. All reaction constants were determined empirically. Next, we developed a Markov model that describes the full motor dynamics mathematically. We derived expressions for a set of characteristic quantities, i.e., the average rate of quarter rotations or "velocity," V, the spread in the average number of quarter rotations, D, and the dimensionless Péclet number, Pe = V/D. Furthermore, we determined the rate of full, four-step rotations (Omega(eff)), from which we derived another dimensionless quantity, the "rotational excess," r.e. This quantity, defined as the relative difference between total forward (Omega(+)) and backward (Omega(-)) full rotations, is a good measure of the unidirectionality of the rotation process. Our model provides a pragmatic tool to optimize motor performance. We demonstrate this by calculating V, D, Pe, Omega(eff), and r.e. for different rates of thermal versus photochemical energy input. We find that for a given light intensity, an optimal temperature range exists in which the motor exhibits excellent efficiency and unidirectional behavior, above or below which motor performance decreases. PMID:19805100

  7. Molecular Visualization of the Spreading Process

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

  8. K-shell processes in heavy-ion collisions in solids and the local plasma approximation

    NASA Astrophysics Data System (ADS)

    Kadhane, Umesh; Montanari, C. C.; Tribedi, Lokesh C.

    2003-03-01

    We have investigated K-shell vacancy production due to ionization and electron transfer processes, in collisions of highly charged oxygen ions with various solid targets such as Cl, K, Ti, Fe, and Cu at energies between 1.5 and 6.0 MeV/u. The K-shell ionization cross sections were derived from the measured K x-ray cross sections. An ab initio theoretical model based on the local plasma approximation (LPA), which is an extension of the dielectric formalism to consider core electrons, provides an explanation of the measured data only qualitatively. In case of asymmetric collisions (Zp/Zt<0.35, Zp, Zt being the atomic numbers of the projectile and target, respectively) and at higher energies, the LPA model explains the data to some extent but deviates for more symmetric collision systems. On the other hand, a perturbed-stationary-state (PSS) calculation (ECPSSR), including the corrective terms due to energy (E) loss, Coulomb (C) deflection, and relativistic (R) wave functions designed for ion-atom collisions agree quite well with the data for different combinations of target and projectile elements. In addition, we have also measured the K(target)-K(projectile) electron transfer cross sections and compared them with a model based on perturbed-stationary-state approximation.

  9. 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.

  10. Charge Transfer Process During Collision of Riming Graupel Pellet with Small Ice Crystals within a Thundercloud

    NASA Technical Reports Server (NTRS)

    Datta, Saswati; De, Utpal K.; Goswami, K.; Jones, Linwood

    1999-01-01

    A charge transfer process during the collision of a riming graupel pellet and an ice-crystal at low temperature is proposed. During riming, the surface structure of graupel deviates from perfect crystalline structure. A concept of quasi-solid layer (QSL) formation on the surface is introduced. This QSL contains defects formed during riming. In absence of impurities, positively charged X-defect abundance is considered in the outer layer. These defects are assumed to be the charge carriers during the charge transfer process. Some part of the QSL is stripped off by the colliding ice crystals, which thereby gain some positive charge, leaving the graupel pellet negatively charged. With the proposed model, fC to pC of charge transfer is observed per collision. A transition temperature between -10 C to -15 C is also noted beyond which the QSL concept does not hold. This transition temperature is dependent on the bulk liquid water content of the cloud.

  11. Internal Energy Exchange and Dissociation Probability in DSMC Molecular Collision Models

    NASA Astrophysics Data System (ADS)

    Chabut, E.

    2008-12-01

    The present work is related to the gas—gas collision models used in DSMC. It especially concerns the relaxation rates and the reactivity for diatomic molecules (but most of the models can be extended to polyatomic molecules). The Larsen-Borgnakke [1] model is often used in DSMC to describe the way of redistribution of the energies during collisions. A lot of information is provided by literature about links existing between macroscopic collision number, the fraction of inelastic collisions and the probability for a molecule to exchange energy during a collision in a specific mode. We then expose the main relations able to reproduce macroscopic relaxation rates. During collisions, the energy brought by the collision partners can be sufficient to generate a chemical reaction. The problematic is at first to determine an energetic condition for a possible reaction: which energy we have to consider and which threshold we have to compare with; and in second how to calculate the reaction probabilities. Then we often use the experimental results which put in light some phenomena (vibration—dissociation coupling for example) to built a qualitative basis for the models and, in a quantitative point of view, we determine probabilities such they can reproduce the macroscopic experimental rates reflected by the modified Arrhenius law. Some of the different chemical models used in DSMC will be exposed as the "TCE" [2]-3], "EAE" [3], "ME" [4] and "VFD" [5] models.

  12. Electron-ion collisions. [Basic physics of inelastic processes of excitation, ionization, and recombination

    SciTech Connect

    Crandall, D.H.

    1982-01-01

    This discussion concentrates on basic physics aspects of inelastic processes of excitation, ionization, and recombination that occur during electron-ion collisions. Except for cases of illustration along isoelectronic sequences, only multicharged (at least +2) ions will be specifically discussed with some emphasis of unique physics aspects associated with ionic charge. The material presented will be discussed from a primarily experimental viewpoint with most attention to electron-ion interacting beams experiments.

  13. Azimuthal Asymmetries of the Drell-Yan Process in pA Collisions

    NASA Astrophysics Data System (ADS)

    Gao, Jian-Hua

    2016-02-01

    We discuss the azimuthal asymmetries of the Drell-Yan process in nucleon-nucleus collisions at the low transverse momentum of the lepton pair. Within the transverse-momentum-dependent (TMD) factorization formalism, the nuclear effects of these azimuthal asymmetries can be from the gauge link of the TMD quark distribution. We estimate all these nuclear effects within the assumption that all the TMD parton distributions or correlations are in Gaussian forms.

  14. 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.

  15. 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

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

    SciTech Connect

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

    2011-09-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  18. 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

  19. 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.

  20. 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. PMID:26263260

  1. 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.

  2. Calculation of rotational transition probabilities in molecular collisions - Application to N2 + N2

    NASA Technical Reports Server (NTRS)

    Itikawa, Y.

    1975-01-01

    A computational method is proposed to obtain rotational transition probabilities in collisions between two diatomic molecules. The potential method of Rabitz and an exponential approximation are used to solve the semiclassical coupled equations without invoking any perturbational technique. The collision trajectory is determined in the classical modified-wave-number approximation. The method can treat systems involving strong interactions and provide probabilities for transitions even with a multiquantum jump. A simultaneous transition in the rotational states of both molecules, i.e., the rotational-rotational energy transfer, is taken into account. An application to the system N2 + N2 is presented.

  3. 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).

  4. 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. PMID:26469322

  5. On quantum mechanical transport coefficients in nonequilibrium nuclear processes with application to heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Hamdouni, Yamen

    2010-12-01

    The elements of the quantum mechanical Markovian diffusion matrix leading to a Gibbs equilibrium state for a set of N coupled quantum harmonic oscillators are derived within Lindblad's axiomatic approach. Consequences of the fundamental constraints on the quantum friction coefficients are discussed. We derive the equations of motion for the expectation values and variances, and we solve them analytically. We apply our results to the description of the charge and mass asymmetry coordinates in heavy-ion collisions, and we investigate the effect of dissipation on tunneling in sub-barrier processes.

  6. 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.

  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. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Kaislaniemi, Lars; van Hunen, Jeroen; Allen, Mark; Neill, Iain

    2014-05-01

    We have studied the role of sub-lithospheric small scale convection in the generation of collision zone magmatism, using combined geodynamic-petrological models. We compare the results with the collisional magmatism of the Turkish-Iranian plateau, where a number of randomly (in both space and time) distributed volcanic centres on has been produced by the active Arabia-Eurasia collision since initial plate collision at ~27-35 Ma. These volcanic rocks have a highly variable geochemical signature, but commonly point to a lithospheric mantle or asthenospheric source. Major and trace element characteristics span the range from OIB-like, to calc-alkali, shoshonitic and even ultrapotassic. We suggest these spatially, temporally and chemically diverse patterns of volcanism are caused by sub-lithospheric small scale convection (SSC), manifested as small (50 to 300 km) convection cells at the lithosphere-asthenosphere boundary and dripping of the lithospheric mantle into the asthenosphere. SSC is activated by the increased amount of water in the lithospheric and asthenospheric mantle and its rheological weakening effect. The increase in water content is caused by the subduction prior to the collision and/or continental subduction during collision. The mantle convection code CitCom, together with a parameterized melting model, is used to model the SSC process. We relate the water content to the mantle solidus and viscosity, and the amount of depletion to the viscosity and buoyancy of the mantle material. We measure the amount of magmatism taking place by assuming direct and instantaneous percolation of mantle melts to the surface. We mimic the dislocation creep mechanism with a diffusion creep mechanism using low activation energy--either one is needed for the SSC to take place under realistic conditions. Results show that SSC is able to produce small degrees (0-2 %) of melting of the mantle through dripping lithosphere, decompression melting, erosion of the overlying

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

    SciTech Connect

    Gianturco, F.A.; Stoeckling, T.

    1997-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  13. 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.

  14. Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study.

    PubMed

    Pepin, Robert; Petrone, Alessio; Laszlo, Kenneth J; Bush, Matthew F; Li, Xiaosong; Tureček, František

    2016-07-21

    Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections. PMID:27389035

  15. 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)

  16. 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.

  17. 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.

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

    PubMed

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

    2001-02-01

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

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

    SciTech Connect

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

    2006-08-15

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

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

    SciTech Connect

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

    1991-07-01

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

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

    SciTech Connect

    Blann, M.

    1986-09-01

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

  2. 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.

  3. Charge transfer in collisions of C{sup 2+} carbon ions with CO and OH targets

    SciTech Connect

    Bene, E.; Martinez, P.; Halsaz, G. J.; Vibok, A.; Bacchus-Montabonel, M. C.

    2009-07-15

    The charge transfer in collisions of C{sup 2+} ions with the CO molecule and the OH radical has been studied theoretically by means of ab initio quantum chemistry molecular methods followed by a semiclassical dynamical treatment in the keV collision energy range. The comparison of the cross sections calculated for these two collision systems exhibits interesting features with regard to the anisotropy of these processes and the influence of the vibration of the molecular target.

  4. Separation of elastic and inelastic processes in the relaxation-time approximation for the collision integral

    NASA Astrophysics Data System (ADS)

    Florkowski, Wojciech; Ryblewski, Radoslaw

    2016-06-01

    We introduce a generalized relaxation-time-approximation form of the collision term in the Boltzmann kinetic equation that allows for using different relaxation times for elastic and inelastic collisions. The efficacy of the proposed framework is demonstrated with the numerical calculations that describe systems with different relations between the two relaxation times and the evolution time of the system.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  6. Collision-induced dissociation of Nb x O{/y +} ( x = 1, 2, y = 2-12) clusters: crossed molecular beams and collision cell studies

    NASA Astrophysics Data System (ADS)

    Mihesan, Claudia; Glodić, Pavle; Velegrakis, Michalis

    2015-03-01

    Oxygen-rich niobium oxide clusters are formed by mixing laser-produced Nb plasma with pure oxygen, and their stability is investigated by mass spectrometry and collision-induced dissociation. We use an experimental configuration recently developed by our group, where the cluster ions beam is crossed with a secondary beam of noble gas atoms, and the fragments are rejected by a retarding field energy analyzer. In this way, the relative collision cross sections of Nb x O{/y +} ( x = 1, 2, y = 2-12) clusters have been measured and information about their fragmentation channels has been obtained.

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

    NASA Astrophysics Data System (ADS)

    Tanaka, K.

    2016-05-01

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

  8. Cold molecules, collisions and reactions

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-05-01

    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

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

    PubMed

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

    2015-11-01

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

  10. 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  13. 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.

  14. Prospects for exploring molecular developmental processes in Haemonchus contortus.

    PubMed

    Nikolaou, S; Gasser, R B

    2006-07-01

    Haemonchus contortus of small ruminants is a parasitic nematode of major socio-economic importance world-wide. While there is considerable knowledge of the morphological changes which take place during the life cycle of H. contortus, very little is understood about the molecular and biochemical processes which govern developmental changes in the parasite. Recent technological advances and the imminent genomic sequence for H. contortus provide unique opportunities to investigate the molecular basis of such processes in parasitic nematodes. This article reviews molecular and biochemical aspects of development in H. contortus, reports on some recent progress on signal transduction molecules in this parasite and emphasises the opportunities that new technologies and the free-living nematode, Caenorhabditis elegans, offer for investigating developmental aspects in H. contortus and related strongylid nematodes, also in relation to developing novel approaches for control. PMID:16759659

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

    PubMed

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

    2016-06-14

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

  16. 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.

  17. [Bone marrow biopsy: processing and use of molecular techniques].

    PubMed

    Quintanilla-Martinez, L; Tinguely, M; Bonzheim, I; Fend, F

    2012-11-01

    The rapid technological development in diagnostic pathology, especially of immunohistochemical and molecular techniques, also has a significant impact on diagnostic procedures for the evaluation of bone marrow trephine biopsies. The necessity for optimal morphology, combined with preservation of tissue antigens and nucleic acids on one hand and the wish for short turnaround times on the other hand require careful planning of the workflow for fixation, decalcification and embedding of trephines. Although any kind of bone marrow processing has its advantages and disadvantages, formalin fixation followed by EDTA decalcification can be considered a good compromise, which does not restrict the use of molecular techniques. Although the majority of molecular studies in haematological neoplasms are routinely performed on bone marrow aspirates or peripheral blood cells, there are certain indications, in which molecular studies such as clonality determination or detection of specific mutations need to be performed on the trephine biopsy. Especially, the determination of B- or T-cell clonality for the diagnosis of lymphoid malignancies requires stringent quality controls and knowledge of technical pitfalls. In this review, we discuss technical aspects of bone marrow biopsy processing and the application of diagnostic molecular techniques. PMID:23085692

  18. 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.

  19. Molecular Ro-vibrational Collision Rates for Infrared Modeling of Warm Interstellar Gas from Full-dimensional Quantum Calculations

    NASA Astrophysics Data System (ADS)

    Stancil, Phillip

    We propose to compute accurate collisional excitation rate coefficients for rovibrational transitions of CS, SiO, SO, NO, H_2O, and HCN due to H_2, He, or H impact. This extends our previous grant which focused on 3- and 4-atom systems to 4- and 5-atom collision complexes, with dynamics to be performed on 6-9 dimensional potential energy surfaces (PESs). This work, which uses fully quantum mechanical methods for inelastic scattering and incorporates full-dimensional PESs, pushes beyond the state-of-the-art for such calculations, as recently established by our group for rovibrational transitions in CO-H_2 in 6D. Many of the required PESs will be computed as part of this project using ab initio theory and basis sets of the highest level feasible and particular attention will be given to the long range form of the PESs. The completion of the project will result in 6 new global PESs and state-to-state rate coefficients for a large range of initial rovibrational levels for temperatures between 1 and 3000 K. The chosen collision systems correspond to cases where data are limited or lacking, are important coolants or diagnostics, and result in observable emission features in the infrared (IR). The final project results will be important for the analysis of a variety of interstellar and extragalactic environments in which the local conditions of gas density, radiation field, and/or shocks drive the level populations out of equilibrium. In such cases, collisional excitation data are critical to the accurate prediction and interpretation of observed molecular IR emission lines in protoplanetary disks, star-forming regions, planetary nebulae, embedded protostars, photodissociation regions, etc. The use of the proposed collisional excitation data will lead to deeper examination and understanding of the properties of many astrophysical environments, hence elevating the scientific return from the upcoming JWST, as well as from current (SOFIA, Herschel, HST) and past IR missions

  20. Molecular barriers to processes of genetic reprogramming and cell transformation.

    PubMed

    Chestkov, I V; Khomyakova, E A; Vasilieva, E A; Lagarkova, M A; Kiselev, S L

    2014-12-01

    Genetic reprogramming by ectopic expression of transcription factor genes induces the pluripotent state in somatic cells. This technology provides an opportunity to establish pluripotent stem cells for each person, as well as to get better understanding of epigenetic mechanisms controlling cell state. Interestingly, some of the molecular processes that accompany somatic cell reprogramming in vitro are also characteristic for tumor manifestation. Thus, similar "molecular barriers" that control the stability of epigenetic state exist for both processes of pluripotency induction and malignant transformation. The reprogramming of tumor cells is interesting in two aspects: first, it will determine the contribution of epigenetic changes in carcinogenesis; second, it gives an approach to evaluate tumor stem cells that are supposed to form the entire cell mass of the tumor. This review discusses the key stages of genetic reprogramming, the similarity and difference between the reprogramming process and malignant transformation. PMID:25716723

  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. Estimate of massive-dimuon production via a Drell-Yan-type process in two-photon collisions

    SciTech Connect

    Sajjad Zahir, M.

    1981-11-01

    This paper presents a theoretical analysis and numerical estimate of the production of massive ..mu../sup +/..mu../sup -/+hadrons in ..gamma gamma.. collision. Although, from the theoretical point of view, the process might have some interesting possibilities, the numerical estimates show that the cross section is too small to be measured with nearly on-shell high-energy photons from either doubly tagged or untagged electrons considering the luminosity of the new generation of machines.

  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. 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.

  5. Processes involving electron capture and multiple ionization in collisions of fast H+ and He2+ ions with lead atoms

    NASA Astrophysics Data System (ADS)

    McCartney, P. C. E.; Shah, M. B.; Geddes, J.; Gilbody, H. B.

    1999-12-01

    A crossed-beam technique incorporating time-of-flight analysis and coincidence counting of the collision products has been used to study Pbq+ formation with q up to 8 in collisions between ground-state Pb atoms and H+ and He2+ ions within the range 50-600 keV amu-1. The separate cross sections for simple charge transfer, transfer ionization, and pure ionization leading to the formation of Pbq+ ions have been obtained and the relative importance of these processes has been established. Accurate measurements and rigorous theoretical descriptions of these multielectron processes in such heavy atoms are difficult and data are still very limited. The present measurements have been designed to extend our previous studies of multiple ionization of a few selected heavy metal atoms and to provide a further check on the extent to which the main collision processes can be described quantitatively in terms of simple models based on an independent electron description. In our previous work with Fe, Cu, and Ga atoms using the same experimental approach, we were able to describe the formation of multiply charged ions through both transfer ionization and pure ionization with a high degree of success using an independent electron model. However, the present results for Pb show that the success of this simple approach is much more limited for these much heavier atoms.

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

    PubMed

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

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

  7. CLASSICAL MODEL FOR ELECTRONICALLY NON-ADIABATIC COLLISION PROCESSES: RESONANCE EFFECTS IN ELECTRONIC-VIBRATIONAL ENERGY TRANSFER

    SciTech Connect

    Orel, Ann E.; Miller, William H.

    1980-11-01

    A recently developed classical model for electronically nonadiabatic collision processes is applied to electronic-vibrational energy transfer in a collinear atom~diatom system, A + BC(v=1) + A*+ BC(v=0), which closely resembles Br-H{sub 2}. This classical model, which treats electronic as well as heavy particle (i.e., translation, rotation, and vibration) degrees of freedom by classical mechanics, is found to describe the resonance features in this process reasonably well. The usefulness of the approach is that it allows one to extend standard Monte Carlo classical trajectory methodology to include electronically non-adiabatic processes in a dynamically consistent way,

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

    PubMed

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

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

  9. A Distonic Radical-Ion for Detection of Traces of Adventitious Molecular Oxygen (O2) in Collision Gases Used in Tandem Mass Spectrometers

    NASA Astrophysics Data System (ADS)

    Jariwala, Freneil B.; Hibbs, John A.; Weisbecker, Carl S.; Ressler, John; Khade, Rahul L.; Zhang, Yong; Attygalle, Athula B.

    2014-09-01

    We describe a diagnostic ion that enables rapid semiquantitative evaluation of the degree of oxygen contamination in the collision gases used in tandem mass spectrometers. Upon collision-induced dissociation (CID), the m/z 359 positive ion generated from the analgesic etoricoxib undergoes a facile loss of a methyl sulfone radical [•SO2(CH3); 79-Da] to produce a distonic radical cation of m/z 280. The product-ion spectrum of this m/z 280 ion, recorded under low-energy activation on tandem-in-space QqQ or QqTof mass spectrometers using nitrogen from a generator as the collision gas, or tandem-in-time ion-trap (LCQ, LTQ) mass spectrometers using purified helium as the buffer gas, showed two unexpected peaks at m/z 312 and 295. This enigmatic m/z 312 ion, which bears a mass-to-charge ratio higher than that of the precursor ion, represented an addition of molecular oxygen (O2) to the precursor ion. The exceptional affinity of the m/z 280 radical cation towards oxygen was deployed to develop a method to determine the oxygen content in collision gases.

  10. 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).

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

    PubMed

    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. PMID:22380231

  12. 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.

  13. The influence of antieigenvalues and antieigenvectors on the correlation between the polarizations of reagents and products of molecular collisions

    NASA Astrophysics Data System (ADS)

    de Miranda, Marcelo P.; Gordon, Sean D. S.; Aldegunde, Jesús

    2012-08-01

    This article raises and answers a question regarding the extent to which correlation between the angular momentum polarizations of reagents and products of a bimolecular collision is or is not uniform. The question is this: how markedly does product (j‧) polarization change when reagent (j) polarization is changed? Using canonical collision mechanisms theory, and the operator-trigonometric concepts of maximal turning angle, antieigenvalue, and antieigenvector, the authors arrive at the following answer: barring complete or nearly complete insensitivity of the collision to steric effects, one should expect a high degree of nonuniformity in two-, three- or four-vector correlations involving j and j‧.

  14. 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.

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

    SciTech Connect

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

    2013-03-25

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

  16. Large scale molecular dynamics modeling of materials fabrication processes

    SciTech Connect

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

    1994-02-01

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

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

    PubMed

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

    2007-06-01

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

  18. Absolute Doubly Differential Cross Sections for Ejection of Electrons in - and Five-Body Collisions of 20 TO 114-KEV Protons on Atomic and Molecular Hydrogen.

    NASA Astrophysics Data System (ADS)

    Kerby, George W., III

    A crossed-beam experiment was performed to detect ejected electrons from ground-state atomic and molecular hydrogen after collisions with 20- to 114-keV protons. Because a pure atomic hydrogen target is not readily attainable, a method has been devised which yields atomic to molecular hydrogen doubly differential cross section (DDCS) ratios. Since the molecular hydrogen DDCS's were independently measured, the atomic cross sections could be directly calculated. Absolute cross sections differential in electron energy and angle were measured for electron energies ranging from 1.5 to 400 eV and scattering angles from 15^circ to 165^circ with respect to the fast beam. Electrons and ions were energy analyzed by an electrostatic hemispherical analyzer, which has an energy resolution of 5% and is rotatable in the scattering plane about the collision center. Atomic hydrogen is produced by a radio-frequency discharge of the type devised by J. Slevin. Hydrogen gas effuses from a 1 mm diameter nozzle in a nearly cos theta distribution. The projectile beam intersects the thermal gas targets 4 mm below the tip of the nozzle. Dissociation fractions of 74% and atomic hydrogen densities of 7 times 10 ^{11} cm^ {-3} were typical. The fraction of dissociated hydrogen was measured by detecting the reduced 9-eV ion signal from the molecular target when the RF is on. This characteristic ion signal originates from the coulomb breakup of the molecule and dissociative channels of excited H _sp{2}{+}. An auxiliary experiment was performed to determine the target densities with the aid of a low-resolution magnetic mass spectrometer after the slow recoil ions were extracted from the collision volume by a weak electric field. Comparisons of the atomic cross sections are made with theories such as the classical-trajectory Monte Carlo (CTMC) method, the plane-wave Born approximation (PWBA) and the continuum-distorted-wave eikonal-initial-state (CDW-EIS) approximation.

  19. 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.

  20. RNA processing-associated molecular mechanisms of neurodegenerative diseases.

    PubMed

    Tang, Anna Y

    2016-08-01

    Dysfunctions of RNA processing and mutations of RNA binding proteins (RBPs) play a fundamental role in the pathogenesis of many neurodegenerative diseases. To elucidate the function of RNA processing and RBPs mutations in neuronal cells and to increase our understanding on the pathogenic mechanisms of neurodegeneration, I have reviewed recent advances on RNA processing-associated molecular mechanisms of neurodegenerative diseases, including RBPs-mediated dysfunction of RNA processing, dysfunctional microRNA (miRNA)-based regulation of gene expression, and oxidative RNA modification. I have focused on neurodegeneration induced by RBPs mutations, by dysfunction of miRNA regulation, and by the oxidized RNAs within neurons, and discuss how these dysfunctions have pathologically contributed to neurodegenerative diseases. The advances overviewed above will be valuable to basic investigation and clinical application of target diagnostic tests and therapies. PMID:26634851

  1. Rotational inelastic cross sections for OCS-Ar, OCS-He, OCS-H2 collisions - A comparison between theory and experiment. [applicable to interstellar processes

    NASA Technical Reports Server (NTRS)

    Broquier, M.; Picard-Bersellini, A.; Whitaker, B. J.; Green, S.

    1986-01-01

    The experimental determination of absorption line profiles for OCS nu3 vibrational transitions broadened by collisions with Ar, He, and H3 buffer gases is reported. The experimental method using diode laser spectroscopy in the five micron region is described. The data are compared with theoretical values obtained using intermolecular potentials previously suggested for these systems and infinite order sudden approximation molecular scattering calculations.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  3. Application of statistical process control to qualitative molecular diagnostic assays.

    PubMed

    O'Brien, Cathal P; Finn, Stephen P

    2014-01-01

    Modern pathology laboratories and in particular high throughput laboratories such as clinical chemistry have developed a reliable system for statistical process control (SPC). Such a system is absent from the majority of molecular laboratories and where present is confined to quantitative assays. As the inability to apply SPC to an assay is an obvious disadvantage this study aimed to solve this problem by using a frequency estimate coupled with a confidence interval calculation to detect deviations from an expected mutation frequency. The results of this study demonstrate the strengths and weaknesses of this approach and highlight minimum sample number requirements. Notably, assays with low mutation frequencies and detection of small deviations from an expected value require greater sample numbers to mitigate a protracted time to detection. Modeled laboratory data was also used to highlight how this approach might be applied in a routine molecular laboratory. This article is the first to describe the application of SPC to qualitative laboratory data. PMID:25988159

  4. Two Molecular Information Processing Systems Based on Catalytic Nucleic Acids

    NASA Astrophysics Data System (ADS)

    Stojanovic, Milan

    Mixtures of molecules are capable of powerful information processing [1]. This statement is in the following way self-evident: it is a hierarchically organized complex mixture of molecules that is formulating it to other similarly organized mixtures of molecules. By making such a statement I am not endorsing the extreme forms of reductionism; rather, I am making what I think is a small first step towards harnessing information processing prowess of molecules and, hopefully, overcoming some limitations of more traditional computing paradigms. There are different ideas on how to understand and use molecular information processing abilities and I will list some below. My list is far from inclusive, and delineations are far from clear-cut; whenever available, I will provide examples from our research efforts. I should stress, for a computer science audience that I am a chemist. Thus, my approach may have much different focus and mathematical rigor, then if it would be taken by a computer scientist.

  5. 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.

  6. 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.

  7. 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.

  8. 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).

  9. Vortex-Surface Collisions^

    NASA Astrophysics Data System (ADS)

    Conlisk, A. T.

    1998-11-01

    The interaction of vortices with solid surfaces occurs in many different situations including, but not limited to tornadoes, propeller wakes, flows over swept wings and missile forebodies, turbomachinery flows, blade-vortex interactions and tip vortex-surface interactions on helicopters. Often, parts of a system must operate within such flows and thus encounter these vortices. In the present paper we discuss the nature of a particular subset of interactions called ``collisions''. A ``collision'' is characterized by the fact that the core of the vortex is permanently altered; usually the core is locally destroyed. The focus is on fully three-dimensional collisions although two-dimensional collisions are discussed as well. Examples of collisions in helicopter aerodynamics and turbomachinery flows are discussed and the dynamics of the vortex core during a collision process are illustrated for a 90^o collision. ^Supported by the US Army Research Office

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

    PubMed

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

    2014-08-01

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

  11. 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.

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

    PubMed

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

    2015-07-01

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

  13. Optical probes of atomic and molecular decay processes.

    SciTech Connect

    Pratt, S. T.

    2008-01-01

    The study of molecular photoionization and photodissociation dynamics provides insight into the intramolecular mechanisms by which energy and angular momentum are exchanged and redistributed among the internal degrees of freedom of highly excited molecules and, more specifically, into the mechanisms that determine the decay pathways and resulting product-state distributions for the excited molecules. These mechanisms lie at the heart of one of the principal subjects of chemistry, that is, understanding and controlling the factors that govern the making and breaking of chemical bonds. The objective of this experimental research program is to elucidate these fundamental mechanisms and to provide useful prototypes for the development of a general qualitative understanding of their ramifications. In this program, the primary focus is on resonant processes in the ionization and dissociation continua, that is, on autoionization and predissociation. These processes are studied as a function of the electronic, vibrational, and rotational quantum numbers of the resonances, allowing a better understanding of their fundamental mechanisms. In the past three years, the primary emphasis of this experimental program has been on understanding the process of vibrational autoionization in Rydberg states of small polyatomic molecules. Vibrational autoionization corresponds to the decay of resonances above the ionization threshold into the continuum through the conversion of vibrational energy into electronic/translational energy of the highly excited/ejected electron. In polyatomic molecules, I am particularly interested in determining how this process depends on both the specific normal vibrational modes involved in the process and the electronic character of the resonances. In this program, the experimental approach relies on laser-based, double-resonance techniques to prepare the selected excited states in the molecules of interest, and on a variety of detection techniques to

  14. Molecular-state treatment of He sup + (2 p ) excitation through electron capture in He sup 2+ -H sub 2 collisions at low energies

    SciTech Connect

    Saha, B.C.; Lane, N.F. ); Kimura, M. Department of Physics, Rice University, Houston, Texas 77251 )

    1991-07-01

    We report the calculation of low-energy state-selective electron-capture cross sections in an {alpha}-particle collision with molecular hydrogen. The semiclassical molecular-orbital expansion method is used and electron translation effects are taken into account. The calculated He{sup +}(2{ital p}) formation cross sections are in good overall agreement with the recent measurements of Hoekstra {ital et} {ital al}. (J. Phys. B 22, L603 (1989)). However, the experimental cross sections show a pronounced plateau between {ital E}=0.7 and 2.0 keV/amu. In the same energy region the calculated results exhibit an oscillatory structure that arises from a combination of Landau-Zener and Rosen-Demkov oscillations.

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. Traveling-molecular-orbital-expansion studies of electron capture in collisions of fully stripped ions (Z = 6--9) with H and H/sub 2/

    SciTech Connect

    Kimura, M.; Lane, N.F.

    1987-01-01

    The traveling-molecular-orbital-expansion description has been employed to investigate electron capture in collisions of fully stripped ions (Z = 6--9) with H and H/sub 2/ in the energy regime from 0.14 to 9 keV/amu. The pseudopotential method was used to represent the H/sub 2/ /sup +/ core which enables us to treat the H/sub 2/ molecule as an atom having an ionization potential for H/sub 2/..-->..H/sub 2/ /sup +/. Features of the adiabatic potentials and corresponding radial coupling matrix elements at the ''reaction window'' as well as the quantitative results of relatively small-scale close-coupling calculations provide a rationale for the interpretation of a recent measurement for these systems by Meyer et al. (Phys. Rev. A 32, 3310 (1985)). For collisions of O/sup 8+/ with H, an extended molecular-orbital-expansion approach has been employed (i) to seek an understanding of the discrepancy evident in two recent independent large-scale calculations for n = 6 partial cross sections, and (ii) to obtain a quantitative test for the mechanism suggested in this paper.

  18. Li2 - Li reactive collisions at high initial j

    NASA Astrophysics Data System (ADS)

    Rosenberry, Mark; Marhatta, Ramesh; Stewart, Brian

    2014-05-01

    Inelastic molecular collisions are a fundamental process in astronomy and chemistry. We are studying collisions of 7Li2 with 7Li in a heat pipe oven, and looking for nuclear parity-changing events that signal a chemical reaction. Previous work in our group studied such reactions for low initial j; we are now working to collect data for the case of high initial j, where quasi-resonant phenomena occur. We have also incorporated new corrections for multiple collisions in our analysis. Quasi-classical trajectory calculations are used to model these reactions and extract physical insight.

  19. Theoretical studies relating to the interaction of radiation with matter: Atomic collision processes occurring in the presence of radiation fields

    NASA Astrophysics Data System (ADS)

    Berman, P. R.

    1981-09-01

    Work is reported in the areas of: Two-Level Atom and Radiation Pulse; Effects of Collisions on Atomic Coherences; Effects of Collisions on Zeeman Coherences; Collision Effects in Degenerate-Four-Wave-Mixing; and Dressed-Atom Picture in Laser Spectroscopy.

  20. DNA Polymerase δ Is Highly Processive with Proliferating Cell Nuclear Antigen and Undergoes Collision Release upon Completing DNA*S⃞

    PubMed Central

    Langston, Lance D.; O'Donnell, Mike

    2008-01-01

    In most cells, 100-1000 Okazaki fragments are produced for each replicative DNA polymerase present in the cell. For fast-growing cells, this necessitates rapid recycling of DNA polymerase on the lagging strand. Bacteria produce long Okazaki fragments (1-2 kb) and utilize a highly processive DNA polymerase III (pol III), which is held to DNA by a circular sliding clamp. In contrast, Okazaki fragments in eukaryotes are quite short, 100-250 bp, and thus the eukaryotic lagging strand polymerase does not require a high degree of processivity. The lagging strand polymerase in eukaryotes, polymerase δ (pol δ), functions with the proliferating cell nuclear antigen (PCNA) sliding clamp. In this report, Saccharomyces cerevisiae pol δ is examined on model substrates to gain insight into the mechanism of lagging strand replication in eukaryotes. Surprisingly, we find pol δ is highly processive with PCNA, over at least 5 kb, on Replication Protein A (RPA)-coated primed single strand DNA. The high processivity of pol δ observed in this report contrasts with its role in synthesis of short lagging strand fragments, which require it to rapidly dissociate from DNA at the end of each Okazaki fragment. We find that this dilemma is solved by a “collision release” process in which pol δ ejects from PCNA upon extending a DNA template to completion and running into the downstream duplex. The released pol δ transfers to a new primed site, provided the new site contains a PCNA clamp. Additional results indicate that the collision release mechanism is intrinsic to the pol3/pol31 subunits of the pol δ heterotrimer. PMID:18635534

  1. DNA polymerase delta is highly processive with proliferating cell nuclear antigen and undergoes collision release upon completing DNA.

    PubMed

    Langston, Lance D; O'Donnell, Mike

    2008-10-24

    In most cells, 100-1000 Okazaki fragments are produced for each replicative DNA polymerase present in the cell. For fast-growing cells, this necessitates rapid recycling of DNA polymerase on the lagging strand. Bacteria produce long Okazaki fragments (1-2 kb) and utilize a highly processive DNA polymerase III (pol III), which is held to DNA by a circular sliding clamp. In contrast, Okazaki fragments in eukaryotes are quite short, 100-250 bp, and thus the eukaryotic lagging strand polymerase does not require a high degree of processivity. The lagging strand polymerase in eukaryotes, polymerase delta (pol delta), functions with the proliferating cell nuclear antigen (PCNA) sliding clamp. In this report, Saccharomyces cerevisiae pol delta is examined on model substrates to gain insight into the mechanism of lagging strand replication in eukaryotes. Surprisingly, we find pol delta is highly processive with PCNA, over at least 5 kb, on Replication Protein A (RPA)-coated primed single strand DNA. The high processivity of pol delta observed in this report contrasts with its role in synthesis of short lagging strand fragments, which require it to rapidly dissociate from DNA at the end of each Okazaki fragment. We find that this dilemma is solved by a "collision release" process in which pol delta ejects from PCNA upon extending a DNA template to completion and running into the downstream duplex. The released pol delta transfers to a new primed site, provided the new site contains a PCNA clamp. Additional results indicate that the collision release mechanism is intrinsic to the pol3/pol31 subunits of the pol delta heterotrimer. PMID:18635534

  2. 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.

  3. 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

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  6. 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

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

    PubMed

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

    2014-05-01

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

  8. 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.

  9. CLASSICAL TRAJECTORY MODELS FOR ELECTRONICALLY NON-ADIABATIC COLLISION PROCESSES: A CLASSICAL VALENCE BOND MODEL FOR ELECTRONIC DEGREES OF FREEDOM

    SciTech Connect

    Miller, William H.; Orel, Ann E.

    1980-11-01

    A classical interpretation of the Dirac-Van Vleck spin version of valence bond theory is used 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-H{sub 2}, F-H{sub 2} , and O-H{sub 2} 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. The attractive feature of this model is that it is as eaaily applicable to electronically non-adiabatic processes as it is to adiabatic ones.

  10. Studies of fluctuation processes in nuclear collisions. Progress report, March 1, 1992--February 28, 1993

    SciTech Connect

    Ayik, S.

    1993-02-01

    Investigations of various aspects of heavy-ion collisions were carried out in the framework of the Boltzmann-Langevin Model (BLM). In a previous work, by projection the BLM onto a collective space, a memory-dependent collective transport model was reduced. This model was applied to thermal fission to investigate the influence of the memory effects on the fission dynamics. Some results of the calculations are presented. In addition a reduction of the relativistic BLM to a two-fluid model was carried out, and transport coefficients associated with fluid dynamical variables was carried out. Then this model was applied to investigate equilabration and fluctuation properties in a counter-streaming nuclear fluid.

  11. Studies of fluctuation processes in nuclear collisions. [Dept. of Physics, Tennessee Technological Univ. , Cookeville, Tennessee

    SciTech Connect

    Ayik, S.

    1993-02-01

    Investigations of various aspects of heavy-ion collisions were carried out in the framework of the Boltzmann-Langevin Model (BLM). In a previous work, by projection the BLM onto a collective space, a memory-dependent collective transport model was reduced. This model was applied to thermal fission to investigate the influence of the memory effects on the fission dynamics. Some results of the calculations are presented. In addition a reduction of the relativistic BLM to a two-fluid model was carried out, and transport coefficients associated with fluid dynamical variables was carried out. Then this model was applied to investigate equilabration and fluctuation properties in a counter-streaming nuclear fluid.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  13. Four-body charge transfer processes in collisions of bare projectile ions with helium atoms

    NASA Astrophysics Data System (ADS)

    Jana, S.; Mandal, C. R.; Purkait, M.

    2015-02-01

    Single-electron capture by a bare ion from a helium atom at intermediate and high energies in the framework of four-body distorted wave (DW-4B) approximation in both prior and post form has been considered. In the entrance channel, the initial bound state wave function is distorted by the incoming projectile ion, and the corresponding distortion is related to the Coulomb continuum states of the active electron and the residual target ion in the field of the projectile ion respectively. Continuum states of the active electron and the projectile ion in the field of the residual target ion are also included in the exit channel. It may be mentioned that the effect of dynamic electron correlation is explicitly taken into account through the complete perturbation potential. The total single-electron capture cross sections are obtained by summing over all contributions up to n = 3 shells and sub-shells respectively. In addition, the differential cross sections for alpha particle-helium collision are calculated at impact energies of 60, 150, 300, 450, and 630 keV amu-1, respectively. The cross sections exhibit a monotonically decreasing angular dependence, with clear peak structures around 0.1 to 0.2 mrad being found at low impact energies. The current theoretical results, both in prior and post forms of the transition amplitude for symmetric and asymmetric collision, are compared with the available theoretical and experimental results. Current computed results have been found to be satisfactory in comparison with other theoretical and experimental findings.

  14. 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.

  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. Detailed seismic velocity structure beneath the Hokkaido corner, NE Japan: Collision process of the forearc sliver

    NASA Astrophysics Data System (ADS)

    Kita, S.; Hasegawa, A.; Okada, T.; Nakajima, J.; Matsuzawa, T.; Katsumata, K.

    2010-12-01

    1. Introduction In south-eastern Hokkaido, the Kuril forearc sliver is colliding with the northeastern Japan arc due to the oblique subduction of the Pacific plate. This collision causes the formation of the Hidaka mountain range since the late Miocene (Kimura, 1986) and delamination of the lower-crust materials of the Kuril forearc sliver, which would be expected to descend into the mantle wedge below (e.g., Ito 2000; Ito and Iwasaki, 2002). In this study, we precisely investigated the three-dimensional seismic velocity structure beneath the Hokkaido corner to examine the collision of two forearcs in this area by using both of data from a dense temporary seismic network deployed in this area (Katsumata et al. [2006]) and those from the Kiban observation network, which covers the entire Japanese Islands with a station separation of 15-20 km. 2. Data and method The double-difference tomography method (Zhang and Thurber, 2003; 2006) was applied to a large number of arrival time data of 201,527 for P-waves and 150,963 for S-waves that were recorded at 125 stations from 10,971 earthquakes that occurred from 1999 to 2010. Grid intervals were set at 10 km in the along-arc direction, 12.5 km perpendicular to it, and 5-10 km in the vertical direction. 3. Results and discussion Inhomogeneous seismic velocity structure was clearly imaged in the Hokkaido corner at depths of 0-120 km. A high-velocity anomaly of P- and S- waves with a volume of 20 km x 90 km x 35km was detected just beneath the main zone of the Hidaka metamorphic belt at depths of 0-35 km. This high-velocity anomaly is continuously distributed from the depths of the mantle wedge to the surface. The western edge of the anomaly exactly corresponds to the Hidaka main thrust (HMT) at the surface. The highest velocity value in the anomaly corresponds to those of the uppermost mantle material (e.g. peridotite). The location of them at depths of 0-35km is also consistent with that of the Horoman-Peridotite belt, which

  17. Extracting Dwell Time Sequences from Processive Molecular Motor Data

    PubMed Central

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

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2016-06-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  1. 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.

  2. Direct numerical simulations of collision efficiency of cohesive sediments

    NASA Astrophysics Data System (ADS)

    Zhang, Jin-Feng; Maa, Jerome P.-Y.; Zhang, Qing-He; Shen, Xiao-Teng

    2016-09-01

    A clear understanding of the collision efficiency of cohesive sediment particles is critical for more accurate simulation of the flocculation processes. It is difficult, if not impossible, to carry out laboratory experiments to determine the collision efficiency for small particles. Direct Numerical Simulation (DNS) is a relatively feasible approach to describe the motion of spherical particles under gravity in calm water, and thus, to study the collision efficiency of these particles. In this study, the Lattice Boltzmann (LB) method is used to calculate the relative trajectories of two approaching particles with different ratios of sizes and densities. Results show that the inter-molecular forces (i.e., van der Waals attractive force, electrostatic repulsive/attractive force, and displacement force), which are usually neglected in previous studies, would affect the trajectories, and thus, lead to an overestimation of the collision efficiency. It is found that to increase the particle size ratio from 0.1 to 0.8 only slightly increases the collision efficiency, since the force caused by fluid-solid interaction between these two particles is reduced. To increase the submerged particle density ratio from 1 to 22, however, would significantly decrease the collision efficiency. Earlier analytical formulations of collision efficiency, which only consider the effects of particle size ratio, have significantly overestimated the collision efficiency (change from 0.01 to 0.6) when the particle size ratio is around 0.5.

  3. Molecular processes from the AGB to the PN stage

    NASA Astrophysics Data System (ADS)

    García-Hernández, D. Anibal

    2012-08-01

    Many complex organic molecules and inorganic solid-state compounds have been observed in the circumstellar shell of stars (both C-rich and O-rich) in the transition phase between Asymptotic Giant Branch (AGB) stars and Planetary Nebulae (PNe). This short (~102-104 years) phase of stellar evolution represents a wonderful laboratory for astrochemistry and provides severe constraints on any model of gas-phase and solid-state chemistry. One of the major challenges of present day astrophysics and astrochemistry is to understand the formation pathways of these complex organic molecules and inorganic solid-state compounds (e.g., polycyclic aromatic hydrocarbons, fullerenes, and graphene in the case of a C-rich chemistry and oxides and crystalline silicates in O-rich environments) in space. In this review, I present an observational review of the molecular processes in the late stages of stellar evolution with a special emphasis on the first detections of fullerenes and graphene in PNe.

  4. 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.

  5. S((1)D) + ortho-D2 Reaction Dynamics at Low Collision Energies: Complementary Crossed Molecular Beam Experiments and Theoretical Investigations.

    PubMed

    Lara, Manuel; Chefdeville, Simon; Larregaray, Pascal; Bonnet, Laurent; Launay, Jean-Michel; Costes, Michel; Naulin, Christian; Bergeat, Astrid

    2016-07-14

    The excitation function of the S((1)D) + D2 reaction was determined in a crossed molecular beam apparatus for collision energies ranging from 1817 to 47 J mol(-1) in the near-cold regime. A very good overall agreement was found between experimental data and the theoretical results obtained using the ab initio potential energy surface built by Ho and coworkers and different methods: time-independent quantum dynamics (QM), semiclassical mean potential capture theory (sc-MPCT), and quasi-classical trajectories (QCT). The general trend of the experimental excitation function is well reproduced in most of the range by a simple capture calculation with an R(-6) dispersion potential. The present results are discussed in the light of previous studies on the isotopic variants S((1)D) + H2 and HD. PMID:26986452

  6. Dissociation of multicharged CO molecular ions produced in collisions with 97-MeV Ar14+: Total-kinetic-energy distributions

    NASA Astrophysics Data System (ADS)

    Sampoll, G.; Watson, R. L.; Heber, O.; Horvat, V.; Wohrer, K.; Chabot, M.

    1992-03-01

    Transient molecular ions of COq+ (where q=2-7) were produced in single collisions of 97-MeV Ar14+ projectiles with neutral CO molecules. The resulting dissociation products were identified by coincidence time-of-flight spectroscopy in which the time of flight of the first ion to reach the detector and the time difference between the first ion and its partner were recorded event by event. An iterative matrix-transformation procedure was employed to convert the time-difference spectra for the prominent dissociation channels into total-kinetic-energy distributions. Analysis of the total-kinetic-energy distributions and comparisons with the available data for CO2+ and CO3+ from synchrotron radiation experiments led to the conclusion that ionization by Ar-ion impact populates states having considerably higher excitation energies than those accessed by photoionization.

  7. Dissociation of multicharged CO molecular ions produced in collisions with 97-MeV Ar14+: Dissociation fractions and branching ratios

    NASA Astrophysics Data System (ADS)

    Wohrer, K.; Sampoll, G.; Watson, R. L.; Chabot, M.; Heber, O.; Horvat, V.

    1992-10-01

    Data on the production and dissociation of COQ+ molecular ions (where Q=1 through 7) obtained by ion-ion coincidence time-of-flight measurements were analyzed to determine production yields, dissociation fractions, and branching ratios. A detailed comparison of the dissociation fractions for CO+ and CO2+ for several collision systems in the same perturbative regime revealed them to be quite similar, whereas the dissociation fraction for CO+ produced by valence-electron photoionization is a factor of 1.8 to 3.6 larger. The results for Q>=2 indicated a preference for dissociation channels leading to symmetric or nearly symmetric charge division. An enhancement of the total ionization yields for Q>4 was observed, and it suggests that electron transfer followed by LMM Auger decay plays an important role in determining the final charges of the dissociation products.

  8. Photoinduced Charge and Energy Transfer Processes in Molecular Aggregates

    SciTech Connect

    John F. Endicott

    2009-10-20

    This project involved the experimental probing of the electronic excited states generated by photoinduced (center-to-center) electron and energy transfer processes in several classes of transition metal donor/acceptor (D/A) complexes. Some of the general properties inferred from these studies should be useful in the design of new systems for energy conversion applications. Pursuit of the project goals has involved the determination of electron transfer efficiencies and the detailed study of variations in the electronic spectra of D/A complexes. This has resulted in the study of some very fundamental issues of photoinduced charge transfer and the identification of some of the constraints on its efficiency. The experimental studies of the competition between the degradative non-radiative unimolecular relaxation of transition metal excited states and their transfer of charge from these excited states to external acceptors have involved a range of techniques such as transient decay kinetics, photoacoustic calorimetry and transient or stationary state spectroscopy. The substrates synthesized for these studies were selected to provide model systems, or series of model systems to probe the validity of models of electronic excited states and their reactivity. The work during the last few years has focused largely, but not exclusively, on the use of emission spectral band shapes to probe the properties of charge transfer (CT) excited states. Bandshape variations are one of the very few approaches for systematically probing electronic excited states and good band shape resolution is necessary in order to gain information about the structural variations that correlate with excited state reactivity. Differences in molecular structure correlate with differences in chemical reactivity, and the variations in emission bandshapes are well known to relate to variations in the molecular structural differences between the excited and ground electronic states. However, it is has been

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  10. 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

  11. 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

  12. Theoretical studies relating to the interaction of radiation with matter: Atomic collision processes occurring in the presence of radiation fields

    NASA Astrophysics Data System (ADS)

    1980-10-01

    Work is reported in the areas of: (1) collisionally-aided radiative excitation; (2) model potential calculations in atom-field-radiation systems; (3) coherence effects in radiative collisions; (4) two level atom radiation pulse; (5) resonance fluorescence in three level systems; (6) modulation spectroscopy; and (7) effects of collisions on atomic coherences.

  13. Theoretical studies relating to the interaction of radiation with matter: Atomic collision processes occurring in the presence of radiation fields

    NASA Astrophysics Data System (ADS)

    Berman, P. R.

    1983-09-01

    Work is reported in the areas of: Saturation Spectroscopy; Heating and Cooling via Laser-Assisted Collisions; Creation of Electronic State Coherences via Laser-Assisted Collisions; Two-Level Atom Plus Radiation Pulse; Photon as Catalyst; and Collisional Effects in Four-Wave Mixing.

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

    NASA Astrophysics Data System (ADS)

    Hsieh, Chang-Tsang William

    In the present research project a systematic study of the collision-induced infrared absorption (CIA) spectra of the binary mixtures of H_2 - D_2 in the region of the double fundamental vibrations of H_2 and D_2, and H_2 - Ar in the fundamental band of H_2, and of pure HD in its fundamental and first overtone regions was undertaken. The experiments were carried out with a 2.0 m high-pressure low-temperature transmission-type absorption cell at 77, 201 and 296 K at total gas densities up to 550 amagat. Infrared prism and grating spectrometers equipped with a microprocessor -controlled stepping motor were used to record the spectra. All the experimental results obtained represent first-time observations in collision-induced absorption. Collision-induced infrared absorption spectra of the double transitions of H_2(v=1>=ts 0) and D_2(v=1>=ts 0) have been observed at 77 and 201 K in the spectral region 7000-8000 cm^{-1} for total gas densities up to 550 amagat with a partial gas density ratio of 1:1 of H_2 and D_2. The observed spectra are interpreted in terms of the transitions, Q_1(J) of H_2+Q_1(J) of D _2, Q_1(J) of H_2+S _1(J) of D_2, S_1(J) of H_2 + Q_1(J) of D_2, and S_1(J) of H_2 + S_1(J) of D_2 for J = 0 and 1 for H _2 and J = 0, 1, and 2 for D_2. Analysis of the experimental absorption profiles was carried out using appropriate lineshape functions. The absorption coefficients, lineshape parameters, etc., are obtained from the analysis. Collision-induced enhancement absorption spectra of the fundamental band of H_2 in H_2 - Ar mixtures were recorded at room temperature for a base density of 72 amagat of H_2 for several partial densities of Ar up to 440 amagat. Hexadecapole-induced U transitions, U_1(1), U_1(2), Q_1(0)+U _0(1), and Q_1(1) + U_0(1) have been identified in the spectral region 5400 -6200 cm^{-1}. A "cage" model has been proposed to account for the double transitions of H_2 - H_2 in the H _2 - Ar enhancement spectra. From the analysis of the

  15. Dipolar degrees of freedom and isospin equilibration processes in heavy ion collisions

    NASA Astrophysics Data System (ADS)

    Papa, M.; Berceanu, I.; Acosta, L.; Amorini, F.; Agodi, C.; Anzalone, A.; Auditore, L.; Cardella, G.; Cavallaro, S.; Chatterjee, M. B.; De Filippo, E.; Francalanza, L.; Geraci, E.; Grassi, L.; Gnoffo, B.; Han, J.; La Guidara, E.; Lanzalone, G.; Lombardo, I.; Maiolino, C.; Minniti, T.; Pagano, A.; Pagano, E. V.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Rosato, E.; Russotto, P.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.

    2015-04-01

    The dipolar degrees of freedom on the 48Ca+27Al system at 40 MeV/nucleon have been investigated for the first time with the 4 π multidetector CHIMERA. The global variable was measured for well-reconstructed events in binary dissipative processes. Both the close link with isospin equilibration processes and its insensitivity to later statistical hot source decays have been discussed. This latter feature provides the opportunity to investigate globally and exclusively the dynamics of the equilibration processes. At this first level of investigation the experimental evidence, supported by the study of the reference system 27Al+40Ca and the auxiliary one 27Ca+48Ca , substantially agree with the CoMD-III calculations by describing the isovectorial forces through stiffness parameter values γ ≈0.8 -1.2 .

  16. 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.

  17. Charged Higgs and neutral Higgs pair production of the weak gauge boson fusion process in electron-positron collisions

    NASA Astrophysics Data System (ADS)

    Morozumi, Takuya; Tamai, Kotaro

    2013-09-01

    Pair production of the neutral and charged Higgs bosons is a unique process that is a signature of the two-Higgs-doublet model. In this paper, we study the pair production and decays of the Higgses in the neutrinophilic two-Higgs-doublet model. The pair production occurs through the W and Z gauge boson fusion process. In the neutrinophilic model, the vacuum expectation value (VEV) of the second Higgs doublet is small and is proportional to the neutrino mass. The smallness of VEV is associated with the approximate global U(1) symmetry, which is slightly broken. Therefore, there is a suppression factor for the U(1) charge breaking process. The second Higgs doublet has U(1) charge; its single production from gauge boson fusion violates the U(1) charge conservation and is strongly suppressed. In contrast to the single production, the pair production of the Higgses conserves U(1) charge and the approximate symmetry does not forbid it. To search for the pair productions in a collider experiment, we study the production cross section of a pair of charged Higgs and neutral Higgs bosons in e^+ e^- collisions with a center of energy from 600 GeV to 2000 GeV. The total cross section varies from 10^{-4} fb to 10^{-3} fb for the degenerate (200 GeV) charged and neutral Higgs mass case. The background process to the signal is the gauge boson pair W^+ + Z production and their decays. We show that the signal over background ratio is about 2-3% by combining the cross section ratio with ratios of branching fractions.

  18. Collision Energy Dependence of Defect Formation in Graphene

    SciTech Connect

    Mao, Fei; Zhang, Chao; Zhang, Yanwen; Zhang, Fenf-Shou

    2012-01-01

    Molecular dynamics simulations are performed using an empirical potential to simulate the collision process of an energetic carbon atom hitting a graphene sheet. According to the different impact locations within the graphene sheet, the incident threshold energies of different defects caused by the collision are determined to be 22 eV for a single vacancy, 36 eV for a divacancy, 60 eV for a Stone-Wales defect, and 65 eV for a hexavacancy. Study of the evolution and stability of the defects formed by these collisions suggests that the single vacancy reconstructs into a pentagon pair and the divacancy transforms into a pentagon-octagon-pentagon configuration. The displacement threshold energy in graphene is investigated by using the dynamical method, and a reasonable value 22.42 eV is clarified by eliminating the heating effect induced by the collision.

  19. 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.

  20. New line narrowing effects in the infrared collision-induced spectra of molecular hydrogens in liquid neon.

    PubMed

    Herrebout, W A; van der Veken, B J; Kouzov, A P

    2008-08-29

    The first spectroscopic observation of the relative (solute-solute) diffusion in a fluid environment is reported. New, unusually sharp Q1q(J) lines developing against the diffuse background in the collision-induced fundamental IR bands of hydrogen isotopomers (H2, D2, and HD) dissolved in liquid Ne (T approximately 25 K) are studied as functions of the solute concentration x. In all cases, the Q1q intensity parabolically scales with x, accompanied by a striking narrowing of the line shapes. The narrowing, as revealed by the p-H2 solution studies, is due to a faster growth with x of the sharper solute-solute induced component of the single Q1q(0) line. The latter as well as other observed solute-solute lines are strongly narrowed by fast velocity decorrelations and are signatures of microscopic-scale diffusion. Also, a first observation of the solute-solvent induced J-->J + 4 transitions is reported. PMID:18851607

  1. 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.

  2. 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

  3. 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.

  4. Nonlinear Breit-Wheeler process in the collision of a photon with two plane waves

    NASA Astrophysics Data System (ADS)

    Wu, Yuan-Bin; Xue, She-Sheng

    2014-07-01

    The nonlinear Breit-Wheeler process of electron-positron pair production off a probe photon colliding with a low-frequency and a high-frequency electromagnetic wave that propagate in the same direction is analyzed. We calculate the pair-production probability and the spectra of the created pair in the nonlinear Breit-Wheeler processes of pair production off a probe photon colliding with two plane waves or one of these two plane waves. The differences of these two cases are discussed. We evidently show, in the two-wave case, the possibility of Breit-Wheeler pair production with simultaneous photon emission into the low-frequency wave and the high multiphoton phenomena: (i) Breit-Wheeler pair production by absorption of the probe photon and a large number of photons from the low-frequency wave, in addition to the absorption of one photon from the high-frequency wave; (ii) Breit-Wheeler pair production by absorption of the probe photon and one photon from the high-frequency wave with simultaneous emission of a large number of photons into the low-frequency wave. The phenomenon of photon emission into the wave cannot happen in the one-wave case. Compared with the one-wave case, the contributions from high multiphoton processes are largely enhanced in the two-wave case. The results presented in this article show a possible way to access the observations of the phenomenon of photon emission into the wave and high multiphoton phenomenon in Breit-Wheeler pair production even with the laser-beam intensity of order 1018 W/cm2.

  5. Cold collisions between boson or fermion molecules

    SciTech Connect

    Kajita, Masatoshi

    2004-01-01

    We theoretically investigate collisions between electrostatically trapped cold polar molecules and compare boson and fermion isotopes. Evaporative cooling seems possible for fermion molecules as the ratio of the collision loss cross section to the elastic collision cross section (R) gets smaller as the molecular temperature T lowers. With boson molecules, R gets larger as T lowers, which makes evaporative cooling difficult. The elastic collision cross section between fermion molecules can be larger than that for boson molecules with certain conditions.

  6. 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.

  7. Recent progress in some exclusive and semi-exclusive processes in proton-proton collisions

    NASA Astrophysics Data System (ADS)

    Szczurek, Antoni; Cisek, Anna; Łuszczak, Marta; Schäfer, Wolfgang

    2016-07-01

    We present the main results of our recent analyses of exclusive production of vector charmonia (J/ψ and ψ') in kt-factorization approach and for γγ production of charged dilepton pairs in exclusive and semiinclusive processes in a new approach, similar in spirit to kt-factorization. The results for charmonia are compared with recent results of the LHCb collaboration. We include some helicity flip contributions and quantify the effect of absorption correction. The effect of cc̅ wave function is illustrated. We present uncertainties related to F2 structure function which are the main ingredient of the approach. Our results are compared with recent CMS data for dilepton production with lepton isolation cuts imposed.

  8. 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.}

  9. Kinematically complete study of electron transfer and rearrangement processes in slow Ar16 +-Ne collisions

    NASA Astrophysics Data System (ADS)

    Xue, Y.; Ginzel, R.; Krauß, A.; Bernitt, S.; Schöffler, M.; Kühnel, K. U.; López-Urrutia, J. R. Crespo; Moshammer, R.; Cai, X.; Ullrich, J.; Fischer, D.

    2014-11-01

    The complete kinematics of single- and double-electron capture from neon to Ar16 + was measured with a reaction microscope at a projectile energy of 3.2 keV/u (velocity vp=0.36 a.u.). Not only the change of the electronic binding energies (the Q value) and the projectile scattering angles, but also (in the case of auto-ionization) the three-dimensional momentum vectors of the emitted electrons were determined. For single-electron capture, the Q -value spectrum shows strong population of both n =7 and 8 states on the projectile, and weak contributions to n =6 and 9 are also observed. In the case of double-electron capture, auto-ionizing double capture (ADC) dominates and the populations of (n ,n') =(5 ,7 ) ,(6 ,6 ),(6 ,7 ) and (6 ,8 ) are observed, while true double capture (TDC) populates the (5 ,7 ) state and asymmetric states of (5 ,n') with n'>10 . The experimental cross sections for Auger decay with the electron energy Ee plotted as a function of the Q value suggest the occurrence of target excitation accompanying the population of configurations (5 ,7 ) and (6 ,6 ) . No essential difference is found in the differential cross sections for ADC and TDC, and the angular distributions suggest that two-step processes dominate the double capture.

  10. 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.

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

    SciTech Connect

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

    1998-06-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    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.

  14. 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.

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

    PubMed

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

    2014-12-01

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

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

    PubMed

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

    2014-05-15

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

  17. Charge exchange and dissociative processes in collisions of slow He{sup 2+} ions with H{sub 2}O molecules

    SciTech Connect

    Seredyuk, B.; McCullough, R.W.; Tawara, H.; Gilbody, H.B.; Bodewits, D.; Hoekstra, R.; Tielens, A.G.G.M.; Sobocinski, P.; Pesic, D.; Hellhammer, R.; Sulik, B.; Stolterfoht, N.; Abu-Haija, O.; Kamber, E.Y.

    2005-02-01

    Experimental and theoretical studies of one-electron capture in collisions of He{sup 2+} ions with H{sub 2}O molecules have been carried out in the range 0.025-12 keV amu{sup -1} corresponding to typical solar wind velocities of 70-1523 km s{sup -1}. Translational energy spectroscopy (TES), photon emission spectroscopy (PES), and fragment ion spectroscopy were employed to identify and quantify the collision mechanisms involved. Cross sections for selective single electron capture into n=1, 2, and 3 states of the He{sup +} ion were obtained using TES while PES provided cross sections for capture into the He{sup +}(2p) and He{sup +}(3p) states. Our model calculations show that He{sup +}(n=2) and He{sup +}(n=3) formation proceeds via a single-electron process governed by the nucleus-electron interaction. In contrast, the He{sup +}(1s) formation mechanism involves an exothermic two-electron process driven by the electron-electron interaction, where the potential energy released by the electron capture is used to remove a second electron thereby resulting in fragmentation of the H{sub 2}O molecule. This process is found to become increasingly important as the collision energy decreases. The experimental cross sections are found to be in reasonable agreement with cross sections calculated using the Demkov and Landau-Zener models.

  18. 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. PMID:21434638

  19. 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.

  20. 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)

  1. 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.

  2. Atmospheric processes on ice nanoparticles in molecular beams

    PubMed Central

    Fárník, Michal; Poterya, Viktoriya

    2014-01-01

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

  3. Linear Collisions

    ERIC Educational Resources Information Center

    Walkiewicz, T. A.; Newby, N. D., Jr.

    1972-01-01

    A discussion of linear collisions between two or three objects is related to a junior-level course in analytical mechanics. The theoretical discussion uses a geometrical approach that treats elastic and inelastic collisions from a unified point of view. Experiments with a linear air track are described. (Author/TS)

  4. 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

  5. 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.

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

    PubMed

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

    2015-12-17

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

  7. 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.

  8. 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.

  9. 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

  10. Post-processing interstitialcy diffusion from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  11. On efficiency of collisions` simulation via particles-in-cells technique

    SciTech Connect

    Ovchenkov, P.A.; Sigov, Yu.S.

    1995-12-31

    Macro-particle technique is widely used to simulate kinetic processes in plasmas and plasma-like media. The common feature of various versions of this technique is tracing phase particles trajectories and detection of macro-characteristics system under modelling as average by particles band. The method is rather costly from the point of view of computer resources needed (as compared with flid calculations) but it permits to simulate complex kinetic processes in cases whet their precise theoretical description is impossible. In particular, the PIC technique allows to simulate spatial-nonuniform (SNU) non-equilibrium systems with self-consistent fields. The pair collisions between macro-particles are often used to model collisions in the frame of particle simulation technique. In so doing the SNU problems are not eliminated. By {open_quotes}pair collisions{close_quotes} we mean the collisions` simulation techniques witch is characterize by use of a collision act between two macro-particles. Such a method is commonly used in molecular dynamic technique. The collision can be treated as either determinate (solid sphere technique) or probabilistic one. There with, as the second interaction agent can be used both the same particle and a hypotetic {open_quotes}average{close_quotes} particle with properties derived from averaging over particles` ensemble. In the first case the technique must include the procedure of choice of pairs for collisions, the second one must include some averaging procedure. In this paper we propose one more method of pair collisions.

  12. 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

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

    PubMed

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

    2014-03-01

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

  14. Singlet molecular oxygen generated in dark biological process.

    PubMed

    Di Mascio, Paolo; Medeiros, Marisa H G

    2014-10-01

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

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

    SciTech Connect

    Professor Francisco Zaera

    2007-08-09

    The main goal of this project had been to use model systems to correlate selectivities in partial oxidation catalysis with the presence of specific sites on the surface of the catalyst. Extensive work was performed this year on characterizing oxygen-treated nickel surfaces by chemical means. Specifically, the surface chemistry of ammonia coadsorbed with atomic oxygen on Ni(110) single-crystal surfaces was studied by temperature-programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). It was determined that at intermediate oxygen coverages direct ammonia adsorption on nickel sites is suppressed, but a new high-temperature reaction regime is generated at 400 K where NHx surface fragments are rehydrogenated concurrently with the production of water and molecular hydrogen. The extensive isotope scrambling and hydrogen transfer seen from nitrogen- to oxygen-containing surface intermediates, and the optimum yields seen for this 400 K state at intermediate oxygen coverages, strongly suggest the direct interaction of the adsorbed ammonia with oxygen atoms at the end of the –Ni–O- rows that form upon reconstruction of the surface. Hydrogen transfer between ammonia and oxygen appears to take place directly via hydrogen bonding, and to be reversible but biased towards water formation. An equilibrium is reached between the produced water and the reacting surface oxygen and hydrogen. The strong influence of the OH surface groups on the thermal chemistry of the adsorbed ammonia was interpreted in terms of the adsorbing geometry of the OH groups on the surface, and of hydrogen bonding between adsorbed OH and NH3 species. In terms of alcohol reactivity, the adsorption of 2-iodoethanol, a precursor for the preparation of 2-hydroxyethyl and oxametallacycle surface species, was found to lead to two configurations involving either just the iodine atom or both iodine and hydroxyl ends of the molecule. A complex chemical behavior starts around 140 K with the

  16. 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.

  17. 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.

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

    SciTech Connect

    Hebner, G.A.

    1998-10-14

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

  19. Ion Collision, Theory

    SciTech Connect

    Shukla, Anil K.

    2013-09-11

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

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

    PubMed

    Keil, Matthias S

    2015-10-01

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

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

    PubMed Central

    Keil, Matthias S.

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  3. Low processivity for DNA translocation by the ISWI molecular motor.

    PubMed

    Eastlund, Allen; Al-Ani, Gada; Fischer, Christopher J

    2015-10-01

    The motor protein ISWI (Imitation SWItch) is the conserved catalytic ATPase domain of the ISWI family of chromatin remodelers. Members of the ISWI family are involved in regulating the structure of cellular chromatin during times of transcription, translation, and repair. Current models for the nucleosome repositioning activity of ISWI and other chromatin remodelers require the translocation of the remodeling protein along double-stranded DNA through an ATP-dependent mechanism. Here we report results from spectrofluorometric stopped-flow experiments which demonstrate that ISWI displays very low processivity for free DNA translocation. By combining these results with those from experiments monitoring the DNA stimulated ATPase activity of ISWI we further demonstrate that the DNA translocation by ISWI is tightly coupled to ATP hydrolysis. The calculated coupling efficiency of 0.067±0.018 ATP/ISWI/bp is seemingly quite low in comparison to similar DNA translocases and we present potential models to account for this. Nevertheless, the tight coupling of ATP hydrolysis to DNA translocation suggests that DNA translocation is not energetically rate limiting for nucleosome repositioning by ISWI. PMID:26116984

  4. Atomic and Molecular Processes in the Solar System and Planetary Atmospheres:. AN Overview and Some Examples

    NASA Astrophysics Data System (ADS)

    Cravens, T. E.

    This chapter provides a brief summary of the overall role of atomic and molecular (ATM) processes in solar system environments and a few examples of Alex Dalgarno's contributions. The bulk of the chapter is devoted to the role of ion-neutral collisional processes at comet Halley and at Saturn's satellites Enceladus and Titan.

  5. Manipulating the proton transfer process in molecular complexes: synthesis and spectroscopic studies.

    PubMed

    Panja, Sumit Kumar; Dwivedi, Nidhi; Saha, Satyen

    2016-08-01

    The proton transfer process in carefully designed molecular complexes has been investigated directly in the solid and solution phase. SCXRD studies have been employed to investigate the N-H-O bonding interaction sites of the molecular complexes, with additional experimental support from FTIR and Raman spectroscopic studies, to gain information on the relative position of hydrogen in between the N and O centers. Further, the proton transfer process in solution is studied using UV-Visible spectroscopy through monitoring the intramolecular charge transfer (ICT) process in these molecular complexes, which is primarily governed by the number of electron withdrawing groups (nitro groups) on proton donor moieties (NP, DNP and TNP). It is found that the magnitude of the ICT process depends on the extent of proton transfer, which on the other hand depends on the relative stabilities of the constituent species (phenolate species). A correlation is observed between an increase in the number of nitro groups and an increase in the melting point of the molecular complexes, indicating the enhancement of ionic character due to the proton transfer process. The aliphatic H-bonding is identified and monitored using (1)H-NMR spectroscopy, which reveals that the identity of molecular complexes in solution interestingly depends on the extent of proton transfer, in addition to the nature of the solvents. The aliphatic C-H-O H-bonding interaction between the oxygen atom of the nitro group and the alkyl hydrogen in piperidinium was also found to play a significant role in strengthening the primary interaction involving a hydrogen transfer process. The conductivity of the molecular complexes increases with an increase in the number of nitro groups, indicating the enhancement in ionic character of the molecular complexes. PMID:27424765

  6. Capture, ionization, and pair-production processes in relativistic heavy-ion collisions in the 1-GeV/nucleon energy range

    NASA Astrophysics Data System (ADS)

    Belkacem, A.; Gould, Harvey; Feinberg, B.; Bossingham, R.; Meyerhof, W. E.

    1997-10-01

    The cross sections for capture, ionization, capture from pair production, and free pair production were measured for 0.96-GeV/nucleon U92+ and 0.405-, 0.96-, and 1.3-GeV/nucleon La57+ ions incident on Au, Ag, and Cu targets. The cross sections for capture from pair production, free pair production, ionization, and total capture (the sum of capture from pair production, radiative electron capture, and nonradiative capture) are analyzed as a function of collision energy, projectile, and target atomic numbers. We find that, when the collision energy is increased from 0.405 GeV/nucleon to 1.3 GeV/nucleon, the capture from pair production and the free pair production cross sections increase by almost a factor of 6, while the capture cross section decreases by two orders of magnitude. The ionization cross section is found to vary very weakly with the collision energy in the 1-GeV/nucleon energy range. We found a dependence of free pair production cross sections on the target and projectile atomic number to be close to Z2, characteristic of an ionizationlike process. We also found a dependence of the capture from pair production cross sections on the target atomic number to be usually steeper than Z2t, and on the projectile atomic number, somewhat steeper than the Z5p, characteristic of a capturelike process. Theory and experiment are in some disagreement for capture from pair production, and free pair production, cross sections, but are in general agreement for the other capture processes and for ionization.

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

    PubMed Central

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

    2009-01-01

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

  8. 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.

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

    PubMed

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

    2014-06-01

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

  10. 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.

  11. 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.

  12. On the filtering and processing of dust by planetesimals. I. Derivation of collision probabilities for non-drifting planetesimals

    NASA Astrophysics Data System (ADS)

    Guillot, Tristan; Ida, Shigeru; Ormel, Chris W.

    2014-12-01

    Context. Circumstellar disks are known to contain a significant mass in dust ranging from micron to centimeter size. Meteorites are evidence that individual grains of those sizes were collected and assembled into planetesimals in the young solar system. Aims: We assess the efficiency of dust collection of a swarm of non-drifting planetesimals with radii ranging from 1 to 103 km and beyond. Methods: We calculate the collision probability of dust drifting in the disk due to gas drag by planetesimal accounting for several regimes depending on the size of the planetesimal, dust, and orbital distance: the geometric, Safronov, settling, and three-body regimes. We also include a hydrodynamical regime to account for the fact that small grains tend to be carried by the gas flow around planetesimals. Results: We provide expressions for the collision probability of dust by planetesimals and for the filtering efficiency by a swarm of planetesimals. For standard turbulence conditions (i.e., a turbulence parameter α = 10-2), filtering is found to be inefficient, meaning that when crossing a minimum-mass solar nebula (MMSN) belt of planetesimals extending between 0.1 AU and 35 AU most dust particles are eventually accreted by the central star rather than colliding with planetesimals. However, if the disk is weakly turbulent (α = 10-4) filtering becomes efficient in two regimes: (i) when planetesimals are all smaller than about 10 km in size, in which case collisions mostly take place in the geometric regime; and (ii) when planetary embryos larger than about 1000 km in size dominate the distribution, have a scale height smaller than one tenth of the gas scale height, and dust is of millimeter size or larger in which case most collisions take place in the settling regime. These two regimes have very different properties: we find that the local filtering efficiency xfilter,MMSN scales with r- 7/4 (where r is the orbital distance) in the geometric regime, but with r- 1/4 to r1/4 in

  13. 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

  14. 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.

  15. 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.

  16. Application of the Convergent Close-Coupling method to collisions of electrons, positrons, and protons with light atomic and molecular targets

    NASA Astrophysics Data System (ADS)

    Bray, Igor

    2015-09-01

    The Convergent Close-Coupling (CCC) method for electron-atom collisions has been applied successfully for around two decades for quasi one- and two-electron atomic targets. The underlying engine is the complete Laguerre basis for treating to convergence the target discrete and continuous spectra via a square-integrable approach, together with a formulation of the close-coupling equations in momentum space. The method has continued to be extended, and now incorporates collisions with positrons with allowance for positronium formation. This is a major advancement because it addresses the complexity associated with treating multi-center collision problems. These techniques have then been readily transferred to collisions with protons, where charge-exchange can be a substantial scattering outcome. The latter also required a move to solving the CCC equations using an impact parameter formalism. Most recently, in addition to the extension of the variety of projectiles, the collision targets have been generalized to molecules. Presently, just the H2+and the H2 molecules have been implemented. In the talk a broad range of applications of the CCC method will be discussed and future developments will be indicated. coauthors: A. S. Kadyrov, D.V. Fursa, I. Abdurakhmanov, M. Zammit.

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

    NASA Astrophysics Data System (ADS)

    Liu, Kun; E906/SeaQuest Collaboration

    2013-10-01

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

  18. 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.

  19. 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.

  20. FAST TRACK COMMUNICATION: Oscillation structures in elastic and electron capture cross sections for H+-H collisions in Debye plasmas

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Wang, J. G.; Krstic, P. S.; Janev, R. K.

    2010-10-01

    We find that the number of vibrational states in the ground potential of a H2+ molecular ion embedded in the Debye plasma and the number of Regge oscillations in the resonant charge transfer cross section of the H+ + H collision system in the plasma are quasi-conserved when the Debye radius D is larger than 1.4a0. The elastic and resonant charge transfer processes in the H+ + H collision have been studied in the 0.1 meV-100 eV collision energy range for a wide range of Debye radii using a highly accurate calculation based on the modified ab initio multireference configuration interaction code. Remarkable plasma screening effects have been found in both the molecular structure and the collision dynamics of this system. Shape resonances, Regge and glory oscillations have been found in the integral cross sections in the considered energy range even for strong interaction screening, showing their ubiquitous nature.

  1. 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).

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

    EPA Science Inventory

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

  3. 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. PMID:27558712

  4. Quantum-state resolved bimolecular collisions of velocity-controlled OH with NO radicals.

    PubMed

    Kirste, Moritz; Wang, Xingan; Schewe, H Christian; Meijer, Gerard; Liu, Kopin; van der Avoird, Ad; Janssen, Liesbeth M C; Gubbels, Koos B; Groenenboom, Gerrit C; van de Meerakker, Sebastiaan Y T

    2012-11-23

    Whereas atom-molecule collisions have been studied with complete quantum-state resolution, interactions between two state-selected molecules have proven much harder to probe. Here, we report the measurement of state-resolved inelastic scattering cross sections for collisions between two open-shell molecules that are both prepared in a single quantum state. Stark-decelerated hydroxyl (OH) radicals were scattered with hexapole-focused nitric oxide (NO) radicals in a crossed-beam configuration. Rotationally and spin-orbit inelastic scattering cross sections were measured on an absolute scale for collision energies between 70 and 300 cm(-1). These cross sections show fair agreement with quantum coupled-channels calculations using a set of coupled model potential energy surfaces based on ab initio calculations for the long-range nonadiabatic interactions and a simplistic short-range interaction. This comparison reveals the crucial role of electrostatic forces in complex molecular collision processes. PMID:23180857

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

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Anirban; Sahu, Satyajit; Fujita, Daisuke

    2009-09-01

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

  6. Improvement of thermoelectric efficiency of the polyaniline molecular junction by the doping process.

    PubMed

    Golsanamlou, Zahra; Tagani, Meysam Bagheri; Soleimani, Hamid Rahimpour

    2015-05-28

    Thermoelectric properties of a polyaniline molecular junction with face centered cubic electrodes are investigated using the Green function formalism in a linear response regime in the presence of the doping process. Doping causes the increase of thermopower and the figure of merit (ZT) and the decrease of electrical conductance as found experimentally in the work of Li et al., (Synthetic. Metals, 2010, 160, 1153-1158). We also find that the ZT increases with the molecular length in short polyanilines. [Golsanamlou et al., Phys. Chem. Chem. Phys., 2000, 35, 3523]. PMID:25929682

  7. Two-center effect on low-energy electron emission in collisions of 1-MeV/u bare ions with atomic hydrogen, molecular hydrogen, and helium. I. Atomic hydrogen

    NASA Astrophysics Data System (ADS)

    Tribedi, Lokesh C.; Richard, P.; Gulyás, L.; Rudd, M. E.; Moshammer, R.

    2001-06-01

    We have investigated ionization mechanisms in fast ion-atom collisions by measuring the low-energy electron emission cross sections in a pure three-body collision involving bare carbon ions (v=6.35 a.u.) colliding with atomic hydrogen targets. The measurements have also been extended to molecular hydrogen and helium targets. In this paper we provide the energy and angular distributions of double differential cross sections of low-energy electron emission for atomic hydrogen targets. The Slevin rf source with a high degree of dissociation was used to produce the atomic H target. It is found that the two-center effect has a major influence on the observed large forward-backward angular asymmetry. A detailed comparison is presented with calculations based on the continuum distorted-wave (CDW) and CDW-EIS (eikonal initial-state) approximations. Both the continuum distorted-wave calculations provide a very good understanding of the data, whereas the first Born calculation predicts almost symmetric forward-backward distributions that do not agree with the data. The two-center effect is slightly better represented by the CDW calculations compared to the CDW-EIS calculation. The total cross sections are, however, in good agreement with the theories used. The results for molecular hydrogen and helium will be discussed in the following paper.

  8. 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

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

    PubMed

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  11. 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.

  12. 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}.

  13. 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. PMID:27435212

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

    SciTech Connect

    Lin, C.D.; Fritsch, W.

    1983-01-01

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

  15. 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.

  16. An optimal polymerization process for low mean molecular weight HBOC with lower dimer.

    PubMed

    Zhou, Wentao; Li, Shen; Hao, Shasha; Liu, Jiaxin; Wang, Hong; Yang, Chengmin

    2015-06-01

    The new research tried to improve the distribution of molecular weight of Hb-based oxygen carriers (HBOC), a bottleneck of glutaraldehyde (GDA)-polymerization process. The orthogonal experiments were done on the basis of the early study of human placenta Hemoglobin (Hb)-crosslinked-GDA and three factors were selected including the molar ratio of GDA and Hb, Hb concentration, and the rate of the feeding GDA. The optimal match condition of polymerization process prepared for the purpose of lower mean molecular weight, content of super-weight molecule, and the content of dimer. The results showed that the molar ratio of GDA and Hb was the greatest influencing factor on the molecular weight distribution of polymerized-Hb, followed by the Hb concentration, and the last is the rate of feeding GDA. The optimum matching conditions had reached the objective that the mean molecular weight with 155.54 ± 5.79, the content of dimer with 17.23 ± 3.71, and content of super-weight molecule with 0.17 ± 0.09, and the results can be repeated in the 30 times expansion experiments. PMID:25519745

  17. 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.

  18. 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.

  19. 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

  20. 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. PMID:27321642

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

    PubMed

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

    2013-09-01

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

  2. 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. PMID:26829664

  3. 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.

  4. 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

  5. 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. PMID:27235773

  6. 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

  7. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: Fractional electron approach

    NASA Astrophysics Data System (ADS)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J.; Yang, Weitao

    2008-03-01

    Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H2O)62+/3+ and Ru(H2O)62+/3+. The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.

  8. Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

    PubMed Central

    Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

    2015-01-01

    The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution. PMID:26177190

  9. 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.

  10. 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.

  11. Theory of slow atomic collisions

    NASA Astrophysics Data System (ADS)

    Nikitin, E. E.; Umanskii, S. Ia.

    The theory presented in this book is self-contained. It can be applied to the interpretation of various processes occurring in atomic collisions over a relatively wide energy range, from thermal energies to hundreds of eV. The general formulation of the scattering problem under quasi-classical conditions is discussed, taking into account scattering amplitudes and cross sections, scattering equations, collisions of two many-electron atoms, and integral cross sections for isotropic collisions. Other topics explored are related to diatomic electronic states, approximate calculations of the electronic states of diatoms, elastic scattering, approximate calculations of a multichannel quasi-classical scattering matrix, the two-state scattering problem, the linear two-state Landau-Zener model, nonlinear two-state models of nonadiabatic coupling, multistate models of nonadiabatic coupling, and a case study involving intramultiplet mixing and depolarization of alkalis in collisions with noble gases.

  12. 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. PMID:24953199

  13. 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

  14. Molecular processes leading to aberrant androgen receptor signaling and castration resistance in prostate cancer

    PubMed Central

    Hu, Rong; Denmeade, Samuel R; Luo, Jun

    2011-01-01

    Hormone therapies targeting androgen receptor signaling are the mainstay of treatment for patients with advanced prostate cancer. The length of clinical remission induced by hormone therapies varies substantially among treated patients. Why some patients progress rapidly after treatment while others benefit with prolonged remission is a question that remains unsolved. The androgen receptor signaling pathway is the key molecular determinant of castration resistance, and a key target for prostate cancer drug design. Recent advances in characterizing molecular processes leading to the development of castration-resistant prostate cancer, including the discovery of multiple androgen receptor splicing variants, offer opportunities for rational development of new clinical tools or approaches to predict, monitor or control/prevent prostate cancer progression in the castrate setting. PMID:21318111

  15. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

    PubMed Central

    Hackl, Hubert; Burkard, Thomas Rainer; Sturn, Alexander; Rubio, Renee; Schleiffer, Alexander; Tian, Sun; Quackenbush, John; Eisenhaber, Frank; Trajanoski, Zlatko

    2005-01-01

    Background Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development. Results Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome. Conclusions Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks. PMID:16420668

  16. Synthesizing primary molecular relaxation processes in excitable gases using a two-frequency reconstructive algorithm.

    PubMed

    Petculescu, Andi G; Lueptow, Richard M

    2005-06-17

    Identifying molecular relaxation processes in excitable gases remains challenging. An algorithm that reconstructs the primary relaxation processes is presented. Based on measurements of acoustic attenuation and sound speed at two frequencies, it synthesizes the entire frequency dependence of the complex effective specific heat of the gas, which is the macroscopic "footprint" of relaxation effects. The algorithm is based on the fact that for a simple relaxation process, such as occurs in many polyatomic gases at temperatures around 300 K, the effective specific heat traces a semicircle in the complex plane as a function of frequency. Knowing the high-frequency or instantaneous value of the specific heat provides the capability to not only sense the presence, but also infer the nature and, for mixtures of unlike-symmetry molecules, the concentration of foreign molecules leaking in a host gas. PMID:16090508

  17. Solution-Processed Small Molecular Organic Light-Emitting Devices with a Mixed Single Layer

    NASA Astrophysics Data System (ADS)

    Wang, Zhaokui; Naka, Shigeki; Okada, Hiroyuki

    2011-01-01

    We investigated the characteristics of solution-processed mixed-single-layer organic light-emitting devices (OLEDs) by mixing an electron injection material, a hole transport material, and a dopant material based on 5,6,11,12-tetraphenylnaphthacene (rubrene). The mixed-single-layer OLEDs showed better performance by optimizing the solution concentration and mixing ratio of organic materials. The performance was further improved by mixing chloroform (95 wt %) and toluene (5 wt %) as a solvent. The maximum luminance and power efficiency obtained were 12,400 cd/m2 and 1.1 lm/W, respectively. The mixed-single-layer OLEDs by solution process can be expected as an alternative route to the fabrication of small-molecular OLEDs with reduced cost of devices and avoiding the complexities of the co-evaporation of multiple organic materials in the vacuum deposition process.

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

    PubMed

    Chaban, Vitaly V; Prezhdo, Oleg V

    2016-07-01

    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. PMID:27340901

  19. Study of applied magnetic field magnetoplasmadynamic thrusters with particle-in-cell code with Monte Carlo collision. I. Computation methods and physical processes

    SciTech Connect

    Tang Haibin; Cheng Jiao; Liu Chang; York, Thomas M.

    2012-07-15

    A two-dimensional axisymmetric electromagnetic particle-in-cell code with Monte Carlo collision conditions has been developed for an applied-field magnetoplasmadynamic thruster simulation. This theoretical approach establishes a particle acceleration model to investigate the microscopic and macroscopic characteristics of particles. This new simulation code was used to study the physical processes associated with applied magnetic fields. In this paper (I), detail of the computation procedure and results of predictions of local plasma and field properties are presented. The numerical model was applied to the configuration of a NASA Lewis Research Center 100-kW magnetoplasmadynamic thruster which has well documented experimental results. The applied magnetic field strength was varied from 0 to 0.12 T, and the effects on thrust were calculated as a basis for verification of the theoretical approach. With this confirmation, the changes in the distributions of ion density, velocity, and temperature throughout the acceleration region related to the applied magnetic fields were investigated. Using these results, the effects of applied field on physical processes in the thruster discharge region could be represented in detail, and those results are reported.

  20. Study of applied magnetic field magnetoplasmadynamic thrusters with particle-in-cell code with Monte Carlo collision. I. Computation methods and physical processes

    NASA Astrophysics Data System (ADS)

    Tang, Hai-Bin; Cheng, Jiao; Liu, Chang; York, Thomas M.

    2012-07-01

    A two-dimensional axisymmetric electromagnetic particle-in-cell code with Monte Carlo collision conditions has been developed for an applied-field magnetoplasmadynamic thruster simulation. This theoretical approach establishes a particle acceleration model to investigate the microscopic and macroscopic characteristics of particles. This new simulation code was used to study the physical processes associated with applied magnetic fields. In this paper (I), detail of the computation procedure and results of predictions of local plasma and field properties are presented. The numerical model was applied to the configuration of a NASA Lewis Research Center 100-kW magnetoplasmadynamic thruster which has well documented experimental results. The applied magnetic field strength was varied from 0 to 0.12 T, and the effects on thrust were calculated as a basis for verification of the theoretical approach. With this confirmation, the changes in the distributions of ion density, velocity, and temperature throughout the acceleration region related to the applied magnetic fields were investigated. Using these results, the effects of applied field on physical processes in the thruster discharge region could be represented in detail, and those results are reported.

  1. 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.

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

    PubMed

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

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H → NaH) and the homonuclear (Na + Na → Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X(1)Σ(+)) is associated into the molecule in the bound states of the excited state (A(1)Σ(+)) 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. PMID:26342366

  3. 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

  4. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

    PubMed Central

    Buch, Ignasi; Giorgino, Toni; De Fabritiis, Gianni

    2011-01-01

    The understanding of protein–ligand binding is of critical importance for biomedical research, yet the process itself has been very difficult to study because of its intrinsically dynamic character. Here, we have been able to quantitatively reconstruct the complete binding process of the enzyme-inhibitor complex trypsin-benzamidine by performing 495 molecular dynamics simulations of free ligand binding of 100 ns each, 187 of which produced binding events with an rmsd less than 2 Å compared to the crystal structure. The binding paths obtained are able to capture the kinetic pathway of the inhibitor diffusing from solvent (S0) to the bound (S4) state passing through two metastable intermediate states S2 and S3. Rather than directly entering the binding pocket the inhibitor appears to roll on the surface of the protein in its transition between S3 and the final binding pocket, whereas the transition between S2 and the bound pose requires rediffusion to S3. An estimation of the standard free energy of binding gives ΔG° = -5.2 ± 0.4 kcal/mol (cf. the experimental value -6.2 kcal/mol), and a two-states kinetic model kon = (1.5 ± 0.2) × 108 M-1 s-1 and koff = (9.5 ± 3.3) × 104 s-1 for unbound to bound transitions. The ability to reconstruct by simple diffusion the binding pathway of an enzyme-inhibitor binding process demonstrates the predictive power of unconventional high-throughput molecular simulations. Moreover, the methodology is directly applicable to other molecular systems and thus of general interest in biomedical and pharmaceutical research. PMID:21646537

  5. Reorganization energy of electron transfer processes in ionic fluids: A molecular Debye-Hueckel approach

    SciTech Connect

    Xiao Tiejun; Song Xueyu

    2013-03-21

    The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hueckel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hueckel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids.

  6. Multiple rescattering processes in high-order harmonic generation from molecular system.

    PubMed

    Zhang, Cai-Ping; Xia, Chang-Long; Jia, Xiang-Fu; Miao, Xiang-Yang

    2016-09-01

    The molecular multiple rescattering processes have been theoretically investigated via solving the time-dependent Schrödinger equation. Not only has the physical model been established, but also the related rescatterings originating from recombination with parent nucleus and with neighboring nucleus have been distinguished. Moreover, it has shown that the rescatterings originating from recombination with parent nucleus are similar with those atomic rescatterings, while those rescatterings from recombination with neighboring nucleus both before and after reversing the direction of the laser field are more sensitive to the internuclear distance. With time-frequency distribution and classical electron dynamics, the underlying mechanisms are revealed. PMID:27607636

  7. 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.

  8. 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. PMID:18338789

  9. Measurement of the differential cross section of the photoinitiated reactive collision of O(1D)+D2 using only one molecular beam: A study by three dimensional velocity mapping

    NASA Astrophysics Data System (ADS)

    Kauczok, S.; Maul, C.; Chichinin, A. I.; Gericke, K.-H.

    2010-06-01

    In order to measure the state selective double differential cross section of a reactive collision, the preparation of the reactants with defined initial velocities and quantum states in number densities high enough to achieve an acceptable count rate is most important. At the same time, secondary collisions have to be prevented in order to ensure that the nascent products are not thermalized. Usually, the best way to control the initial conditions is to use crossed molecular beams, but the number density decreases quadratically with the distance from the nozzle orifice which can be a problem, especially if a molecular product with a large number of populated states is to be analyzed state specifically by REMPI spectroscopy. In this contribution we would like to present a method for measuring the quantum state selective differential cross section of a photoinitiated reaction that combines the advantages of the PHOTOLOC technique (high reactant densities) and the parallel beams technique used by the groups of Kitsopoulos, Orr-Ewing, and Suits (defined relative velocity of the reactants). Moreover, an algorithm based on a Bayesian backward reconstruction developed by W. H. Richardson [J. Opt. Soc. Am. 62, 55 (1972)] has been derived. Both, one reactant and the precursor of the other reactant, are present in the same molecular beam and the center of mass velocity is selected by shifting the dissociation and the detection laser in time and space. Like in comparable methods, this produces a bias in the measured velocity distribution due to the fact that the reaction takes place in the whole volume surrounding the laser beams. This has been also reported by Toomes et al. in the case of the parallel beams technique and presents a general problem of probing reaction products by REMPI spectroscopy. To account for this, we develop a general approach that can be easily adapted to other conditions. The bias is removed in addition to deconvolution from the spread in reactant

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Analyzing Collisions in Terms of Newton's Laws

    NASA Astrophysics Data System (ADS)

    Roeder, John L.

    2003-02-01

    Although the principle of momentum conservation is a consequence of Newton's second and third laws of motion, as recognized by Newton himself, this principle is typically applied in analyzing collisions as if it is a separate concept of its own. This year I sought to integrate my treatment of collisions with my coverage of Newton's laws by asking students to calculate the effect on the motion of two particles due to the forces they exerted for a specified time interval on each other. For example, "A 50-kg crate slides across the ice at 3 m/s and collides with a 25-kg crate at rest. During the collision process the 50-kg crate exerts a 500 N time-averaged force on the 25 kg for 0.1 s. What are the accelerations of the crates during the collision, and what are their velocities after the collision? What are the momenta of the crates before and after collision?"

  17. 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

  18. Signal processing for molecular and cellular biological physics: an emerging field.

    PubMed

    Little, Max A; Jones, Nick S

    2013-02-13

    Recent advances in our ability to watch the molecular and cellular processes of life in action--such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer--raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied. PMID:23277603

  19. Dislocation processes in the deformation of nanocrystalline aluminium by molecular-dynamics simulation.

    PubMed

    Yamakov, Vesselin; Wolf, Dieter; Phillpot, Simon R; Mukherjee, Amiya K; Gleiter, Herbert

    2002-09-01

    The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying--in a degree of detail not possible experimentally--the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size. PMID:12618848

  20. Acceleration of Early-Photon Fluorescence Molecular Tomography with Graphics Processing Units

    PubMed Central

    Wang, Xin; Zhang, Bin; Cao, Xu; Liu, Fei; Luo, Jianwen; Bai, Jing

    2013-01-01

    Fluorescence molecular tomography (FMT) with early-photons can improve the spatial resolution and fidelity of the reconstructed results. However, its computing scale is always large which limits its applications. In this paper, we introduced an acceleration strategy for the early-photon FMT with graphics processing units (GPUs). According to the procedure, the whole solution of FMT was divided into several modules and the time consumption for each module is studied. In this strategy, two most time consuming modules (Gd and W modules) were accelerated with GPU, respectively, while the other modules remained coded in the Matlab. Several simulation studies with a heterogeneous digital mouse atlas were performed to confirm the performance of the acceleration strategy. The results confirmed the feasibility of the strategy and showed that the processing speed was improved significantly. PMID:23606899

  1. Molecular mobility and relaxation process of isolated lignin studied by multifrequency calorimetric experiments.

    PubMed

    Guigo, Nathanael; Mija, Alice; Vincent, Luc; Sbirrazzuoli, Nicolas

    2009-02-28

    The glass transition of lignin has been studied by multifrequency calorimetric measurements in order to highlight the morphological changes and the dynamic aspects associated to this relaxation process. Influences of water sorption and thermal annealing on molecular mobility have been considered. Additional investigations by thermogravimetry, infra-red spectroscopy and rheometry have been performed to corroborate the claims. The relaxation process of annealed lignin shows a different behaviour as the consequence of micro-structural modifications of lignin. These are explained by redistribution of secondary bonds as well as formation of new interunit linkages. Concerning the dynamic aspects, apparent activation energy, E, and sizes of cooperatively rearranging region, V(crr), have been evaluated respectively from the frequency dependence and heat capacity measurements of the glass transition. Compared to dried lignin, both E and V(crr) significantly decrease in a water-sorbed matrix indicating that the three-dimensional structure presents a higher mobility and is less confined. PMID:19209367

  2. Dislocation processes in the deformation of nanocrystalline aluminum by molecular-dynamics simulation.

    SciTech Connect

    Yamakov, V.; Wolf, D.; Phillpot, S. R.; Mukherjee, A. K.; Gleiter, H.; Materials Science Division; Univ. of California; Forschungszentrum Karlsruhe

    2002-09-01

    The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying-in a degree of detail not possible experimentally-the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size.

  3. Molecular Interdiffusion between Stacked Layers by Solution and Thermal Annealing Processes in Organic Light Emitting Devices.

    PubMed

    Ohisa, Satoru; Pu, Yong-Jin; Yamada, Norifumi L; Matsuba, Go; Kido, Junji

    2015-09-23

    In organic light emitting devices (OLEDs), interfacial structures between multilayers have large impacts on the characteristics of OLEDs. Herein, we succeeded in revealing the interdiffusion in solution processed and thermal annealed OLEDs by neutron reflectometry. We investigated interfaces between a polymer under layer and small molecules upper layer. The small molecules diffused into the swollen polymer layer during the interfacial formation by the solution process, but the polymer did not diffuse into the small molecules layer. At temperatures close to the glass transition temperatures of the materials, asymmetric molecular diffusion was observed. We elucidated the effects of the interdiffusion on the characteristics of OLEDs. Partially mixing the interface improved the current efficiencies due to suppressed triplet-polaron quenching at the interface. Controlling and understanding the interfacial structures of the miultilayers will be more important to improve the OLED characteristics. PMID:26331696

  4. 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.

  5. Observation of the amorphous zinc oxide recrystalline process by molecular dynamics simulation

    PubMed Central

    Lin, Ken-Huang; Sun, Shih-Jye; Ju, Shin-Pon; Tsai, Jen-Yu; Chen, Hsin-Tsung; Hsieh, Jin-Yuan

    2013-01-01

    The detailed structural variations of amorphous zinc oxide (ZnO) as well as wurtzite (B4) and zinc blende (B3) crystal structures during the temperature elevation process were observed by molecular dynamics simulation. The amorphous ZnO structure was first predicted through the simulated-annealing basin-hopping algorithm with the criterion to search for the least stable structure. The density and X-ray diffraction profiles of amorphous ZnO of the structure were in agreement with previous reports. The local structural transformation among different local structures and the recrystalline process of amorphous ZnO at higher temperatures are observed and can explain the structural transformation and recrystalline mechanism in a corresponding experiment [Bruncko et al., Thin Solid Films 520, 866-870 (2011)]. PMID:23509413

  6. Relaxation processes and glass transition in confined 1,4-polybutadiene films: A Molecular Dynamics study

    NASA Astrophysics Data System (ADS)

    Paul, Wolfgang; Solar, Mathieu

    We will present results from Molecular Dynamics simulations of a chemically realistic model of 1,4-polybutadiene (PB) chains confined by graphite walls. Relaxation processes in this system are heterogeneous and anisotropic. We will present evidence for a slow additional relaxation process related to chain desorption from the walls. We also study the structural relaxation resolved with respect to the distance from the graphite walls and show the influence of structural changes on the relaxation behavior. The temperature dependence of the dielectric relaxation in layers of different thickness near the walls shows no indication of a shift of Tg as a function of thickness when analyzed with a Vogel-Fulcher fit. We explain this by the importance of intramolecular dihedral barriers for the glass transition in PB which dominate over the density changes next to a wall except for a 1 nm thick layer directly at the wall.

  7. Effect of water separation layer on metal nanoforming process investigated using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Wu, Cheng-Da; Chang Chin, Po-Yuan; Chiang, Chia-Chin; Lai, Rong-Jer; Fang, Te-Hua

    2013-11-01

    The effects of water separation layer and temperature on the nanoforming process of Al films are studied using molecular dynamics simulations. These effects are evaluated in terms of molecular/atomic trajectories, potential energy, slip vectors, and the radial distribution function. The simulation results show that Al films can automatically fill cavities via heating without requiring an external loading exerted on them. At the complete filling stage, the most compact structure is obtained for forming with no water; however, the pattern collapses during the demolding process due to strong adhesion with the mold. In nanoforming in a humid environment, water molecules between the mold and Al film act as a buffer which relieves the forming pressure on the Al film, slowing down the deformation. During demolding, the buffer effectively prevents the formation of pattern defects induced by adhesion. Water molecules gradually vaporize with increasing temperature, which causes pattern failure due to a decrease in humidity. Moderate water layers are beneficial for better order and a compact pattern structure.

  8. Structure of a simple molecular dynamics FORTRAN program optimized for CRAY vector processing computers

    NASA Astrophysics Data System (ADS)

    Schoen, Martin

    1989-01-01

    A program structure for efficient vectorization of molecular dynamics FORTRAN programs on CRAY vector processing computers is described. Though coded for a very simple pure atomic fluid in a cubic cell with periodic boundary conditions the program can easily be modified to handle more complicated systems. A detailed analysis shows that the present program is faster by 36% for N = 256 particles and faster by more than a factor of 3 for N = 2048 compared with a fully vectorized molecular dynamics program written for the CYBER 205 vector processing machine. In comparison with a link cell MD program also written for a CRAY the program described here runs three times faster for a large particle number N = 6912. This factor increases with decreasing N to 6.3 for N = 1372. The speedup is achieved by i) long vectors in inner loops wherever possible; ii) limiting the number of arithmetic operations in inevitably short loops as much as possible; iii) appropriate library routines; iv) integer index vector neighbour lists.

  9. 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.

  10. 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

  11. 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

  12. Convergent-close-coupling calculations for excitation and ionization processes of electron-hydrogen collisions in Debye plasmas

    SciTech Connect

    Zammit, Mark C.; Fursa, Dmitry V.; Bray, Igor

    2010-11-15

    Electron-hydrogen scattering in weakly coupled hot-dense plasmas has been investigated using the convergent-close-coupling method. The Yukawa-type Debye-Hueckel potential has been used to describe the plasma screening effects. The target structure, excitation dynamics, and ionization process change dramatically as the screening is increased. Excitation cross sections for the 1s{yields}2s,2p,3s,3p,3d and 2s{yields}2p,3s,3p,3d transitions and total and total ionization cross sections for the scattering from the 1s and 2s states are presented. Calculations cover the energy range from thresholds to high energies (250 eV) for various Debye lengths. We find that as the screening increases, the excitation and total cross sections decrease, while the total ionization cross sections increase.

  13. First-Principles Molecular Dynamics Studies of Organometallic Complexes and Homogeneous Catalytic Processes.

    PubMed

    Vidossich, Pietro; Lledós, Agustí; Ujaque, Gregori

    2016-06-21

    Computational chemistry is a valuable aid to complement experimental studies of organometallic systems and their reactivity. It allows probing mechanistic hypotheses and investigating molecular structures, shedding light on the behavior and properties of molecular assemblies at the atomic scale. When approaching a chemical problem, the computational chemist has to decide on the theoretical approach needed to describe electron/nuclear interactions and the composition of the model used to approximate the actual system. Both factors determine the reliability of the modeling study. The community dedicated much effort to developing and improving the performance and accuracy of theoretical approaches for electronic structure calculations, on which the description of (inter)atomic interactions rely. Here, the importance of the model system used in computational studies is highlighted through examples from our recent research focused on organometallic systems and homogeneous catalytic processes. We show how the inclusion of explicit solvent allows the characterization of molecular events that would otherwise not be accessible in reduced model systems (clusters). These include the stabilization of nascent charged fragments via microscopic solvation (notably, hydrogen bonding), transfer of charge (protons) between distant fragments mediated by solvent molecules, and solvent coordination to unsaturated metal centers. Furthermore, when weak interactions are involved, we show how conformational and solvation properties of organometallic complexes are also affected by the explicit inclusion of solvent molecules. Such extended model systems may be treated under periodic boundary conditions, thus removing the cluster/continuum (or vacuum) boundary, and require a statistical mechanics simulation technique to sample the accessible configurational space. First-principles molecular dynamics, in which atomic forces are computed from electronic structure calculations (namely, density

  14. ATOMIC AND MOLECULAR PHYSICS: Interference Angle on Quantum Rotational Energy Transfer in Na + Na2 (A1 Σ+u, v = 8 ~ b3п0u, v = 14) Molecular Collision System

    NASA Astrophysics Data System (ADS)

    Wang, Wei-Li; Miao, Gang; Li, Jian; Ma, Feng-Cai

    2009-12-01

    In order to study the collisional quantum interference (CQI) on rotational energy transfer in atom-diatom system, we have studied the relation of the integral interference angle and differential interference angle in Na + Na2 (A1 σ+u, v = 8 ~ b3п0u, v = 14) collision system. In this paper, based on the first-Born approximation of time-dependent perturbation theory and taking into accounts the anisotropic effect of Lennard-Jones interaction potentials, we present a theoretical model of collisional quantum interference in intramolecular rotational energy transfer, and a relationship between differential and integral interference angles.

  15. Ternary drop collisions

    NASA Astrophysics Data System (ADS)

    Hinterbichler, Hannes; Planchette, Carole; Brenn, Günter

    2015-10-01

    It has been recently proposed to use drop collisions for producing advanced particles or well-defined capsules, or to perform chemical reactions where the merged drops constitute a micro-reactor. For all these promising applications, it is essential to determine whether the merged drops remain stable after the collision, forming a single entity, or if they break up. This topic, widely investigated for binary drop collisions of miscible and immiscible liquid, is quite unexplored for ternary drop collisions. The current study aims to close this gap by experimentally investigating collisions between three equal-sized drops of the same liquid arranged centri-symmetrically. Three drop generators are simultaneously operated to obtain controlled ternary drop collisions. The collision outcomes are observed via photographs and compared to those of binary collisions. Similar to binary collisions, a regime map is built, showing coalescence and bouncing as well as reflexive and stretching separation. Significant differences are observed in the transitions between these regimes.

  16. Molecular methods to assess Listeria monocytogenes route of contamination in a dairy processing plant.

    PubMed

    Alessandria, Valentina; Rantsiou, Kalliopi; Dolci, Paola; Cocolin, Luca

    2010-07-31

    In this study we investigated the occurrence of Listeria monocytogenes in a dairy processing plant during two sampling campaigns in 2007 and 2008. Samples represented by semifinished and finished cheeses, swabs from the equipment and brines from the salting step, were subjected to analysis by using traditional and molecular methods, represented mainly by quantitative PCR. Comparing the results obtained by the application of the two approaches used, it became evident how traditional microbiological analysis underestimated the presence of L. monocytogenes in the dairy plant. Especially samples of the brines and the equipment swabs were positive only with qPCR. For some equipment swabs it was possible to detect a load of 10(4)-10(5) cfu/cm(2), while the modified ISO method employed gave negative results both before and after the enrichment step. The evidences collected during the first sampling year, highlighting a heavy contamination of the brines and of the equipment, lead to the implementation of specific actions that decreased the contamination in these samples during the 2008 campaign. However, no reduction in the number of L. monocytogenes positive final products was observed, suggesting that a more strict control is necessary to avoid the presence of the pathogen. All the isolates of L. monocytogenes were able to attach to abiotic surfaces, and, interestingly, considering the results obtained from their molecular characterization it became evident how strains present in the brines, were genetically connected with isolates from the equipment and from the final product, suggesting a clear route of contamination of the pathogen in the dairy plant. This study underlines the necessity to use appropriate analytical tools, such as molecular methods, to fully understand the spread and persistence of L. monocytogenes in food producing companies. PMID:20193970

  17. Calculation of the Trubnikov and Nanbu Collision Kernels: Implications for Numerical Modeling of Coulomb Collisions

    SciTech Connect

    Dimits, A M; Wang, C; Caflisch, R; Cohen, B I; Huang, Y

    2008-08-06

    We investigate the accuracy of and assumptions underlying the numerical binary Monte-Carlo collision operator due to Nanbu [K. Nanbu, Phys. Rev. E 55 (1997)]. The numerical experiments that resulted in the parameterization of the collision kernel used in Nanbu's operator are argued to be an approximate realization of the Coulomb-Lorentz pitch-angle scattering process, for which an analytical solution for the collision kernel is available. It is demonstrated empirically that Nanbu's collision operator quite accurately recovers the effects of Coulomb-Lorentz pitch-angle collisions, or processes that approximate these (such interspecies Coulomb collisions with very small mass ratio) even for very large values of the collisional time step. An investigation of the analytical solution shows that Nanbu's parameterized kernel is highly accurate for small values of the normalized collision time step, but loses some of its accuracy for larger values of the time step. Careful numerical and analytical investigations are presented, which show that the time dependence of the relaxation of a temperature anisotropy by Coulomb-Lorentz collisions has a richer structure than previously thought, and is not accurately represented by an exponential decay with a single decay rate. Finally, a practical collision algorithm is proposed that for small-mass-ratio interspecies Coulomb collisions improves on the accuracy of Nanbu's algorithm.

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

    PubMed

    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. PMID:25527956

  19. 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.

  20. Bidirectional Transport by Molecular Motors: Enhanced Processivity and Response to External Forces

    PubMed Central

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

    2010-01-01

    Abstract Intracellular transport along cytoskeletal filaments is often mediated by two teams of molecular motors that pull on the same cargo and move in opposite directions along the filaments. We have recently shown theoretically that this bidirectional transport can be understood as a stochastic tug-of-war between the two motor teams. Here, we further develop our theory to investigate the experimentally accessible dynamic behavior of cargos transported by strong motors such as kinesin-1 or cytoplasmic dynein. By studying the run and binding times of such a cargo, we show that the properties of biological motors, such as the large ratio of stall/detachment force and the small ratio of superstall backward/forward velocity, are favorable for bidirectional cargo transport, leading to fast motion and enhanced diffusion. In addition, cargo processivity is shown to be strongly enhanced by transport via several molecular motors even if these motors are engaged in a tug-of-war. Finally, we study the motility of a bidirectional cargo under force. Frictional forces arising, e.g., from the viscous cytoplasm, lead to peaks in the velocity distribution, while external forces as exerted, e.g., by an optical trap, lead to hysteresis effects. Our results, in particular our explicit expressions for the cargo binding time and the distance of the peaks in the velocity relation under friction, are directly accessible to in vitro as well as in vivo experiments. PMID:20513405

  1. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

    PubMed Central

    2013-01-01

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

  2. 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

  3. Dissolving process of a cellulose bunch in ionic liquids: a molecular dynamics study.

    PubMed

    Li, Yao; Liu, Xiaomin; Zhang, Suojiang; Yao, Yingying; Yao, Xiaoqian; Xu, Junli; Lu, Xingmei

    2015-07-21

    In recent years, a variety of ionic liquids (ILs) were found to be capable of dissolving cellulose and mechanistic studies were also reported. However, there is still a lack of detailed information at the molecular level. Here, long time molecular dynamics simulations of cellulose bunch in 1-ethyl-3-methylimidazolium acetate (EmimAc), 1-ethyl-3-methylimidazolium chloride (EmimCl), 1-butyl-3-methylimidazolium chloride (BmimCl) and water were performed to analyze the inherent interaction and dissolving mechanism. Complete dissolution of the cellulose bunch was observed in EmimAc, while little change took place in EmimCl and BmimCl, and nothing significant happened in water. The deconstruction of the hydrogen bond (H-bond) network in cellulose was found and analyzed quantitatively. The synergistic effect of cations and anions was revealed by analyzing the whole dissolving process. Initially, cations bind to the side face of the cellulose bunch and anions insert into the cellulose strands to form H-bonds with hydroxyl groups. Then cations start to intercalate into cellulose chains due to their strong electrostatic interaction with the entered anions. The H-bonds formed by Cl(-) cannot effectively separate the cellulose chain and that is the reason why EmimCl and BmimCl dissolve cellulose more slowly. These findings deepen people's understanding on how ILs dissolve cellulose and would be helpful for designing new efficient ILs to dissolve cellulose. PMID:26095890

  4. The molecular signature of AML mesenchymal stromal cells reveals candidate genes related to the leukemogenic process.

    PubMed

    Binato, Renata; de Almeida Oliveira, Nathalia Correa; Du Rocher, Barbara; Abdelhay, Eliana

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process. PMID:26279521

  5. Deciphering the molecular and biologic processes that mediate histone deacetylase inhibitor-induced thrombocytopenia.

    PubMed

    Bishton, Mark J; Harrison, Simon J; Martin, Benjamin P; McLaughlin, Nicole; James, Chloé; Josefsson, Emma C; Henley, Katya J; Kile, Benjamin T; Prince, H Miles; Johnstone, Ricky W

    2011-03-31

    Histone deacetylase inhibitor (HDACI)-induced thrombocytopenia (TCP) is a major dose-limiting toxicity of this new class of drugs. Using preclinical models to study the molecular and biologic events that underpin this effect of HDACI, we found that C57BL/6 mice treated with both the HDAC1/2-selective HDACI romidepsin and the pan-HDACI panobinostat developed significant TCP. HDACI-induced TCP was not due to myelosuppression or reduced platelet lifespan, but to decreased platelet release from megakaryocytes. Cultured primary murine megakaryocytes showed reductions in proplatelet extensions after HDACI exposure and a dose-dependent increase in the phosphorylation of myosin light chain 2 (MLC2). Phosphorylation of MLC to phospho-MLC (pMLC) and subsequent proplatelet formation in megakaryocytes is regulated by the Rho-GTPase proteins Rac1, CDC42, and RhoA. Primary mouse megakaryocytes and the human megakaryoblastic cell line Meg-01 showed reductions in Rac1, CDC42, and RhoA protein levels after treatment with HDACIs. We were able to overcome HDACI-induced TCP by administering the mouse-specific thrombopoietin (TPO) mimetic AMP-4, which improved platelet numbers to levels similar to untreated controls. Our report provides the first detailed account of the molecular and biologic processes involved in HDACI-mediated TCP. Moreover, our preclinical studies provide evidence that dose-limiting TCP induced by HDACIs may be circumvented using a TPO mimetic. PMID:21292776

  6. 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.

  7. 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.

  8. Molecular imaging with radionuclides, a powerful technique for studying biological processes in vivo

    NASA Astrophysics Data System (ADS)

    Cisbani, E.; Cusanno, F.; Garibaldi, F.; Magliozzi, M. L.; Majewski, S.; Torrioli, S.; Tsui, B. M. W.

    2007-02-01

    Our team is carrying on a systematic study devoted to the design of a SPECT detector with submillimeter resolution and adequate sensitivity (1 cps/kBq). Such system will be used for functional imaging of biological processes at molecular level in small animal. The system requirements have been defined by two relevant applications: study of atherosclerotic plaques characterization and stem cells diffusion and homing. In order to minimize costs and implementation time, the gamma detector will be based—as much as possible—on conventional components: scintillator crystal and position sensitive PhotoMultipliers read by individual channel electronics. A coded aperture collimator should be adapted to maximize the efficiency. The optimal selection of the detector components is investigated by systematic use of Monte-Carlo simulations (and laboratory validation tests); and finally preliminary results are presented and discussed here.

  9. Fine microstructure of processed chitosan nanofibril networks preserving directional packing and high molecular weight.

    PubMed

    Osorio-Madrazo, Anayancy; David, Laurent; Peniche-Covas, Carlos; Rochas, Cyrille; Putaux, Jean-Luc; Trombotto, Stéphane; Alcouffe, Pierre; Domard, Alain

    2015-10-20

    Crystalline chitosan nanofibril networks were prepared, preserving the native structural packing and the polymer high molecular weight. The fine microstructure of the nanomaterial, obtained by mild hydrolysis of chitosan (CHI), was characterized by using synchrotron small- and wide-angle X-ray scattering (SAXS and WAXS), transmission electron microscopy (TEM) and electron diffraction. Hydrolysis of chitosan yielded a network of crystalline nanofibrils, containing both allomorphs of chitosan: hydrated and anhydrous. The comparison of WAXS data in transmission and reflection mode revealed the preferential orientation of the CHI crystals when subjected to mechanical compression constrains. The results are in agreement with the existence of a network nanostructure containing fiber-like crystals with the principal axis parallel to the polymer chain axis. The evolution of the CHI allomorphic composition with temperature was studied to further elucidate the mechanism of structural transitions occurring during CHI nanofibril network processing. PMID:26256153

  10. 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.

  11. Early stage oxynitridation process of Si(001) surface by NO gas: Reactive molecular dynamics simulation study

    NASA Astrophysics Data System (ADS)

    Cao, Haining; Srivastava, Pooja; Choi, Keunsu; Kim, Seungchul; Lee, Kwang-Ryeol

    2016-03-01

    Initial stage of oxynitridation process of Si substrate is of crucial importance in fabricating the ultrathin gate dielectric layer of high quality in advanced MOSFET devices. The oxynitridation reaction on a relaxed Si(001) surface is investigated via reactive molecular dynamics (MD) simulation. A total of 1120 events of a single nitric oxide (NO) molecule reaction at temperatures ranging from 300 to 1000 K are statistically analyzed. The observed reaction kinetics are consistent with the previous experimental or calculation results, which show the viability of the reactive MD technique to study the NO dissociation reaction on Si. We suggest the reaction pathway for NO dissociation that is characterized by the inter-dimer bridge of a NO molecule as the intermediate state prior to NO dissociation. Although the energy of the inter-dimer bridge is higher than that of the intra-dimer one, our suggestion is supported by the ab initio nudged elastic band calculations showing that the energy barrier for the inter-dimer bridge formation is much lower. The growth mechanism of an ultrathin Si oxynitride layer is also investigated via consecutive NO reactions simulation. The simulation reveals the mechanism of self-limiting reaction at low temperature and the time evolution of the depth profile of N and O atoms depending on the process temperature, which would guide to optimize the oxynitridation process condition.

  12. Platinum(II)-bis(aryleneethynylene) complexes for solution-processible molecular bulk heterojunction solar cells.

    PubMed

    Dai, Feng-Rong; Zhan, Hong-Mei; Liu, Qian; Fu, Ying-Ying; Li, Jin-Hua; Wang, Qi-Wei; Xie, Zhiyuan; Wang, Lixiang; Yan, Feng; Wong, Wai-Yeung

    2012-01-27

    Four new solution-processible small-molecular platinum(II)-bis(aryleneethynylene) complexes consisting of benzothiadiazole as the electron acceptor and triphenylamine and/or thiophene as the electron donor were conveniently synthesized and characterized by physicochemical and computational methods, and utilized as the electron-donor materials in the fabrication of solution-processed bulk heterojunction (BHJ) solar cells. The effect of different electron-donor groups in these small molecules on the optoelectronic and photovoltaic properties was also examined. The optical and time-dependent density functional theory studies showed that the incorporation of stronger electron-donor groups significantly enhanced the solar-absorption abilities of the complexes. These molecular complexes can serve as good electron donors for fabricating BHJ devices by blending them with the [6,6]-phenyl-C(71)-butyric acid methyl ester (PC(70)BM) as the electron acceptor. The best power conversion efficiency of 2.37% was achieved with the open-circuit voltage of 0.83 V, short-circuit current density of 7.10 mA cm(-2) and fill factor of 0.40 under illumination of an AM 1.5 solar-cell simulator. The spin-coated thin films showed p-channel field-effect charge transport with hole mobilities of up to 2.4×10(-4) cm(2) V(-1) s(-1) for these molecules. The present work illuminates the potential of well-defined organometallic complexes in developing light-harvesting small molecules for efficient power generation in organic photovoltaics implementation. PMID:22213333

  13. Biogeochemical Processes in Late Archean Marine Biosphere Revealed by Isotopic and Molecular Records

    NASA Astrophysics Data System (ADS)

    Eigenbrode, J. L.; Freeman, K. H.; Summons, R. E.

    2004-12-01

    The presence of shallow-marine oxygen oases and associated aerobic ecosystems in an otherwise anoxic and anaerobic world has been proposed by researchers to explain the anomalous 40 permil spread in organic-carbon isotope values during the late Archean. To test this hypothesis, we studied isotopic, molecular, and lithologic records of 2.7-2.5 Ga rocks of different depositional facies from the Hamersley Province, Western Australia. Kerogen carbon-isotopic compositions indicate that extreme 13C-depletion (more than -45 permil) was associated with shallow-marine-carbonate environments at 2.72 Ga and with deepwater environments thereafter. Moreover, kerogen-carbon-isotope values associated with carbonate environments became enriched by more than 10 permil over 100-150 Ma. These observations suggest that microbial processes responsible for extreme 13C-depletion became less significant in shallow carbonate environments, but remained important in deeper settings. Molecular biomarker ratios determined for associated bitumens: 1) strongly correlate to kerogen carbon-isotope values and other biomarker ratios, and, 2) show relationships with depositional facies and dolomite abundance giving credence to a syngenetic relationship with host rocks. The biomarker data confirm aerobic methanotrophs in the Late Archean biosphere, but not in strong association with extreme 13C-depletion. Biomarker patterns reflect a greater association of aerobic respiration and oxygenic photosynthesis in shallow carbonate environments compared to deeper settings. Collectively, the data record dramatic changes in carbon cycling associated with environmental partitioning of microbial processes and ecosystems over 100-150 Ma. Most likely, this represents increased bioavailability of strong electron acceptors with the expansion of oxidant-rich oases prior to rise in atmospheric oxygen.

  14. 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

  15. 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)

  16. Conformation and orientation dependence in ion-induced collisions with DNA and RNA building blocks

    NASA Astrophysics Data System (ADS)

    Bacchus-Montabonel, Marie-Christine

    2015-04-01

    Action of radiations on biological tissues is of major concern in cancer therapy development. Understanding the mechanisms involved at the molecular level in such reactions may be of crucial interest. In particular ion-induced ionization processes appear at the early stage of damage and a detailed analysis has been performed on the charge transfer dynamics of carbon ions with the different DNA and RNA building blocks in order to analyze their respective behavior in ion-induced collisions. We have considered the pyrimidine nucleobases uracil and thymine and the 5-halouracil molecules corresponding to the same skeleton, as well as the sugar moiety 2-deoxy-D-ribose. The calculations have been performed by means of ab initio quantum chemistry molecular methods followed by a semi-classical collision treatment in a wide collision energy range. Considerations of the structure of the biological target as well as analysis of the anisotropy of the process have been performed. The comparison with proton collisions has been developed with regard to previous results. Qualitative trends of interest for DNA building blocks damage may be pointed out.

  17. 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

  18. Mast cell procarboxypeptidase A. Molecular modeling and biochemical characterization of its processing within secretory granules.

    PubMed

    Springman, E B; Dikov, M M; Serafin, W E

    1995-01-20

    Previously, we characterized murine mast cell procarboxypeptidase A (MC-proCPA) as an inactive zymogen. To investigate the mechanisms for this lack of enzymatic activity and the processing of the zymogen to the active form, we now have performed molecular modeling of the tertiary structure of murine MC-proCPA based on the x-ray crystallographic structures of porcine pancreatic procarboxypeptidases A and B. Our model predicts that MC-proCPA retains a high degree of structural similarity to its pancreatic homologues. The globular propeptide physically blocks access to the fully formed active site of the catalytic domain and contains a salt bridge to the substrate-binding region that precludes docking of even small substrates. Based on consideration of the predicted tertiary structure and charge field characteristics of the model, the activation site (between GluA94 and Ile1) appears to be highly exposed even after MC-proCPA binds to secretory granule proteoglycans. Based on the steady-state levels of MC-proCPA versus MC-CPA, cycloheximide inhibition of protein synthesis, and brefeldin A blockage of protein sorting, we show that MC-proCPA is processed rapidly in murine mast cell line KiSV-MC14 with a half-life of 26 +/- 5 min (mean +/- S.D., n = 3), and the processing occurs within the secretory granules. The enzyme responsible for this processing may be a thiol protease since treatment of the KiSV-MC14 with 200 microM E-64d, a selective thiol-protease inhibitor, increases MC-proCPA by 2.7 +/- 0.2-fold (mean +/- S.D., n = 3) within 6 h of application. PMID:7836395

  19. A modular molecular framework for utility in small-molecule solution-processed organic photovoltaic devices

    SciTech Connect

    Welch, Gregory C.; Perez, Louis A.; Hoven, Corey V.; Zhang, Yuan; Dang, Xuan-Dung; Sharenko, Alexander; Toney, Michael F.; Kramer, Edward J.; Nguyen, Thuc-Quyen; Bazan, Guillermo C.

    2011-07-22

    We report on the design, synthesis and characterization of light harvesting small molecules for use in solution-processed small molecule bulk heterojunction (SM-BHJ) solar cell devices. These molecular materials are based upon an acceptor/donor/acceptor (A/D/A) core with donor endcapping units. Utilization of a dithieno(3,2-b;2',3'-d)silole (DTS) donor and pyridal[2,1,3]thiadiazole (PT) acceptor leads to strong charge transfer characteristics, resulting in broad optical absorption spectra extending well beyond 700 nm. SM-BHJ solar cell devices fabricated with the specific example 5,5'-bis{7-(4-(5-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolo[3,4-c]pyridine}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (6) as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) as the acceptor component showed short circuit currents above -10 mA cm-2 and power conversion efficiencies (PCEs) over 3%. Thermal processing is a critical factor in obtaining favorable active layer morphologies and high PCE values. A combination of UV-visible spectroscopy, conductive and photo-conductive atomic force microscopies, dynamic secondary mass ion spectrometry (DSIMS), and grazing incident wide angle X-ray scattering (GIWAXS) experiments were carried out to characterize how thermal treatment influences the active layer structure and organization.

  20. Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship

    SciTech Connect

    Giannone, Richard J; Huber, Dr. Harald; Karpinets, Tatiana V; Heimerl, Dr. Thomas; Kueper, Dr. Ulf; Rachel, Dr. Reinhard; Keller, Martin; Hettich, Robert {Bob} L; Podar, Mircea

    2011-01-01

    Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis.

  1. Proteomic Characterization of Cellular and Molecular Processes that Enable the Nanoarchaeum equitans-Ignicoccus hospitalis Relationship

    PubMed Central

    Giannone, Richard J.; Huber, Harald; Karpinets, Tatiana; Heimerl, Thomas; Küper, Ulf; Rachel, Reinhard; Keller, Martin; Hettich, Robert L.; Podar, Mircea

    2011-01-01

    Nanoarchaeum equitans, the only cultured representative of the Nanoarchaeota, is dependent on direct physical contact with its host, the hyperthermophile Ignicoccus hospitalis. The molecular mechanisms that enable this relationship are unknown. Using whole-cell proteomics, differences in the relative abundance of >75% of predicted protein-coding genes from both Archaea were measured to identify the specific response of I. hospitalis to the presence of N. equitans on its surface. A purified N. equitans sample was also analyzed for evidence of interspecies protein transfer. The depth of cellular proteome coverage achieved here is amongst the highest reported for any organism. Based on changes in the proteome under the specific conditions of this study, I. hospitalis reacts to N. equitans by curtailing genetic information processing (replication, transcription) in lieu of intensifying its energetic, protein processing and cellular membrane functions. We found no evidence of significant Ignicoccus biosynthetic enzymes being transported to N. equitans. These results suggest that, under laboratory conditions, N. equitans diverts some of its host's metabolism and cell cycle control to compensate for its own metabolic shortcomings, thus appearing to be entirely dependent on small, transferable metabolites and energetic precursors from I. hospitalis. PMID:21826220

  2. 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).

  3. 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

  4. 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

  5. Collision experiments with fullerenes

    NASA Astrophysics Data System (ADS)

    Campbell, E. E. B.; Ehlich, R.; Westerburg, M.; Hertel, I. V.

    1993-12-01

    Relative fragmentation cross sections for fullerene ion collisions with rare gas atoms and SF6 are presented over a range of collision energies. Structure in the cross sections and threshold energy determinations can shed some light on the fragmentation dynamics. Cluster cluster collisions with fullerenes are also described which show evidence of fusion reactions.

  6. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

    PubMed Central

    Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

  7. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming.

    PubMed

    Levine, Benjamin G; Stone, John E; Kohlmeyer, Axel

    2011-05-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

  8. 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.

  9. Molecular and Genomic Characterization of Vibrio mimicus Isolated from a Frozen Shrimp Processing Facility in Mexico.

    PubMed

    Guardiola-Avila, Iliana; Acedo-Felix, Evelia; Sifuentes-Romero, Itzel; Yepiz-Plascencia, Gloria; Gomez-Gil, Bruno; Noriega-Orozco, Lorena

    2016-01-01

    Vibrio mimicus is a gram-negative bacterium responsible for diseases in humans. Three strains of V. mimicus identified as V. mimicus 87, V. mimicus 92 and V. mimicus 93 were isolated from a shrimp processing facility in Guaymas, Sonora, Mexico. The strains were analyzed using several molecular techniques and according to the cluster analysis they were different, their similarities ranged between 51.3% and 71.6%. ERIC-PCR and RAPD (vmh390R) were the most discriminatory molecular techniques for the differentiation of these strains. The complete genomes of two strains (V. mimicus 87, renamed as CAIM 1882, and V. mimicus 92, renamed as CAIM 1883) were sequenced. The sizes of the genomes were 3.9 Mb in both strains, with 2.8 Mb in ChI and 1.1 Mb in ChII. A 12.7% difference was found in the proteome content (BLAST matrix). Several virulence genes were detected (e.g. capsular polysaccharide, an accessory colonization factor and genes involved in quorum-sensing) which were classified in 16 categories. Variations in the gene content between these genomes were observed, mainly in proteins and virulence genes (e.g., hemagglutinin, mobile elements and membrane proteins). According to these results, both strains were different, even when they came from the same source, giving an insight of the diversity of V. mimicus. The identification of various virulence genes, including a not previously reported V. mimicus gene (acfD) in ChI in all sequenced strains, supports the pathogenic potential of this species. Further analysis will help to fully understand their potential virulence, environmental impact and evolution. PMID:26730584

  10. 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

  11. Roles of deformation and orientation in heavy-ion collisions induced by light deformed nuclei at intermediate energy

    SciTech Connect

    Cao, X. G.; Zhang, G. Q.; Cai, X. Z.; Ma, Y. G.; Guo, W.; Chen, J. G.; Tian, W. D.; Fang, D. Q.; Wang, H. W.

    2010-06-15

    The reaction dynamics of axisymmetric deformed {sup 24}Mg+{sup 24}Mg collisions has been investigated systematically by an isospin-dependent quantum molecular dynamics model. It is found that different deformations and orientations result in apparently different properties of reaction dynamics. We reveal that some observables such as nuclear stopping power (R), multiplicity of fragments, and elliptic flow are very sensitive to the initial deformations and orientations. There exists an eccentricity scaling of elliptic flow in central body-body collisions with different deformations. In addition, the tip-tip and body-body configurations turn out to be two extreme cases in central reaction dynamical process.

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

    PubMed

    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 Xe(q+) (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 Xe(q+) 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 v(1/2) (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

  13. 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.

  14. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. PMID:15218250

  15. Annihilation of nematic point defects: Pre-collision and post-collision evolution

    NASA Astrophysics Data System (ADS)

    Svetec, M.; Kralj, S.; Bradač, Z.; Žumer, S.

    2006-05-01

    The annihilation of the nematic hedgehog and anti-hedgehog within an infinite cylinder of radius R is studied. The semi-microscopic lattice-type model and Brownian molecular dynamics are used. We distinguish among the i) early pre-collision, ii) late pre-collision, iii) early post-collision, and iv) late post-collision stages. In the pre-collision stage our results agree qualitatively with the existing experimental observations and also continuum-type simulations. The core of each defect exhibits a ring-like structure, where the ring axis is set perpendicular to the cylinder symmetry axis. For ξ(0)d/(2R) > 1 the interaction between defects is negligible, where ξ(0)d describes the initial separation of defects. Consequently, the defects annihilate within the simulation time window for ξ(0)d/(2R) < 1. For close enough defects their separation scales as ξd \\varpropto (tc - t)0.4±0.1, where tc stands for the collision time. In elastically anisotropic medium the hedgehog is faster than the anti-hedgehog. In the early pre-collision stage the defects can be treated as point-like particles, possessing inherent core structure, that interact via the nematic director field. In the late pre-collision stage the cores reflect the interaction between defects. After the collision a charge-less ring structure is first formed. In the early post-collision stage the ring adopts an essentially untwisted circular structure of the radius ξr. In the late post-collision stage we observe two qualitatively different scenarios. For μ = ξr/R < μc ˜ 0.25 the ring collapses leading to the escaped radial equilibrium structure. For μ > μc the chargeless ring triggers the nucleation growth into the planar polar structure with line defects.

  16. Ab initio study of charge-transfer dynamics in collisions of C{sup 2+} ions with hydrogen chloride

    SciTech Connect

    Rozsalyi, E.; Vibok, A.; Bene, E.; Halasz, G. J.; Bacchus-Montabonel, M. C.

    2011-05-15

    Ab initio quantum chemistry molecular calculations followed by a semiclassical dynamical treatment in the keV collision energy range have been developed for the study of the charge-transfer process in collisions of C{sup 2+} ions with hydrogen chloride. The mechanism has been investigated in detail in connection with avoided crossings between states involved in the reaction. A simple mechanism driven by a strong nonadiabatic coupling matrix element has been pointed out for this process. A comparative analysis with the halogen fluoride target corresponding to a similar electronic configuration shows a quite different charge-transfer mechanism leading to a very different behavior of the cross sections. Such behavior may be correlated to specific nonadiabatic interactions observed in these collision systems.

  17. Single charge exchange in collision of fast protons with hydrogen molecules

    NASA Astrophysics Data System (ADS)

    Ghanbari-Adivi, Ebrahim; Sattarpour, Seyedeh Hedyeh

    2015-11-01

    Single charge transfer process in collision of energetic protons with molecular hydrogens is theoretically studied using a first-order two-effective-center Born approximation. The correct boundary conditions are incorporated in the formalism and the Hartree-Fock molecular wave function for molecular targets and the residual ions are used to calculate the transition amplitude. The interference patterns in the capture differential cross-sections (DCSs) for a given fixed orientation of the molecule, due to the scattering from the two-atomic centers in the molecular targets, are examined. The dependence of the DCSs upon the angle between the molecular axis and the direction of the incident velocity is theoretically investigated. Both average differential and integral cross-sections are calculated. The obtained results are compared with the available experimental data.

  18. A model for energy transfer in collisions of atoms with highly excited molecules.

    PubMed

    Houston, Paul L; Conte, Riccardo; Bowman, Joel M

    2015-05-21

    A model for energy transfer in the collision between an atom and a highly excited target molecule has been developed on the basis of classical mechanics and turning point analysis. The predictions of the model have been tested against the results of trajectory calculations for collisions of five different target molecules with argon or helium under a variety of temperatures, collision energies, and initial rotational levels. The model predicts selected moments of the joint probability distribution, P(Jf,ΔE) with an R(2) ≈ 0.90. The calculation is efficient, in most cases taking less than one CPU-hour. The model provides several insights into the energy transfer process. The joint probability distribution is strongly dependent on rotational energy transfer and conservation laws and less dependent on vibrational energy transfer. There are two mechanisms for rotational excitation, one due to motion normal to the intermolecular potential and one due to motion tangential to it and perpendicular to the line of centers. Energy transfer is found to depend strongly on the intermolecular potential and only weakly on the intramolecular potential. Highly efficient collisions are a natural consequence of the energy transfer and arise due to collisions at "sweet spots" in the space of impact parameter and molecular orientation. PMID:25907301

  19. Solution-phase laser processing of π-conjugated polymers: Switching between different molecular states

    NASA Astrophysics Data System (ADS)

    Takada, K.; Tomioka, A.

    2012-04-01

    Liquid-phase laser processing, where the laser-irradiated target material is immersed in water for cooling, has been reported as a promising processing technique for thermally fragile organic materials. Although nanometer-sized particles have been reported to be obtained with the liquid-phase laser processing, the physical property did not change because quantum-mechanical size effect does not exhibit itself in the zero-radius Frenkel excitons. In the present study, we step further to use solution droplets as a target material, where organic molecules are molecularly dispersed in organic solvent and, therefore, expected to easily alter the conformation and the energy state upon laser irradiation. Small volume organic solvent is quickly evaporated upon laser irradiation, letting the bare organic molecule placed in water and rapidly cooled. To prevent the chemical decomposition of the target π-conjugated molecule, the specimen was resonantly irradiated by a ns-pulse green laser, not by a conventional UV laser. When the solid state spin-coat film made from MEH-PPV chloroform solution was used as a irradiation target immersed in water, resulting MEH-PPV particles showed similar photoluminescence (PL) like the PL of the spin-coat film and PL of the chloroform solution, including the 0→1, 0→2 vibrational transitions: this indicates that the energy levels were not modified from the spin-coat film. In comparison, when tiny droplets of MEH-PPV chloroform solution (orange color) were suspended in water, laser irradiation gave rise to yellow MEH-PPV particles which showed 550 nm and 530 nm PL (type B), blue-shifted from the spin-coat film PL 580 nm (type A), suggesting a successful phase transition of MEH-PPV polymer to type B. Further solution-phase laser processing left the type B state unchanged. The irreversible phase transition from type A to type B suggests that the type B ground state has lower energy than type A, which is consistent with the blue-shifted PL of

  20. Elastic Collisions and Gravity

    NASA Astrophysics Data System (ADS)

    Ball, Steven

    2009-04-01

    Elastic collisions are fascinating demonstrations of conservation principles. The mediating force must be conservative in an elastic collision. Truly elastic collisions take place only when the objects in collision do not touch, e.g. magnetic bumpers on low friction carts. This requires that we define a collision as a momentum transfer. Elastic collisions in 1-D can be solved in general and the implications are quite remarkable. For example, a heavy object moving initially towards a light object followed by an elastic collision results in a final velocity of the light object greater than either initial velocity. This is easily demonstrated with low friction carts. Gravitational elastic collisions involving a light spacecraft and an extremely massive body like a moon or planet can be approximated as 1-D collisions, such as the ``free return'' trajectory of Apollo 13 around the moon. The most fascinating gravitational collisions involve the gravitational slingshot effect used to boost spacecraft velocities. The maximum gravitational slingshot effect occurs when approaching a nearly 1-D collision, revealing that the spacecraft can be boosted to greater than twice the planet velocity, enabling the spacecraft to travel much further away from the Sun.

  1. Diffractive processes in antiproton-proton collision at s**(1/2) = 1.96 TeV in the D0 experiment

    SciTech Connect

    Otec, Roman; /Prague, Tech. U.

    2006-09-01

    A first study of single diffractive central high-p{sub T} dijet events in p{bar p} collisions at center-of-mass energy {radical}s = 1.96 TeV is presented, using data recorded by the D0 detector at the Tevatron during RunIIa in 2002-2004. The total integrated luminosity corresponding to the data sample is 398 pb{sup -1}. A diffractive sample is selected using a rapidity gap approach. A precise definition of the rapidity gap constitutes the first part of the thesis. The rapidity gap is defined by means of two parts of the D0 detector--luminosity detectors and calorimeter. Luminosity detectors serve as a basic indicators of diffractive candidates and the calorimeter is used to confirm the low energy activity in the forward region (a rapidity gap). Presented studies of energy deposited in forward part of calorimeter by various types of events yield two rapidity gap definitions. Both of them use a fixed rapidity interval in calorimeter |{eta}| {element_of} [2.6,5.2] and introduce an upper limit on the energy deposited in this region. First definition, which corresponds to the lowest systematical errors, uses a limit of 10 GeV, an energy limit in the second definition is set to 3 GeV. This alternative definition corresponds to the lowest contamination of diffractive sample by non-diffractive events, on the other hand it is accompanied with rejection of high percentage of diffractive candidates. Using the gap definition dijet diffractive data are then selected and compared to inclusive dijet events in various distributions. The main focus is to measure the difference in azimuthal angles between two leading jets in events with at least two high p{sub t} central jets. This variable is sensitive to the dynamics of the process. Indeed, the results show the different behavior of {Delta}{phi} distributions between the inclusive and diffractive samples. It is also shown that this difference is bigger for lower p{sub T} jets. Other distributions presented in the thesis show that

  2. 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

  3. Molecular characterization of dissolved organic matter through a desalination process by high resolution mass spectrometry.

    PubMed

    Cortés-Francisco, Nuria; Caixach, Josep

    2013-09-01

    The effect of different water treatments such as ultrafiltration (UF) and reverse osmosis (RO) on dissolved organic matter (DOM) is still unknown. Electrospray ionization Fourier transform orbitrap mass spectrometry has been used to provide valuable information of marine DOM evolution through a desalination process on a molecular scale. In the present manuscript, the characterization of four real composite water samples from a desalination pilot plant installed in the coast of Barcelona (Spain) has been carried out. The sampling was performed on each point of the pilot plant: raw seawater (RSW), UF effluent, brine RO and permeate RO. The mass spectra of the different samples show several thousand peaks, however for the present screening study, only the mass range m/z 200-500 and the main signals in this mass range (relative intensities ≥1%) have been considered. The analysis of RSW and UF samples reveal that there is little effect on DOM by the UF pilot. However, when the water is treated on the RO an important change on DOM has been observed. The recurring periodical patterns found in RSW and UF are lost in Permeate RO sample. Compounds with more aliphatic character, with higher H/C ratio (H/Cav 1.72) are present in the Permeate and some of them have been tentatively identified as fatty acids. PMID:23879562

  4. Ultrafast two-dimensional NMR relaxometry for investigating molecular processes in real time.

    PubMed

    Ahola, Susanna; Telkki, Ville-Veikko

    2014-06-01

    Nuclear spin-lattice (T1) and spin-spin (T2) relaxation times provide versatile information about the dynamics and structure of substances, such as proteins, polymers, porous media, and so forth. Multidimensional experiments increase the information content and resolution of NMR relaxometry, but they also multiply the measurement time. To overcome this issue, we present an efficient strategy for a single-scan measurement of a 2D T1-T2 correlation map. The method shortens the experimental time by one to three orders of magnitude as compared to the conventional method, offering an unprecedented opportunity to study molecular processes in real-time. We demonstrate that, despite the tremendous speed-up, the T1-T2 correlation maps determined by the single-scan method are in good agreement with the maps measured by the conventional method. The concept of the single-scan T1-T2 correlation experiment is applicable to a broad range of other multidimensional relaxation and diffusion experiments. PMID:24634359

  5. Molecular characterization of six intermediate proteins in the processing of mouse protamine P2 precursor.

    PubMed

    Chauvière, M; Martinage, A; Debarle, M; Sautière, P; Chevaillier, P

    1992-03-01

    In mouse spermatozoa, DNA is compacted by two protamines mP1 and mP2. Protamine mP2 (63 residues) is synthesized in spermatid nuclei as a precursor pmP2 (106 residues) which is subsequently processed at the end of spermiogenesis [Yelick, P.C., Balhorn, R., Johnson, P.A., Corzett, M., Mazrimas, J.A., Kleene, K.C. & Hecht, N.B. (1987) Mol. Cell. Biol. 7, 2173-2179]. Six proteins, three of which were described earlier [Chauvière, M., Martinage, A., Debarle, M., Alimi, E., Sautière, P. & Chevaillier, Ph. (1991) C.R. Acad. Sci. 313, 107-112], have molecular and electrophoretic properties similar to those of pmP2. They were isolated from purified testis nuclei and characterized by amino acid composition, N-terminal sequence and peptide mapping. From the amino acid compositions, it appears that all six proteins are rich in arginine, cysteine and histidine and are closely related to pmP2 and mP2. The N-terminal sequence of each protein overlaps a distinct region of the N-terminal part of pmP2. The C-terminal part of protamine mP2 starting at arginine 15 is common to all proteins as assessed by amino acid compositions and peptide maps. All these structural data demonstrate that the six isolated proteins are products of pmP2 precursor processing. The six intermediate proteins pmP2/5, pmP2/11, pmP2/16, pmP2/20, pmP2/26 and pmP2/32 which contain 102, 96, 91, 87, 81 and 75 residues, respectively, are generated from the pmP2 precursor after N-terminal excision of 4, 10, 15, 19, 25 and 31 residues, respectively. The C-terminal sequence of protamine mP2 is strictly identical to that of its precursor; therefore, no maturation occurs in this part of the molecule. At the present time, the proteolytic pathway involved in the amino-terminal processing leading to the mature form of the protamine mP2 (63 residues) has not been elucidated. However, the different representation of six intermediates in the testis suggests that some stages of processing are faster than others or that some

  6. 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

  7. 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

  8. Information processing in parallel through directionally resolved molecular polarization components in coherent multidimensional spectroscopy

    NASA Astrophysics Data System (ADS)

    Yan, Tian-Min; Fresch, Barbara; Levine, R. D.; Remacle, F.

    2015-08-01

    We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, kl, k l = ∑ i l i k i where ki is the propagation direction of the ith pulse and {li} is a set of integers that encodes the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, which are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by nonlinear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible.

  9. Self-Assembly, Molecular Ordering, and Charge Mobility in Solution-Processed Ultrathin Oligothiophene Films

    SciTech Connect

    Murphy,A.; Chang, P.; VanDyke, P.; Liu, J.; Frechet, J.; Subramanian, V.; Delongchamp, D.; Sambasivan, S.; Fischer, D.; Lin, E.

    2005-01-01

    Symmetrical {alpha}, {omega}-substituted quarter-(T4), penta-(T5), sexi-(T6), and heptathiophene (T7) oligomers containing thermally removable aliphatic ester solubilizing groups were synthesized, and their UV-vis and thermal characteristics were compared. Spun-cast thin films of each oligomer were examined with atomic force microscopy and near-edge X-ray absorption fine structure spectroscopy to evaluate the ability of the material to self-assemble from a solution-based process while maintaining complete surface coverage. Films of the T5-T7 oligomers self-assemble into crystalline terraces after thermal annealing with higher temperatures required to affect this transformation as the size of the oligomers increases. A symmetrical {alpha}, {omega}-substituted sexithiophene (T6-acid) that reveals carboxylic acids after thermolysis was also prepared to evaluate the effect of the presence of hydrogen-bonding moieties. The charge transport properties for these materials evaluated in top-contact thin film transistor devices were found to correlate with the observed morphology of the films. Therefore, the T4 and the T6-acid performed poorly because of incomplete surface coverage after thermolysis, while T5-T7 exhibited much higher performance as a result of molecular ordering. Increases in charge mobility correlated to increasing conjugation length with measured mobilities ranging from 0.02 to 0.06 cm2/(V{center_dot}s). The highest mobilities were measured when films of each oligomer had an average thickness between one and two monolayers, indicating that the molecules become exceptionally well-ordered during the thermolysis process. This unprecedented ordering of the solution-cast molecules results in efficient charge mobility rarely seen in such ultrathin films.

  10. Stochastic dynamics of small ensembles of non-processive molecular motors: The parallel cluster model

    NASA Astrophysics Data System (ADS)

    Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S.

    2013-11-01

    Non-processive molecular motors have to work together in ensembles in order to generate appreciable levels of force or movement. In skeletal muscle, for example, hundreds of myosin II molecules cooperate in thick filaments. In non-muscle cells, by contrast, small groups with few tens of non-muscle myosin II motors contribute to essential cellular processes such as transport, shape changes, or mechanosensing. Here we introduce a detailed and analytically tractable model for this important situation. Using a three-state crossbridge model for the myosin II motor cycle and exploiting the assumptions of fast power stroke kinetics and equal load sharing between motors in equivalent states, we reduce the stochastic reaction network to a one-step master equation for the binding and unbinding dynamics (parallel cluster model) and derive the rules for ensemble movement. We find that for constant external load, ensemble dynamics is strongly shaped by the catch bond character of myosin II, which leads to an increase of the fraction of bound motors under load and thus to firm attachment even for small ensembles. This adaptation to load results in a concave force-velocity relation described by a Hill relation. For external load provided by a linear spring, myosin II ensembles dynamically adjust themselves towards an isometric state with constant average position and load. The dynamics of the ensembles is now determined mainly by the distribution of motors over the different kinds of bound states. For increasing stiffness of the external spring, there is a sharp transition beyond which myosin II can no longer perform the power stroke. Slow unbinding from the pre-power-stroke state protects the ensembles against detachment.

  11. Molecular Mechanisms Mediating the Adaptive Regulation of Intestinal Riboflavin Uptake Process

    PubMed Central

    Subramanian, Veedamali S.; Ghosal, Abhisek; Kapadia, Rubina; Nabokina, Svetlana M.; Said, Hamid M.

    2015-01-01

    The intestinal absorption process of vitamin B2 (riboflavin, RF) is carrier-mediated, and all three known human RF transporters, i.e., hRFVT-1, -2, and -3 (products of the SLC52A1, 2 & 3 genes, respectively) are expressed in the gut. We have previously shown that the intestinal RF uptake process is adaptively regulated by substrate level, but little is known about the molecular mechanism(s) involved. Using human intestinal epithelial NCM460 cells maintained under RF deficient and over-supplemented (OS) conditions, we now show that the induction in RF uptake in RF deficiency is associated with an increase in expression of the hRFVT-2 & -3 (but not hRFVT-1) at the protein and mRNA levels. Focusing on hRFVT-3, the predominant transporter in the intestine, we also observed an increase in the level of expression of its hnRNA and activity of its promoter in the RF deficiency state. An increase in the level of expression of the nuclear factor Sp1 (which is important for activity of the SLC52A3 promoter) was observed in RF deficiency, while mutating the Sp1/GC site in the SLC52A3 promoter drastically decreased the level of induction in SLC52A3 promoter activity in RF deficiency. We also observed specific epigenetic changes in the SLC52A3 promoter in RF deficiency. Finally, an increase in hRFVT-3 protein expression at the cell surface was observed in RF deficiency. Results of these investigations show, for the first time, that transcriptional and post-transcriptional mechanisms are involved in the adaptive regulation of intestinal RF uptake by the prevailing substrate level. PMID:26121134

  12. 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.

  13. 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.

  14. 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.

  15. 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...

  16. 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...

  17. Teaching the Process of Molecular Phylogeny and Systematics: A Multi-Part Inquiry-Based Exercise

    ERIC Educational Resources Information Center

    Lents, Nathan H.; Cifuentes, Oscar E.; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from "Homo sapiens" and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these…

  18. Molecular dynamics investigation of the adhesion mechanism acting between dopamine and the surface of dopamine-processed aramid fibers.

    PubMed

    Chai, Dongliang; Xie, Zhimin; Wang, Youshan; Liu, Li; Yum, Young-Jin

    2014-10-22

    Dopamine, as a universal material for surface treatment, can effectively improve the surface performance of aramid fibers. However, directly processing the surface of aramid fibers using dopamine currently incurs a high cost. To seek dopamine substitutes, one must first explore the adhesion mechanism responsible for binding the dopamine to the surface of the fiber. In this study, we construct an all-atomic molecular dynamics model of an aramid fiber before and after surface modification using dopamine. A force field based on condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) is used. Using it, we analyze the surface adhesion mechanism of polydopamines aggregated by 21 kinds of molecular structures typically found on the surface of aramid fibers. The results show that a clear and smooth interface is formed between the polydopamine nanofilm layer and the surface of the aramid fiber. The high atomic density of the polydopamine in the small interface region is found to be conducive to noncovalent bonds of polydopamines with the surface of the aramid fiber. In addition, we investigate the works of adhesion of the 21 molecular structures typically found on the surface of aramid fibers. The results suggest that the work of adhesion of 5,6-indolequinone is the highest, followed by annular eumelanin molecules with annular planar structure. Straight-chain shaped dimers proved to be the molecules with the highest adhesion ability of the dihydroxyindole chain oligomers. Therefore, there is reason to suppose that more molecular structures (as above) can be formed by processing the surface of aramid fibers using dopamine by controlling the processing conditions. These molecular structures help improve the adhesion ability of the dopamine on the surface of the aramid fiber. Additionally, if these polydopamine molecules with high adhesion ability can be synthesized on a large scale, then new surface-processing materials are possible. PMID

  19. Mechanism of fragmentation and atomization of molecular ions in gasdynamic transport cell

    NASA Astrophysics Data System (ADS)

    Bazhenov, A. N.; Bulovich, S. V.; Gall, L. N.; Kretinina, A. V.; Lapushkin, M. N.; Gall, N. R.

    2010-04-01

    The fragmentation of molecular ions formed upon the electrospraying of a sample and transported through the gasdynamic system of a mass spectrometer equipped with an IESAP (Ion Extraction from Solution at Atmospheric Pressure) source has been experimentally studied. It is established that ion fragmentation in a Kantorowicz-Gray type cell takes place in the immediate vicinity of a skimmer port, apparently, as a result of collisions between ions (accelerated in an electric field) and stagnant gas. Molecular mechanisms of fragmentation are considered and it is concluded that this process can take place in a single ion-molecule collision event.

  20. Transport processes at alpha-quartz-water interfaces: insights from first-principles molecular dynamics simulations.

    PubMed

    Adeagbo, Waheed A; Doltsinis, Nikos L; Klevakina, Ksenia; Renner, Jörg

    2008-05-16

    Car-Parrinello molecular dynamics (CP-MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the alpha-quartz-water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H(2)O molecules into H(+) and OH(-) is observed at the Si-terminated surface. The OH(-) fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO(2) present as Si(OH)(4) in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)(4) molecule as would have been indicated by a substantial lowering of the Si(OH)(4) diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP-MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si--O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si--O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si--O bond. The final solute species is Si(OH)(4). PMID:18404743

  1. Molecular characterization of activated sludge from a seawater‐processing wastewater treatment plant

    PubMed Central

    Sánchez, Olga; Garrido, Laura; Forn, Irene; Massana, Ramon; Maldonado, Manuel Ignacio; Mas, Jordi

    2011-01-01

    Summary The prokaryotic community composition of activated sludge from a seawater‐processing wastewater treatment plant (Almeria, Spain) was investigated by using the rRNA approach, combining different molecular techniques such as denaturing gradient gel electrophoresis (DGGE), clone libraries and in situ hybridization (FISH and CARD‐FISH). Most of the sequences retrieved in the DGGE and the clone libraries were similar to uncultured members of different phyla. The most abundant sequence recovered from Bacteria in the clone library corresponded to a bacterium from the Deinococcus–Thermus cluster (almost 77% of the clones), and the library included members from other groups such as the Alpha, Gamma and Delta subclasses of Proteobacteria, the Bacteroidetes and Firmicutes. Concerning the archaeal clone library, we basically found sequences related to different orders of methanogenic Archaea, in correspondence with the recovered DGGE bands. Enumeration of DAPI (4′,6‐diamidino‐2‐phenylindole) stained cells from two different activated sludge samples after a mechanical flocculation disruption revealed a mean cell count of 1.6 × 109 ml−1. Around 94% of DAPI counts (mean value from both samples) hybridized with a Bacteria specific probe. Alphaproteobacteria were the dominant bacterial group (36% of DAPI counts), while Beta‐, Delta‐ and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes contributed to lower proportions (between 0.5–5.7% of DAPI counts). Archaea accounted only for 6% of DAPI counts. In addition, specific primers for amplification of the amoA (ammonia monooxygenase) gene were used to detect the presence of Beta, Gamma and archaeal nitrifiers, yielding positive amplifications only for Betaproteobacteria. This, together with negative in situ hybridizations with probes for well‐known nitrifiying bacteria, suggests that nitrification is performed by still undetected microorganisms. In summary, the combination of the

  2. A study of the collisional dynamics for collisions of UF with atoms and molecules

    NASA Astrophysics Data System (ADS)

    Doverspike, L. D.; Champion, R. D.

    1980-08-01

    Absolute total cross sections for the collisional decomposition of the negative ion of uranium hexafluoride into its three lowest asymptotic channels in collisions with the rare gases were measured for collision energies ranging from below thresholds for decomposition up to a laboratory collision energy of 500 eV. The experimental results were found to be consistent with the predictions of a two step collision model where the unimolecular decomposition of the excited molecular negative ions is described with a statistical theory.

  3. The effect of gold nanoparticles on exchange processes in collision complexes of triplet and singlet oxygen molecules with excited eosin molecules

    NASA Astrophysics Data System (ADS)

    Bryukhanov, V. V.; Minaev, B. M.; Tsibul'nikova, A. V.; Slezhkin, V. A.

    2015-07-01

    We have studied exchange processes in contact complexes of triplet eosin molecules with oxygen molecules in the triplet (3Σ{/g -}) and singlet (1Δ g ) states in thin polyvinylbutyral films in the presence of gold nanoparticles. Upon resonant excitation of surface plasmons in gold nanoparticles into the absorption band of eosin molecules-singlet oxygen sensitizers-we have obtained an increase in the intensity of the delayed fluorescence and an increase in the lifetime of the dye with simultaneous quenching of the luminescence of singlet oxygen. The kinetics of the delayed fluorescence of the dye as a result of singlet-triplet annihilation of triplet eosin molecules with singlet oxygen molecules has been investigated. To compare theoretical and experimental data, we have numerically simulated energy transfer processes. Rate constants of energy transfer and of singlet-triplet annihilation, as well as quenching constants of triplet states of the dye by molecular oxygen, have been calculated. Luminescence quantum yield 1Δ g of polyvinylbutyral has been estimated. We have analyzed quantum-chemically electronic mechanisms of singlet-triplet annihilation of oxygen and eosin.

  4. The dynamics of electronic to vibrational, rotational, and translational energy transfer in collision of Ba( sup 1 P sub 1 ) with diatomic molecules

    SciTech Connect

    Suits, A.G.; de Pujo, P.; Sublemontier, O.; Visticot, J.; Berlande, J.; Cuvellier, J.; Gustavsson, T.; Mestdagh, J.; Meynadier, P. ); Lee, Y.T. )

    1992-09-15

    Doppler measurements taken over a range of probe-laser angles in a crossed-beam experiment were used, in conjunction with forward convolution analysis, to obtain flux--velocity contour maps for Ba({sup 3}{ital P}{sub 2}) produced in a collision of Ba({sup 1}{ital P}{sub 1}) with H{sub 2}, N{sub 2}, O{sub 2}, and NO. The contour maps suggest a general model for the dynamics of this process in which large impact parameter collisions result in a near-resonant transfer of initial electronic energy into final vibrational energy, while close collisions produce sideways scattering and effectively couple electronic energy to translation. The molecular collision partners fall into two categories: for one group, comprising O{sub 2} and NO, the existence of a well-defined molecular anion with favorable Franck--Condon factors linking excited vibrational levels to the ground vibrational state of the neutral results in greatly enhanced coupling for the near-resonant process. Molecules for which there exist no stable anions, such as N{sub 2} and H{sub 2}, represent a second category. The electronically inelastic collision for this group is instead dominated by the nonresonant process yielding the ground vibrational state and large translational energy release.

  5. Exotics from Heavy Ion Collisions

    SciTech Connect

    Ohnishi, Akira; Jido, Daisuke; Cho, Sungtae; Furumoto, Takenori; Yazaki, Koichi; Hyodo, Tetsuo; Ko, Che Ming; Lee, Su Houng; Nielsen, Marina; Sekihara, Takayasu; Yasui, Shigehiro

    2011-10-21

    Discriminating hadronic molecular and multi-quark states is a long standing problem in hadronic physics. We propose here to utilize relativistic heavy ion collisions to resolve this problem, as exotic hadron yields are expected to be strongly affected by their structures. Using the coalescence model, we find that the exotic hadron yield relative to the statistical model result is typically an order of magnitude smaller for a compact multi-quark state, and larger by a factor of two or more for a loosely bound hadronic molecule. We further find that some of the newly proposed heavy exotic states could be produced and realistically measured at RHIC and LHC.

  6. A collision avoidance system for workpiece protection

    SciTech Connect

    Schmitt, D.J.; Weber, T.M.; Novak, J.L.; Maslakowski, J.E.

    1995-04-01

    This paper describes an application of Sandia`s non-contact capacitive sensing technology for collision avoidance during the manufacturing of rocket engine thrust chambers. The collision avoidance system consists of an octagon shaped collar with a capacitive proximity sensor mounted on each face. The sensors produced electric fields which extend several inches from the face of the collar and detect potential collisions between the robot and the workpiece. A signal conditioning system processes the sensor output and provides varying voltage signals to the robot controller for stopping the robot.

  7. Cosmic string collision in cosmological backgrounds

    SciTech Connect

    Firouzjahi, Hassan; Khoeini-Moghaddam, Salomeh; Khosravi, Shahram

    2010-06-15

    The collisions of cosmic string loops and the dynamics of junction formations in expanding backgrounds are studied. The key parameter controlling the dynamics of junction formation, the cosmic strings zipping and unzipping, is the relative size of the loops compared to the Hubble radius at the time of collision. We study analytically and numerically these processes for large superhorizon size loops, for small subhorizon size loops as well as for loops with the radii comparable to the Hubble radius at the time of collision.

  8. Tumor-Specific Proteolytic Processing of Cyclin E Generates Hyperactive Lower-Molecular-Weight Forms

    PubMed Central

    Porter, Donald C.; Zhang, Ning; Danes, Christopher; McGahren, Mollianne J.; Harwell, Richard M.; Faruki, Shamsa; Keyomarsi, Khandan

    2001-01-01

    Cyclin E is a G1 cyclin essential for S-phase entry and has a profound role in oncogenesis. Previously this laboratory found that cyclin E is overexpressed and present in lower-molecular-weight (LMW) isoforms in breast cancer cells and tumor tissues compared to normal cells and tissues. Such alteration of cyclin E is linked to poor patient outcome. Here we report that the LMW forms of cyclin E are hyperactive biochemically and they can more readily induce G1-to-S progression in transfected normal cells than the full-length form of the protein can. Through biochemical and mutational analyses we have identified two proteolytically sensitive sites in the amino terminus of human cyclin E that are cleaved to generate the LMW isoforms found in tumor cells. Not only are the LMW forms of cyclin E functional, as they phosphorylate substrates such as histone H1 and GST-Rb, but also their activities are higher than the full-length cyclin E. These nuclear localized LMW forms of cyclin E are also biologically functional, as their overexpression in normal cells increases the ability of these cells to enter S and G2/M. Lastly, we show that cyclin E is selectively cleaved in vitro by the elastase class of serine proteases to generate LMW forms similar to those observed in tumor cells. These studies suggest that the defective entry into and exit from S phase by tumor cells is in part due to the proteolytic processing of cyclin E, which generates hyperactive LMW isoforms whose activities have been modified from that of the full-length protein. PMID:11509668

  9. Numerical simulations of evaporation and condensation processes of giant molecular clouds in a hot plasma

    NASA Astrophysics Data System (ADS)

    Vieser, Wolfgang; Hensler, Gerhard

    We are performing 2D hydrodynamic simulations to examine the evaporation and condensation processes of giant molecular clouds in the hot phase of the interstellar medium (ISM). The evolution of cold and dense clouds (T=1000K, n_H=3{cm}^{-3}, M=6\\cdot10^4 {M}_{\\odot}) is calculated in the subsonic streaming of a hot rarefied plasma (T=5\\cdot10^6K, n_H=6\\cdot10^{-4}{cm}^{-3}). Our code includes self-gravity, heating and cooling effects and heat conduction by electrons. We are using the thermal conductivity of a fully ionized hydrogen plasma (\\propto {T}^{5/2}, Spitzer, 1962, Physics of Fully Ionized Gases) and a saturated heat flux (Cowie & McKee, 1977, ApJ 211, 135) in regions where the mean free path of the electrons is long compared to the temperature scale height. Significant differences occur between simulations with and without heat conduction. In the simulations without heat conduction, the cloud edge is stired up by Kelvin-Helmholtz (K-H) instabilities after only a few dynamical times. It is not possible to incorporate a significant amount of hot gas in the cloud core before the cloud is destroyed by instabilities. The simulations including heat conduction show an evolution that proceeds not as violent as the case without heat conduction. The edge of the cloud remains nearly unsusceptible to K-H instabilities. In this scenario it is possible to mix the formerly hot streaming gas very effectively with the cloud material.

  10. 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.

  11. Molecular basis of processing-induced changes in protein structure in relation to intestinal digestion in yellow and green type pea (Pisum sativum L.): A molecular spectroscopic analysis.

    PubMed

    Yu, Gloria Qingyu; Warkentin, Tom; Niu, Zhiyuan; Khan, Nazir A; Yu, Peiqiang

    2015-12-01

    The objectives of this study were (1) to quantify the protein inherent molecular structural features of green cotyledon (CDC Striker) and yellow cotyledon (CDC Meadow) pea (Pisum sativum L.) seeds using molecular spectroscopic technique (FT/IR-ATR); (2) measure the denaturation of protein molecular makeup in the two types of pea during dry roasting (120°C for 60 min), autoclaving (120°C for 60 min) or microwaving (for 5 min); and (3) correlate the heat-induced changes in protein molecular makeup to the corresponding changes in protein digestibility determined using modified three-step in vitro procedure. Compared with yellow-type, the green-type peas had higher (P<0.05) ratios of amide I to II peak height (1.698 vs. 1.805) and area (1.843 vs. 2.017). A significant correlation was observed between the amide I and II peak height (r=0.48) and peak area (r=-0.42) ratio with protein content. Compared with yellow-type, the green-type peas had lower (P<0.05) α-helix:β-sheet ratio (1.015 vs. 0.926), indicating varietal difference in protein secondary structure makeup. All processing applications increased α-helix:β-sheet ratio, with the largest (P<0.05) increase being observed with roasting and microwaving. The heat-induced changes in α-helix:β-sheet ratio was strongly correlated to intestinal digestibility of protein within the green (r=-0. 86) and yellow (r=0.81) pea-types. However, across the pea types the correlation was not significant. Principal component and hierarchical cluster analyses on the entire spectral data from the amide region (ca. 1727-1480 cm(-1)) were able to visualize and discriminate the structural difference between pea varieties and processing treatments. This study shows that the molecular spectroscopy can be used as a rapid tool to screen the protein value of raw and heat-treated peas. PMID:26188704

  12. Spectroscopic study of molecular-hydrogen processes in a mirror-confined plasma

    SciTech Connect

    Moran, T.G. |

    1995-04-01

    Visible and near-ultraviolet molecular hydrogen emission from the Tara Tandem Mirror central cell plasma was investigated in order to determine molecular densities, ionization rates, and continuum dissociation rates. Measurements of H{sub 2} {ital G}{r_arrow}{ital B} band emission were used to infer spatial density and ionization profiles, maximum densities of 4{times}10{sup 12} cm{sup {minus}3} at the gas injection port, and a total molecular ionization rate of 254 A. Continuum emission in the near ultraviolet was identified as the H{sub 2} dissociative continuum through its wavelength distribution, time behavior, and intensity. Wavelength-integrated continuum emission measurements were used to obtain the dissociation rate associated with the continuum: 6 A. The power expended in molecular ionization, dissociation, and radiation is estimated to be 8.4 kW out of 300 kW of rf power injected.

  13. Enantiopure Functional Molecular Motors Obtained by a Switchable Chiral-Resolution Process.

    PubMed

    van Leeuwen, Thomas; Gan, Jefri; Kistemaker, Jos C M; Pizzolato, Stefano F; Chang, Mu-Chieh; Feringa, Ben L

    2016-05-17

    Molecular switches, rotors, and motors play an important role in the development of nano-machines and devices, as well as responsive and adaptive functional materials. For unidirectional rotors based on chiral overcrowded alkenes, their stereochemical homogeneity is of crucial importance. Herein, a method to obtain new and functionalizable overcrowded alkenes in enantiopure form is presented. The procedure involves a short synthesis of three steps and a solvent-switchable chiral resolution by using a readily available resolving agent. X-ray crystallography revealed the mode of binding of the motor with the resolving agent, as well as the absolute configuration of the motor. (1) H NMR and UV/Vis spectroscopy techniques were used to determine the dynamic behavior of this molecular motor. This method provides rapid access to ample amounts of enantiopure molecular motors, which will greatly facilitate the further development of responsive molecular systems based on chiral overcrowded alkenes. PMID:27072290

  14. Molecular dynamics simulation for the cluster formation process of Lennard-Jones particles: Magic numbers and characteristic features

    NASA Astrophysics Data System (ADS)

    Ikeshoji, Tamio; Hafskjold, Bjørn; Hashi, Yuichi; Kawazoe, Yoshiyuki

    1996-09-01

    Cluster formation of Lennard-Jones particles (65 536 atoms in a unit cell with an overall number density equal to 0.0149) was simulated by molecular dynamics. The temperature was set to decrease linearly with time by various thermostats, starting from a gas state temperature and ending at zero temperature. With the Nosé-Hoover thermostat, it was found that the translational temperature of the clusters suddenly decreased almost to zero when the cluster formation drastically increased around a reduced temperature (T*) of 0.5, while the internal temperature decreased linearly. Using the Andersen thermostat, which could simulate the aggregation of particles in an inert gas, both the internal and translational temperatures decreased almost linearly with time. When these thermostats were used, cluster-cluster and cluster-atom collisions did not give any magic number peaks in the size distribution up to 250 atoms/cluster at any temperature. Careful tracing of the cluster growth of 13-atom clusters showed no difference in reactivity between icosahedral and nonicosahedral clusters. To simulate cooling in a supersonic jet, a thermostat which controlled only the translational temperature was introduced. After the clusters were formed by cooling the system with this thermostat, their internal temperature stayed at T*≊0.5, while the translational temperature decreased linearly to zero with time as it was controlled. A long-time evaporation from these high-temperature clusters gave peaks at 13 and 19 (and less significantly at 23 and 26) which are magic number sizes corresponding to single, double, triple, and quadruple icosahedra, respectively. The internal temperatures of 13- and 19-atom clusters were higher than those of other size clusters. Higher evaporation energy was observed for the clusters of 13, 19, 23, and 26 atoms than for other size clusters after the long-time evaporation, but only the 13-atom clusters had the higher evaporation energy after cooling by the

  15. Spatial Kerr soliton collisions at arbitrary angles.

    PubMed

    Chamorro-Posada, P; McDonald, G S

    2006-09-01

    The theory of spatial Kerr solitons is extended to colliding beams that are neither almost-exactly copropagating nor almost-exactly counterpropagating. Our new Helmholtz formalism yields results that are consistent with the inherent symmetry of the collision process and that are not predicted by existing paraxial descriptions. Full numerical and approximate analytical results are presented. These show excellent agreement. In particular, Kerr solitons are found to be remarkably robust under nonparaxial collisions. PMID:17025766

  16. Transition rates in proton - Rydberg atom collisions

    NASA Astrophysics Data System (ADS)

    Vrinceanu, Daniel

    2016-05-01

    Monte Carlo simulations for energy and angular momentum transfer processes in proton - Ryderg atom collisions were performed and the corresponding rates are reported.The relevance of these rates in the context of cosmological recombination is discussed. The rates are contrasted with the similar rates in electron - Rydberg atom collisions. This work has been supported by National Science Foundation through grants for the Center for Research on Complex Networks (HRD-1137732) and Research Infrastructure for Science and Engineering (RISE) (HRD-1345173).

  17. Disequilibration by Planetary Collision

    NASA Astrophysics Data System (ADS)

    Asphaug, E. I.; Jutzi, M.

    2010-12-01

    Molten planets equilibrate gravitationally, chemically, and thermally. Large scale collisions (a.k.a. giant impacts, similar-sized collisions) can upset the apple cart by bringing core material, late in the game, into mixture with mantle products, and by shredding stratified planets into strands of mantle and clumps of core (c.g. Asphaug et al. Nature 2006). Atmophiles and volatiles come along for the ride, and can find themselves in disequilibrium mixtures not anticipated by one-dimensional models of planetary evolution, or by planet growth models in which planets stick, merge, and mix perfectly in the aftermath of a collision. We present very high resolution case studies of such collisions.

  18. Biomimetic materials processing: Implementation of molecular imprinting and study of biomineralization through the development of an agarose gel assay

    NASA Astrophysics Data System (ADS)

    Boggavarapu, Sajiv

    Biomimetics is defined as an approach in which naturally occurring materials processes are mimicked in laboratory situations. The ultimate goal is to develop synthetic analogues of naturally occurring materials such as bone and teeth, classified as biocomposites, which possess similar chemical and mechanical properties. The work presented here provides the initial work in furthering the progress of biomimetic materials processing. The first element of the work utilizes molecular imprinting as a selective recognition, or sensing tool, for detection of low molecular weight organic molecules. Molecular imprinting is a phenomenon in which crosslinked synthetic polymers exhibit selective binding towards small organic molecules. Initial work in the field was done in which numerous processing steps were involved with bulk polymer samples while the achievement here lies in the development of molecular imprinted polymer films which greatly facilitate the processing and characterization. Molecularly imprinted polymers are sometimes referred to as artificial antibodies due to the selective binding aspects that are highly analogous to natural antibodies. Additional work involves transforming the recognition aspects of molecular imprinting into a biomineralization analogue. Biomineralization is the process in which organisms convert freely soluble minerals (namely calcium carbonates and calcium phosphates) into solid parts, such as bones and teeth, at ambient conditions via the influence of organic molecules such as proteins and carbohydrates. The molecular imprinting approach with biomineralization led to limited success but formed the foundation for a more detailed study into the effects of small organic functional groups (COOH-, OH-) on the growth of calcium carbonates and calcium phosphates, the core components of important biocomposites such as bone. In order to study the effects of organic molecules on the calcium based crystals, a mineralization assay was developed in an

  19. Basins in ARC-continental collisions

    USGS Publications Warehouse

    Draut, Amy E.; Clift, Peter D.

    2012-01-01

    Arc-continent collisions occur commonly in the plate-tectonic cycle and result in rapidly formed and rapidly collapsing orogens, often spanning just 5-15 My. Growth of continental masses through arc-continent collision is widely thought to be a major process governing the structural and geochemical evolution of the continental crust over geologic time. Collisions of intra-oceanic arcs with passive continental margins (a situation in which the arc, on the upper plate, faces the continent) involve a substantially different geometry than collisions of intra-oceanic arcs with active continental margins (a situation requiring more than one convergence zone and in which the arc, on the lower plate, backs into the continent), with variable preservation potential for basins in each case. Substantial differences also occur between trench and forearc evolution in tectonically erosive versus tectonically accreting margins, both before and after collision. We examine the evolution of trenches, trench-slope basins, forearc basins, intra-arc basins, and backarc basins during arc-continent collision. The preservation potential of trench-slope basins is low; in collision they are rapidly uplifted and eroded, and at erosive margins they are progressively destroyed by subduction erosion. Post-collisional preservation of trench sediment and trench-slope basins is biased toward margins that were tectonically accreting for a substantial length of time before collision. Forearc basins in erosive margins are usually floored by strong lithosphere and may survive collision with a passive margin, sometimes continuing sedimentation throughout collision and orogeny. The low flexural rigidity of intra-arc basins makes them deep and, if preserved, potentially long records of arc and collisional tectonism. Backarc basins, in contrast, are typically subducted and their sediment either lost or preserved only as fragments in melange sequences. A substantial proportion of the sediment derived from

  20. 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.

  1. Use of molecular typing methods to trace the dissemination of Listeria monocytogenes in a shrimp processing plant.

    PubMed Central

    Destro, M T; Leitão, M F; Farber, J M

    1996-01-01

    Molecular typing of bacteria has been widely used in epidemiological studies but not as extensively for tracing the transmission of pathogenic bacteria in food plants. This study was conducted to examine the potential use of two molecular typing methods, random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE), to trace Listeria monocytogenes contamination in a shrimp processing plant. Ribotyping and phase typing were also performed on a select number of strains. One hundred fifteen strains of L. monocytogenes collected in different areas of a shrimp processing plant were first serotyped and then subtyped by molecular typing. RAPD and PFGE showed great promise for typing L. monocytogenes isolates since distinguishable and reproducible DNA polymorphisms were obtained. When the composite profile from both (RAPD and PFGE) methods was generated, there was an increase in the discriminatory power to discern differences between strains of L. monocytogenes. The results indicated that environmental strains all fell into composite profile groupings unique to the environment, while strains from both water and utensils shared another composite profile group. L. monocytogenes fresh shrimp isolates belonging to one profile group were found in different areas of the processing line. This same profile group was also present in food handlers from the processing and packaging areas of the plant. PMID:8593073

  2. Gravity-induced cellular and molecular processes in plants studied under altered gravity conditions

    NASA Astrophysics Data System (ADS)

    Vagt, Nicole; Braun, Markus

    With the ability to sense gravity plants possess a powerful tool to adapt to a great variety of environmental conditions and to respond to environmental changes in a most beneficial way. Gravity is the only constant factor that provides organisms with reliable information for their orientation since billions of years. Any deviation of the genetically determined set-point angle of the plants organs from the vector of gravity is sensed by specialized cells, the statocytes of roots and shoots in higher plants. Dense particles, so-called statoliths, sediment in the direction of gravity and activate membrane-bound gravireceptors. A physiological signalling-cascade is initiated that eventually results in the gravitropic curvature response, namely, the readjust-ment of the growth direction. Experiments under microgravity conditions have significantly contributed to our understanding of plant gravity-sensing and gravitropic reorientation. For a gravity-sensing lower plant cell type, the rhizoid of the green alga Chara, and for statocytes of higher plant roots, it was shown that the interactions between statoliths and the actomyosin system consisting of the actin cytoskeleton and motor proteins (myosins) are the basis for highly efficient gravity-sensing processes. In Chara rhizoids, the actomyosin represents a guid-ing system that directs sedimenting statoliths to a specific graviperception site. Parabolic flight experiments aboard the airbus A300 Zero-G have provided evidence that lower and higher plant cells use principally the same statolith-mediated gravireceptor-activation mechanism. Graviper-ception is not dependent on mechanical pressure mediated through the weight of the sedimented statoliths, but on direct interactions between the statoliths's surface and yet unknown gravire-ceptor molecules. In contrast to Chara rhizoids, in the gravity-sensing cells of higher plants, the actin cytoskeleton is not essentially involved in the early phases of gravity sensing. Dis

  3. Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration.

    PubMed

    Avenhaus, Ulrike; Cabeza, Ricardo A; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

    2015-01-01

    Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be

  4. Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration

    PubMed Central

    Avenhaus, Ulrike; Cabeza, Ricardo A.; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

    2016-01-01

    Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be

  5. Calcium isotope fractionation in groundwater: Molecular scale processes influencing field scale behavior

    NASA Astrophysics Data System (ADS)

    Druhan, Jennifer L.; Steefel, Carl I.; Williams, Kenneth H.; DePaolo, Donald J.

    2013-10-01

    It is the purpose of this study to demonstrate that the molecular scale reaction mechanisms describing calcite precipitation and calcium isotope fractionations under highly controlled laboratory conditions also reproduce field scale measurements of δ44Ca in groundwater systems. We present data collected from an aquifer during active carbonate mineral precipitation and develop a reactive transport model capturing the observed chemical and isotopic variations. Carbonate mineral precipitation and associated fluid δ44Ca data were measured in multiple clogged well bores during organic carbon amended biogenic reduction of a uranium contaminated aquifer in western Colorado, USA. Secondary mineral formation induced by carbonate alkalinity generated during the biostimulation process lead to substantial permeability reduction in multiple electron-donor injection wells at the field site. These conditions resulted in removal of aqueous calcium from a background concentration of 6 mM to <1 mM while δ44Ca enrichment ranged from 1‰ to greater than 2.5‰. The relationship between aqueous calcium removal and isotopic enrichment did not conform to Rayleigh model behavior. Explicit treatment of the individual isotopes of calcium within the CrunchFlow reactive transport code demonstrates that the system did not achieve isotopic reequilibration over the time scale of sample collection. Measured fluid δ44Ca values are accurately reproduced by a linear rate law when the Ca2+:CO32- activity ratio remains substantially greater than unity. Variation in the measured δ44Ca between wells is shown to originate from a difference in carbonate alkalinity generated in each well bore. The influence of fluid Ca2+:CO32- ratio on the precipitation rate and δ44Ca is modeled by coupling the CrunchFlow reactive transport code to an ion by ion growth model. This study presents the first coupled ion-by-ion and reactive transport model for isotopic enrichment and demonstrates that reproducing field

  6. Dynamical resonant electron capture in atom surface collisions: H- formation in H-Al(111) collisions

    NASA Astrophysics Data System (ADS)

    Borisov, A. G.; Teillet-Billy, D.; Gauyacq, J. P.

    1992-05-01

    The formation of H- ion by grazing-angle collisions of hydrogen on an Al(111) surface is investigated with the newly developed coupled angular mode method. The capture process involves a dynamical resonant process induced by the collision velocity. All the resonance properties of the H- level in front of an Al(111) surface are determined: position, width, and angular distribution of ejected electrons. The results are shown to account for the recent observations on H- formation by Wyputta, Zimny, and Winter.

  7. Spectroscopic investigation of the NO C 2Π de-excitation process by collision with O2 X 3Σg- in a low-pressure N2-O2 mixture microwave discharge

    NASA Astrophysics Data System (ADS)

    Tan, Hao; Nezu, Atsushi; Akatsuka, Hiroshi

    2016-01-01

    We use a spectroscopic method to diagnose the microwave discharge plasma of N2-O2 mixtures. We succeed in observing NO δ-band radiation peaks when the oxygen partial pressure is smaller than 3%. In order to quantitatively investigate the de-excitation processes of the NO C 2Π excited state, we improve our self-consistent kinetic model to include some of the main excited states of NO molecules. In providing our numerical results, we discuss a reasonable NO C 2Π de-population process by that involves collision with the O2 X 3Σg- state molecule, which leads to the disappearance of δ-band radiation. We propose an indirect proof that this de-population process results in an increase in the vibrational temperature of NO A 2Σ+.

  8. MOLSCAT: MOLecular SCATtering

    NASA Astrophysics Data System (ADS)

    Hutson, Jeremy M.; Green, Sheldon

    2012-06-01

    MOLSCAT is a FORTRAN code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem and was developed to obtain collision rates for molecules in the interstellar gas which are needed to understand microwave and infrared astronomical observations. The code is implemented for various types of collision partners. In addition to the essentially exact close coupling method several approximate methods, including the Coupled States and Infinite Order Sudden approximations, are provided.

  9. 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.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  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

    2016-01-01

    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

  14. 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

  15. An isomerization-induced cage-breaking process in a molecular glass former below T{sub g}

    SciTech Connect

    Teboul, V.; Saiddine, M.; Accary, J.-B.; Nunzi, J.-M.

    2011-03-21

    A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials.

  16. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  17. Rovibrationally Inelastic Collisions of Ultracold Lithium Dimer

    NASA Astrophysics Data System (ADS)

    Jasmine, William; Stewart, Brian

    2016-05-01

    We have calculated cross sections for rovibrationally inelastic collisions of Li2 A(1) 1Σu+ colliding with neon and xenon on ab initio potentials. We find that the inelastic cross section can be very large and increasing at low collision velocity. This behavior is very well modeled as a Langevin process. The total inelastic cross section is a sizable fraction of the total capture cross section, typically about a third. For Li2 - Xe, the total inelastic rate constants are several thousand square angstroms, and level-to-level rate constants are several hundred square angstroms at collision speeds below 1000 cm/s, implying that such collisions might be observable in photoassociated lithium dimer.

  18. 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. PMID:26245857

  19. 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.

  20. Collision-spike sputtering of Au nanoparticles

    DOE PAGESBeta

    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