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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. 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.

  3. 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.

  4. 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.

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

    PubMed

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

    2014-12-21

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

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

    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

  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. 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.

  10. 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

  11. Secondary Molecular Ion Emission In Binary Projectile-Surface Collisions

    NASA Astrophysics Data System (ADS)

    Jalowy, T.; Neugebauer, R.; Farenzena, L. S.; Collado, V. M.; Schmidt-Böcking, H.; da Silveira, E. F.; Groeneveld, K. O.

    2003-08-01

    Secondary molecular ions, emitted from a LiF target bombarded by a MeV argon beam, are analyzed by a XY-TOF detection system. This new method allows, for each emitted ion, simultaneous measurement of its time-of flight (TOF) and its impact coordinates (XY) on the detector surface, after acceleration by a homogenous electric field. Angular distributions and initial velocities for atomic (H+ , Li+, C+) and for molecular (Hn+, CmHn+) ions are determined. The analysis reveals different emission processes, among them a unexpected emission of fast molecular ions from binary collisions.

  12. 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,

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

    NASA Astrophysics Data System (ADS)

    Peach, Gillian; Dimitrijevic, Milan S.

    2012-04-01

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

  14. Division B Commission 14 Working Group: Collision Processes

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  15. Giant Molecular Cloud Collisions as Triggers of Star Formation

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  16. 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}

  17. 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.

  18. Continuum and molecular-dynamics simulation of nanodroplet collisions

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  19. 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.

  20. 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.

  1. 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.

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

    PubMed

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

    2016-05-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Optimal separable bases and molecular collisions

    SciTech Connect

    Poirier, L W

    1997-12-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Quéméner, Goulven; Bohn, John L.

    2016-01-01

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

  10. 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

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

    PubMed

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

    2016-09-07

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

  13. 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

  14. 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

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

    NASA Technical Reports Server (NTRS)

    Ioup, J.

    1979-01-01

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

  16. 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.

  17. 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.

  18. Multichannel quantum defect theory for cold molecular collisions

    SciTech Connect

    Croft, James F. E.; Wallis, Alisdair O. G.; Hutson, Jeremy M.; Julienne, Paul S.

    2011-10-15

    Multichannel quantum defect theory (MQDT) is shown to be capable of producing quantitatively accurate results for low-energy atom-molecule scattering calculations. With a suitable choice of reference potential and short-range matching distance, it is possible to define a matrix that encapsulates the short-range collision dynamics and is only weakly dependent on energy and magnetic field. Once this has been produced, calculations at additional energies and fields can be performed at a computational cost that is proportional to the number of channels N and not to N{sup 3}. MQDT thus provides a promising method for carrying out low-energy molecular scattering calculations on systems where full exploration of the energy dependence and the field dependence is currently impractical.

  19. 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

  20. Effect of laser frequency on a collision-induced radiative process

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

    A review is presented of the principles of collision induced radiative processes, followed by an examination of the effects of laser frequencies on these processes. A one-dimensional problem involving two electron states is considered, and it is found that the Hamiltonian of the radiation field is dominated by electric-dipole interaction which couples states of different parity. Transitions are noted to be dependent on collisions, and the complexities of three-dimensional systems are expressed as considerations of the angular momentum of the photon, the necessity of treating different states simultaneously, and the fact that a radiation field destroys rotational invariance. Changing the radiation frequency alters the crossing point and offers opportunities to study the interplay of potential surfaces with molecular dynamics. Experiments on Na+A systems are outlined for several collision energies and various laser frequencies. Multiple crossings were obtained, although the total cross-section, at all energies, decreased at 18,350/cm.

  1. 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.

  2. 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.

  3. Fragmentation processes of OCS in collision with highly charged ions

    NASA Astrophysics Data System (ADS)

    Matsumoto, J.; Tezuka, T.; Fukutome, A.; Karimi, R.; Wales, B.; Sanderson, J. H.; Shiromaru, H.

    2014-04-01

    Fragmentation of (OCS)3+ and (OCS)4+ produced by 120 keV Ar8+ collision was studied by using a position-sensitive time-of-flight (PS-TOF) method. We identified stepwise processes involving CO2+ and CS2+ metastable species as well as the concerted process (simultaneous breakup of the two bonds). For the (OCS)4+ events, the stepwise processes were found for fragmentation channels containing a doubly-charged terminal atom.

  4. 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.

  5. 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.

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

    SciTech Connect

    Larriba, Carlos Hogan, Christopher J.

    2013-10-15

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

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

    NASA Technical Reports Server (NTRS)

    Green, S.

    1984-01-01

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

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

    SciTech Connect

    Inoue, Tsuyoshi; Fukui, Yasuo

    2013-09-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

    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.

  10. Quasidiatomic Approach to the Collisions of Low KEV Molecular Ions with Atoms

    NASA Astrophysics Data System (ADS)

    Yenen, Orhan

    The polarization of L(,(alpha)) radiation is measured in coincidence with a charged particle scattered at specific laboratory angles, resulting from the collision induced dissociation of low keV H(,2)('+) and H(,3)('+) incident on target gases. Coincidence measurements of the polarization pattern are made for a variety of scattering angles for 3.22 keV H(,2)('+) incident on He and Ne, and for 4.83 keV H(,3)('+) incident on He. The molecular states excited during the collision are determined from the alignment of the observed polarization patterns. A quasidiatomic collision model, which is an extension of the electron promotion model of ion-atom collisions at low keV energies to molecule-atom collisional systems, is developed to interpret the experimental results. The rules of building simple quasidiatomic correlation diagrams, to qualitatively estimate the dynamical behavior of molecular collisions, are presented. The general idea of treating the molecule as an atom under certain circumstances, is applied to a molecular two-state calculation of the differential charge-transfer probabilities in H('+)-H(,2) collisions. This calculation reproduces the essential features of previous experiments.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

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

  19. 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)

  20. 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.

  1. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1979-01-01

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

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  5. The n-p bremsstrahlung in heavy ion collision processes

    NASA Astrophysics Data System (ADS)

    Blann, M.

    1990-01-01

    The goal is to summarize the current status of the interpretation of energetic gamma-rays in heavy ion collisions via the n-p-bremsstrahlung mechanism. An essential element of the topic is a transport equation to approximate the fast non-equilibrium nucleon-nucleon cascade/emission stage of the heavy ion reactions. It is during this stage that it was expected that the n-p-bremsstrahlung processes produced energetic photons. The Boltzmann master equation (BME) model which will be used as the transport code is briefly described, deferring to earlier works for a more complete description, and present but a single representative comparison with an experimental neutron emission spectrum. The status of the elementary n-p-gamma cross section needed to extend the transport code to photon emission in heavy ion reactions, and the status of these comparisons with data are summarized.

  6. Correlated electron processes in ion-atom collisions

    SciTech Connect

    McColm, D.W. . Dept. of Physics)

    1990-02-01

    This final report covers the work carried out under the LLNL Contract P.O. Number B055762, Subcontractor Regents University of California at Davis. The research carried out under this contract investigated electron processes occurring in collisions between heavy ions and atoms. The doubly-differential secondary electron yield following the impact of 3.5 to 8 MeV/uU{sup q+}(q = 38,68) ion impact on thin carbon foil targets has been investigated experimentally. The absolute electron emission yields were determined for ejection angles varied between 22.5{degree} and 157{degree} and electron energies ranging from 10 eV to 8 keV. The electron spectra are compared to previous investigations and new experimental data using lighter ion impact at MeV projectile energies. 14 refs., 5 figs.

  7. 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.

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

    SciTech Connect

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

    2009-04-03

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

  9. Initial results of a full kinetic simulation of RF H- source including Coulomb collision process

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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 ne ˜ 1018 m-3 and high gas pressure pH2 = 3 Pa, while it is necessary to include Coulomb collision under high electron density and low gas pressure conditions.

  10. Nuclear collision processes around the Bragg peak in proton therapy.

    PubMed

    Matsuzaki, Yuka; Date, Hiroyuki; Sutherland, Kenneth Lee; Kiyanagi, Yoshiaki

    2010-01-01

    In the physical processes of proton interaction in bio-materials, most of the proton energy is transferred to electrons. Ionization and excitation occur most frequently around the Bragg peak region, where nuclear reactions also exist. In this study, we investigated the processes of energy deposition by considering interactions including the nuclear reactions between protons and water molecules by a Monte Carlo simulation for proton therapy. We estimated the number of particles produced by a variety of nuclear reactions, and we focused on the interaction in the low-energy region (below 1 MeV). Furthermore, we considered the charge-changing processes in the low-energy region (less than a few hundred keV). Finally, we evaluated the total dose and the contribution of primary protons and secondary particles through nuclear reactions to the absorbed dose. The results showed that the protons generate numerous neutrons via nuclear reactions. Particularly, neutrons with relatively low energies produce recoil protons by elastic collisions with the hydrogen atoms. Around the Bragg peak, low-energy primary protons (slowed-down protons) are prevalent, whereas recoil (secondary) protons gradually become dominant behind the distal falloff region of the Bragg peak. Therefore, around the Bragg peak, the main contribution to the absorbed dose is that of the primary protons (from 80 to 90%), whereas secondary protons created by primary proton-induced reactions contribute to the dose from 20 to 5%. Behind the distal endpoint of the Bragg peak, the absorbed dose is mainly due to the protons produced by (1)H(n, p), and the contribution of these is about 70%. PMID:20821107

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

    NASA Astrophysics Data System (ADS)

    Smith, Winthrop; Wells, James

    2009-05-01

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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. ATOMIC AND MOLECULAR PHYSICS: Lie Algebraic Approach to Energy Transfer for Collinear Collision of Two Anharmonic Diatomic Molecules

    NASA Astrophysics Data System (ADS)

    Wang, Xiao-Yan; Wang, Peng-Cheng; Qiu, Jian-Feng; Wang, Jin-Xi; Hou, Li-Xia; Xie, Jin-Dong Ding, Shi-Liang

    2010-02-01

    An anharmonic oscillator algebra model is used to study the collinear collisions of two diatomic molecules. The transition probability for vibration-vibration energy transfer is presented. For an application of the method, we talk about the collision of N2+CO, N2+O2, and N2+N2. Through long time averaging, the transition probability changes to the function of total energy of the system. Comparing the results with the quantum results, we can see that the dynamical Lie algebraic method is useful for describing the anharmonic diatomic molecular collision.

  17. Half-Collision Dynamics of Excited Metal Atom Quenching Processes

    NASA Astrophysics Data System (ADS)

    Wallace, Ingvar Axel, II

    Half-collision studies of the quenching of excited states of Zn by Xe and Cd by H_2, CH_4 and i-C_4H _{10} have been undertaken and have provided information concerning the role of alignment of the excited metal atom p-orbital as well as other dynamical information and details about the potential energy surfaces (curves) involved in the quenching process. Van der Waals complexes of a single metal atom with a rare gas atom or quencher molecule are prepared using a supersonic expansion of the metal vapor, carrier gas and quencher gas. To provide a more detailed understanding of van der Waals bonding involving closed shell metal atoms, spectroscopic investigations of the MgcdotNe, Zncdot Ar and ZncdotKr C ^1Pi_1 and X^1 Sigma_0^+ states as well as the ZncdotXe D^1Sigma _0^+ and X^1Sigma _0^+ states via laser induced fluorescence have also been performed. No fluorescence is observed from the Zn cdotXe C^1Pi_1 state which predissociates to Zn(4s4p^3 P_{rm J}) + Xe, permitting the C state to be characterized via a Zn(4s4p^3P_2) "action spectrum." Modeling of the deeply bound C state and the shallow D state using Morse potentials suggests that the long range tail of the C state curve crosses the inner wall of the D state curve. For the CdcdotCH _4 and CdcdotC _4H_{10} complexes, fluorescence is not observed from either the C or D states. However, Cd(5s5p^3P _{rm J}) action spectra are obtained for C and D state excitation. A Cd(5s5p ^3P_0) action spectrum is observed as a result of CdcdotCH _4 A and B state excitation. Rotational structure is observed in the vibrational bands and has permitted characterization of the Cdcdot CH_4 X and A states within a pseudodiatomic approximation and provided evidence for hindered rotation of the methane molecule. When CdcdotH_2 or CdcdotD_2 is excited to the red of the Cd(5s5p^1 P_1 >=ts 5s5s^1S_0) atomic transition, fluorescence is again absent while Cd(5s5p ^3P_{rm J}) action spectra are observed. The observation in the spectra of

  18. 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.

  19. Molecular emission towards RCW38 and RCW120; Possible candidates of the star formation via cloud-cloud collision

    NASA Astrophysics Data System (ADS)

    Torii, Kazufumi; Fukui, Yasuo; Furukawa, Naoko; Akio, Ohama; Hasegawa, Keisuke

    2012-04-01

    Understanding the formation of high-mass stars is one of the most pressing issues in modern astronomy. Recent observations towards the young cluster Trifid Neubla (M20) have revealed that two molecular clouds of 10^3 Mo are physically associated with the cluster, and the cloud-cloud collision process as the mechanism of the cluster formation was proposed (Torii et al. 2011). A large relative velocity of ~10 km/s between these two clouds is much larger than the permitted gravitational binding velocity of the constituent clouds. It is a crucial next step that we identify other examples of cloud-cloud collision to further constrain triggered-formed stars. In this proposal, we will observe two well-known bubble-shaped HII regions RCW 38 and RCW 120, located within 2 kpc, from the Sun in CO J=1-0 with Mopra. High spatial resolutions of ~0.1-0.2 pc enable to describe the detailed velocity components and therefore to establish unambiguous association with the optical and infrared nebula just like in M20. We request 26 hours in total.

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  1. 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.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Tsuboi, Masato; Miyazaki, Atsushi; Uehara, Kenta

    2015-12-01

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

  4. 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.

  5. 1982 bibliography of atomic and molecular processes

    SciTech Connect

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A.

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  6. 1985 bibliography of atomic and molecular processes

    SciTech Connect

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J.

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  7. 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.

  8. 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.

  9. 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.

  10. Single- and double-electron capture processes in low-energy collisions of N{sup 3+} with He

    SciTech Connect

    Liu, X. J.; Wang, J. G.; Qu, Y. Z.; Buenker, R. J.

    2011-10-15

    Single-electron capture (SEC) and double-electron capture (DEC) processes in collisions of ground state N{sup 3+} (2s{sup 2} {sup 1}S) ions with He are investigated by using the quantum-mechanical molecular-orbital close-coupling (QMOCC) method. The ab initio adiabatic potentials, radial and rotational coupling matrices utilized in QMOCC calculations, are obtained from the multireference single- and double-excitation configuration interaction approach. Total and state-selective SEC and DEC cross sections are presented in the low-energy range from 0.1 eV to 15 keV (i.e., 0.007 eV/u -1.07 keV/u) and rate coefficients in the temperature range from 10{sup 4} to 10{sup 7} K. Our results indicate that the SEC dominates the charge-transfer process in the considered energy region of this collision system and the SEC cross sections are nearly constant in the relatively high-collision energy region, while the DEC cross sections are about 2 orders of magnitude smaller. It is found that, for the SEC processes, in the dominant mechanisms, electrons are captured to exoergic channels N{sup 2+} (2s2p{sup 2} {sup 2}D,{sup 2}S), and for the DEC processes, they are captured to N{sup +} (2s{sup 2}2p{sup 2} {sup 1}D,{sup 1}S). Our calculations also reveal that rotational couplings become important at E > 10 eV/u for SEC and E > 200 eV/u for DEC processes.

  11. Anion production in high-velocity cluster-atom collisions; the electron capture process revisited

    NASA Astrophysics Data System (ADS)

    Béroff, K.; Chabot, M.; Martinet, G.; Pino, T.; Bouneau, S.; Le Padellec, A.; Féraud, G.; Do Thi, N.; Calvo, F.; Bordas, C.; Lépine, F.

    2013-01-01

    Anion production cross sections in collisions between Cn+, Cn carbon clusters (n ≤ 5) and helium atoms have been measured in high-velocity collisions (v = 2.25 and 2.6 au). This paper focuses on two of the three processes responsible for the Cn- production, namely double electron capture (DEC) onto Cn+ cations and single electron capture onto neutral (SECN) Cn. They were experimentally distinguished from a gaseous thickness dependence study. Dissociative and non-dissociative cross sections were measured and, in the case of DEC, all dissociative branching ratios measured; for these small systems, the C2- fragment was found magical. Data concerning electron capture in neutral-neutral collisions are extremely rare, especially at high velocity. Introduction of this measured process in the independent atom and electron (IAE) model allowed us to revisit and satisfactorily reproduce the so-far unexplained size evolution of single electron capture (SEC) cross sections in 2.6 au Cn+-He (n ≤ 10) collisions (Chabot et al 2006 J. Phys. B: At. Mol. Opt. Phys. 39 2593-603). IAE calculations for DEC cross sections and their comparison with experiment suggest a loss of electron in anionic Cn- species after the collision, competing with fragmentation and depending on the size.

  12. 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)

  13. Molecular processes in cellular arsenic metabolism

    SciTech Connect

    Thomas, David J.

    2007-08-01

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

  14. Molecular sieving silica membrane fabrication process

    DOEpatents

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

    1999-08-10

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

  15. 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.

  16. 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.

  17. Cascade statistics in the binary collision approximation and in full molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hou, M.; Pan, Z.-Y.

    1995-08-01

    The Binary Collision Approximation (BCA) and Molecular Dynamics (MD) are used to simulate low energy atomic collision cascades in solids. Results are compared and discussed on the example of copper and gold self irradiation. For MD, long range N-body potentials are built, similar to those deduced from the second moment semi-empirical tight binding model. The pair interaction contribution is splined to a Molière screened Coulomb potential at small separation distances. This hybrid potential is checked for consistency with the already assessed N-body potential by means of thermal dynamics calculations in both the canonical (NVT) and the micro canonical (NVE) ensembles. Its use for long time enhanced diffusion simulations is discussed. The BCA calculations are performed with the MARLOWE program, using the same Molière potential as for MD, and modelling the N-body contribution by a binding of the atoms to their equilibrium lattice sites. The scattering integrals are estimated by means of a 4 points Gauss-Mehler quadrature. In MD, the NVT equations of motion are integrated with a constant time step of 2 fs. For the NVE cascade simulations, the Newton equations of motion are solved with a dynamically adjusted time step, kept lower than 2 fs. The influence of the time step on the simulated trajectories is discussed. The mean number of moving atoms with total energy above threshold values ranging from 1 to 100 eV is estimated as a function of time over 300 fs both with MARLOWE and by MD. This estimate is repeated for external primary energies ranging from 250 eV to 1 keV. In the case of copper, the BCA results are found to be in remarkable agreement with MD over about 200 fs cascade development, provided the size of the crystallite used in MD is sufficiently large in order to account for the early mechanical response of the close environment. This agreement between the two methods is found to be the best when the binding energy of the target atoms as modelled in the BCA

  18. 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.

  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. Correlation between molecular recoil and molecular orientation in collisions of symmetric top molecules with hot hydrogen atoms

    NASA Astrophysics Data System (ADS)

    Ni, C. K.; Flynn, G. W.

    1992-05-01

    Nascent Doppler profiles are measured for hot H-atom—molecule collisions in numerous rotational sublevels of two symmetric tops. Linewidths for CDF 3 molecules due to hot H-atom collisions increase with the quantum number K. In contrast, linewidths for CD 3F molecules due to hot H-atom collisions decrease with the quantum number K. A simple model is proposed to explain the K dependent linewidths.

  1. 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.

  2. 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.

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

    PubMed

    Tscherbul, T V; Dalgarno, A

    2010-11-14

    An efficient method is presented for rigorous quantum calculations of atom-molecule and molecule-molecule collisions in a magnetic field. The method is based on the expansion of the wave function of the collision complex in basis functions with well-defined total angular momentum in the body-fixed coordinate frame. We outline the general theory of the method for collisions of diatomic molecules in the (2)Σ and (3)Σ electronic states with structureless atoms and with unlike (2)Σ and (3)Σ molecules. The cross sections for elastic scattering and Zeeman relaxation in low-temperature collisions of CaH((2)Σ(+)) and NH((3)Σ(-)) molecules with (3)He atoms converge quickly with respect to the number of total angular momentum states included in the basis set, leading to a dramatic (>10-fold) enhancement in computational efficiency compared to the previously used methods [A. Volpi and J. L. Bohn, Phys. Rev. A 65, 052712 (2002); R. V. Krems and A. Dalgarno, J. Chem. Phys. 120, 2296 (2004)]. Our approach is thus well suited for theoretical studies of strongly anisotropic molecular collisions in the presence of external electromagnetic fields. PMID:21073210

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

    PubMed

    Tscherbul, T V; Dalgarno, A

    2010-11-14

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

  5. 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.

  6. Growth rates of atmospheric molecular clusters determined from cluster appearance times and collision-evaporation fluxes

    NASA Astrophysics Data System (ADS)

    Kontkanen, Jenni; Olenius, Tinja; Lehtipalo, Katrianne; Vehkamäki, Hanna; Kulmala, Markku

    2015-04-01

    The probability of freshly formed particles to survive to climatically relevant sizes is determined by the competition between the coagulation loss rate and the particle growth rate. Therefore, various methods have been developed to deduce the growth rates from measured particle size distributions. Recently, the growth rates of sub-3nm clusters have been determined based on the appearance times of different cluster sizes. However, it is not clear to what extent these growth rates are consistent with the growth rates corresponding to molecular fluxes between clusters. In this work, we simulated the time evolution of a population of sub-3 nm molecular clusters and compared the growth rates determined (1) from the cluster appearance times and (2) from the collision-evaporation fluxes between different cluster sizes. We performed a number of simulations by varying the ambient conditions and the properties of the model substance. In the first simulation set, the Gibbs free energy of the formation of the clusters was assumed to have a single maximum and no minima, corresponding to a monotonically increasing stability as a function of cluster size. The saturation vapor pressure was selected so that the growth proceeded solely via monomer additions. The growth rates were determined separately for each cluster. However, to see the effect of finite size resolution, we also performed simulations where the clusters were grouped into size bins, for which we determined the growth rates. In the second simulation set, the saturation vapor pressure was lowered so that the collisions of small clusters significantly contributed to the growth. As the growth rate of a single cluster is ambiguous in this case, the growth rates were determined only for different size bins. We performed simulations using a similar free energy profile as in other simulations but we also used a free energy profile containing a local minimum, corresponding to small stable clusters. Our simulations show that

  7. 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.

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

    SciTech Connect

    Suits, Arthur G.

    2015-08-31

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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Hsieh, Horngming; Averback, R. S.; Sellers, Harrell; Flynn, C. P.

    1992-02-01

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

  11. 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.

  12. Tensorial slip theory for gas flows and comparison with molecular dynamics simulations using an anisotropic gas-wall collision mechanism.

    PubMed

    Pham, Thanh Tung; To, Quy Dong; Lauriat, Guy; Léonard, Céline

    2013-05-01

    In this paper we examine the anisotropic slip theory for gas flows based on tangential accommodation coefficients and compare it with molecular dynamics (MD) results. A special gas-wall boundary condition is employed within MD simulations to mimic the anisotropic gas-wall collision mechanism. Results from MD simulations with different surface orientations show good agreement with the slip quantification proposed in this work.

  13. Collisions between tunable halo dimers: exploring an elementary four-body process with identical bosons.

    PubMed

    Ferlaino, F; Knoop, S; Mark, M; Berninger, M; Schöbel, H; Nägerl, H-C; Grimm, R

    2008-07-11

    We study inelastic collisions in a pure, trapped sample of Feshbach molecules made of bosonic cesium atoms in the quantum halo regime. We measure the relaxation rate coefficient for decay to lower-lying molecular states and study the dependence on scattering length and temperature. We identify a pronounced loss minimum with varying scattering length along with a further suppression of loss with decreasing temperature. Our observations provide insight into the physics of a few-body quantum system that consists of four identical bosons at large values of the two-body scattering length. PMID:18764179

  14. Experimental analysis of the coalescence process via head-on collisions in a time-dependent flow

    NASA Astrophysics Data System (ADS)

    Borrell, Marcos; Yoon, Y.; Leal, L. Gary

    2004-11-01

    The present study experimentally investigates the mechanisms involved in the flow-induced coalescence process for two equal-sized drops (polybutadiene drops suspended in a polydimethylsiloxane matrix), by taking advantage of the capability of the computer-controlled "four-roll mill" to carry out head-on collisions. In this work, head-on collision experiments have been carried out for a time-dependent flow that is designed so that the force along the line of centers mimics the force history due to rotation of the two droplets in a glancing collision. One primary goal of these experiments is to assess the importance of global deformation of the drops in the coalescence process. Specifically, we seek to determine whether global deformation plays a role in the observation that coalescence often occurs during the portion of a glancing collision when the drops are actually being pulled apart by the external flow. By comparison of the results for head-on and glancing collisions, we find that coalescence occurs in an apparently identical fashion in spite of the fact that the overall shape of the drops must be different since the velocity gradient is steady during the glancing collision but time dependent in the head-on collision. Specifically, the (near) axisymmetric film drainage process achieved in a head-on collision is apparently a very good approximation to the same process in a nonaxisymmetric glancing collision, suggesting that the coalescence process is dominated by the time history of the force along the line of centers and is at least approximately independent of the degree of asymmetry in the overall collision process.

  15. Three-dimensional analysis of the collision process of a bead on a granular packing

    NASA Astrophysics Data System (ADS)

    Ammi, Madani; Oger, Luc; Beladjine, Djaoued; Valance, Alexandre

    2009-02-01

    We present results of the collision process of a bead onto a static granular packing. We provide, in particular, a three-dimensional (3D) extensive characterization of this process from a model experiment that allows us to propel a spherical bead onto a granular packing with a well-controlled velocity and impact angle. A collision typically produces a high-energy particle (rebound particle) and several low-energy grains (ejected particles). The collision process is recorded by means of two fast video cameras. The sequence of images from both cameras are then analyzed via image processing and the trajectories of all particles are reconstructed in 3D space. We show that the incident particle does not remain in the vertical incident plane after the rebound and that the deviation angle increases with increasing impact angle. Concerning the ejected particles, we demonstrated that the ejection angle (measured with respect to the horizontal plane) is surprisingly independent of both the impact angle and velocity of the incident particle, and is very close to 60°. The horizontal component of the ejection speed of the splashed particles is found to be weakly dependent on the incident speed and impact angle, and is relatively isotropic (no particular horizontal direction is favored). This last feature suggests that the bead packing acts as a perfect diffusive medium with respect to energy propagation.

  16. 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.

  17. Electron-Nuclear Dynamics of atomic and molecular collisions: Charge exchange and energy loss

    NASA Astrophysics Data System (ADS)

    Cabrera-Trujillo, Remigio; Sabin, John R.; Ohrn, Yngve; Deumens, Erik

    2004-05-01

    Processes like electron exchange (capture and loss), bond breaking, and chemical reactions are difficult to visualize and treat in a time-independent approach. In this work, we present the Electron-Nuclear Dynamics (END) method for the study of time-dependent scattering processes. The END is a general approach for treating time-dependent problems which includes the dynamics of electrons and nuclei simultaneously by considering the full electron-nuclear coupling in the system and thus eliminates the necessity of constructing potential-energy surfaces. The theory approximates the time dependent Schrödinger equation starting from the time dependent variational principle (TDVP) by deriving a Hamiltonian dynamical system for time dependent nuclear and electronic wave function parameters. The wave function is described in a coherent state manifold, which leads to a system of Hamilton's equations of motion. The resulting system of coupled, first order, ordinary differential equations approximates the Schrödinger equation. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. Emphasis is put on electron exchange, differential cross section and energy loss (stopping cross section) of collision of ions, atoms and molecules involving H, He, C, N, O, and Ne atoms. We compare our results to available experimental data.

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

    PubMed

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

    2005-08-01

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

  19. Influence of nuclear exchange on nonadiabatic electron processes in H(+)+H2 collisions.

    PubMed

    Errea, L F; Illescas, Clara; Macías, A; Méndez, L; Pons, B; Rabadán, I; Riera, A

    2010-12-28

    H(+)+H(2) collisions are studied by means of a semiclassical approach that explicitly accounts for nuclear rearrangement channels in nonadiabatic electron processes. A set of classical trajectories is used to describe the nuclear motion, while the electronic degrees of freedom are treated quantum mechanically in terms of a three-state expansion of the collision wavefunction. We describe electron capture and vibrational excitation, which can also involve nuclear exchange and dissociation, in the E = 2-1000 eV impact energy range. We compare dynamical results obtained with two parametrizations of the potential energy surface of H(3)(+) ground electronic state. Total cross sections for E > 10 eV agree with previous results using a vibronic close-coupling expansion, and with experimental data for E < 10 eV. Additionally, some prototypical features of both nuclear and electron dynamics at low E are discussed.

  20. Laser-modified charge-transfer processes in He2++H collisions

    NASA Astrophysics Data System (ADS)

    Liu, C. L.; He, B.; Zou, S. Y.; Wang, J. G.

    2016-10-01

    Laser-modified electron capture processes are studied for the He2++H collision system in the low projectile energy region by solving the time-dependent Schrödinger equation. An obvious enhancement of the total and dominant state-selective charge-transfer cross sections are observed with respect to laser-free and weaker laser cases for low projectile energy. The influence of the laser pulse phase upon the cross sections is also studied and the reduction of the cross section is observed at some pulse phases with the increasing of the projectile energy. The time evolution for the dynamics of the collision system is analyzed in order to explore the dependence of the cross sections upon the pulse phase.

  1. 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.

  2. 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.

  3. Molecular dynamics simulations of wear processes

    NASA Astrophysics Data System (ADS)

    Yu, Hualiang

    Wear has been recognized as a vital problem in many industries. It results in a loss of durability, reliability, and efficiency and costs tens of billions of dollars annually. Significant effort has been devoted in both experimental and theoretical studies. However, the mechanisms of wear are still poorly understood and therefore wear control is far behind its demand. One way to study wear process is via computer simulation, which has become more powerful with the rapid development in computer facilities and efficient algorithms. It allows observation of atomic scale deformation and therefore it is a very good tool to study wear mechanisms at the nano-scale. This study presents a series of molecular dynamic simulation of some nano-scale wear processes, such as indentation and plowing, with the goal of exploring the factors that affect wear and predicting wear for different conditions. Molecular Dynamics simulations were carried out on a system that includes an aluminum substrate and a hard tip. Embedded atom method (EAM) and Lennard-Jones potentials were used to describe interactions between atoms. For nano-indentation simulations, both constant indent force and constant loading speed were applied to study the wear mechanisms as well as material properties. Some phenomenon, such as jump-to-contact, local melting, and dislocation nucleation were observed. More importantly, the effects of system temperature, indent force, substrate orientation, tip-substrate bond, indenter shape, boundary condition, and defect concentrations of the substrate were systematically investigated during indentation. The results are in qualitative agreement with limited experimental data. Similar simulations were carried out for plowing. The effects of plowing force, substrate orientation, the tip-substrate bond, and alloy elements are discussed based on the simulation results. In addition, a simple analytic model of plowing behavior is provided. The model reveals two parameters, static

  4. Principles of the Quantum Control of Molecular Processes

    NASA Astrophysics Data System (ADS)

    Shapiro, Moshe; Brumer, Paul

    2003-02-01

    Principles and Applications of Quantum Control Over the past fifteen years, significant developments have been made in utilizing quantum attributes of light and matter to assume unprecedented control over the dynamics of atomic and molecular systems. This growth reflects a confluence of factors including the maturation of quantum mechanics as a tool for chemistry and physics, the development of new laser devices increasing our ability to manipulate light, and the recognition that coherent laser light can be used to imprint information on atoms and molecules for practical purposes. Written by two of the world's leading researchers in the field, Principles of the Quantum Control of Molecular Processes offers a systematic introduction to the fundamental principles of coherent control, and to the physics and chemistry necessary to master it. Designed as both a resource for self-study and as a graduate textbook, this survey of the subject provides a step-by-step discussion of light-matter interactions along with coverage of such essential topics as: Molecular dynamics and control The dynamics of photodissociation Bimolecular collision processes The control of chirality and asymmetric synthesis Application of control using moderate and strong fields Tuning the system and laser parameters to achieve optimal control Decoherence and methods for countering it Both authoritative and comprehensive, this first in-depth treatment of coherent control is destined to become the standard reference in an increasingly influential field. PAUL W. BRUMER, PhD, is University Professor-Theoretical Chemical Physics and holds the Roel Buck Chair in Chemical Physics at the University of Toronto. He received his BSc. from Brooklyn College and his PhD from Harvard University. MOSHE SHAPIRO, PhD, is the Jacques Mimran Professor of Chemical Physics at the Weizmann Institute of Science, Rehovot, Israel, and a Professor of Chemistry and Physics at the University of British Columbia. He received his

  5. 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.

  6. 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.

  7. Statistical kinetics of processive molecular motors

    NASA Astrophysics Data System (ADS)

    Schnitzer, Mark Jacob

    1999-10-01

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

  8. 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.

  9. 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.

  10. Molecular beam studies of elementary chemical processes.

    PubMed

    Lee, Y T

    1987-05-15

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

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

    ERIC Educational Resources Information Center

    Donnelly, Denis P.; And Others

    1971-01-01

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

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

    PubMed

    Opatrný, T; Kurizki, G

    2001-04-01

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

  13. 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.

  14. 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

  15. ATOMIC AND MOLECULAR PHYSICS: Collision-Induced Coherence Effect on Coherent Population Transfer

    NASA Astrophysics Data System (ADS)

    Yang, Xi-Hua; Zhang, Jun; Zhang, Hui-Fang; Yan, Xiao-Na

    2009-07-01

    We investigate the effect of collision-induced coherence on coherent population transfer with the stimulated Raman adiabatic passage technique in a double A-type four-level system with a widely separated excited doublet. It is shown that when the two pulsed lasers with Rabi frequencies nearly comparable to the energy separation of the doublet are tuned to the particular frequency where the condition for quantum interference is satisfied, the very low transfer efficiency due to the nonadiabatic coupling between the two degenerate adiabatic states could be enhanced significantly with the increase of the collisional decay rates in a moderate range. The enhanced transfer efficiency results from the weakening of the nonadiabatic coupling between the two degenerate adiabatic states realized through collision-induced destructive quantum interference.

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  18. 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.

  19. 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.

  20. 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.

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

    SciTech Connect

    Hahn, M.; Savin, D. W.

    2015-08-20

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

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

    PubMed

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

    2001-02-01

    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.

  3. 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

  4. 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.

  5. Electron-Nuclear Dynamics of collision processes: Charge exchange and energy loss

    NASA Astrophysics Data System (ADS)

    Cabrera-Trujillo, Remigio; Sabin, John R.; Öhrn, Yngve; Deumens, Erik

    2004-03-01

    We present the Electron-Nuclear Dynamics (END) method for the study of time-dependent scattering processes. The END is a general approach for treating time-dependent problems which includes the dynamics of electrons and nuclei simultaneously by considering the full electron-nuclear coupling in the system and thus eliminates the necessity of constructing potential-energy surfaces. The theory approximates the time dependent Schrödinger equation starting from the time dependent variational principle by deriving a Hamiltonian dynamical system for time dependent nuclear and electronic wave function parameters. The wave function is described in a coherent state manifold, which leads to a system of Hamilton's equations of motion. Emphasis is put on electron exchange, differential cross section and energy loss (stopping cross section) of collision of ions, atoms and molecules involving H, He, C, N, O, and Ne atoms. We compare our results to available experimental data.

  6. 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.

  7. 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.

  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. 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.

  10. Electron capture and excitation processes in H+‑H collisions in dense quantum plasmas

    NASA Astrophysics Data System (ADS)

    Jakimovski, D.; Markovska, N.; Janev, R. K.

    2016-10-01

    Electron capture and excitation processes in proton–hydrogen atom collisions taking place in dense quantum plasmas are studied by employing the two-centre atomic orbital close-coupling (TC-AOCC) method. The Debye–Hückel cosine (DHC) potential is used to describe the plasma screening effects on the Coulomb interaction between charged particles. The properties of a hydrogen atom with DHC potential are investigated as a function of the screening strength of the potential. It is found that the decrease in binding energy of nl levels with increasing screening strength is considerably faster than in the case of the Debye–Hückel (DH) screening potential, appropriate for description of charged particle interactions in weakly coupled classical plasmas. This results in a reduction in the number of bound states in the DHC potential with respect to that in the DH potential for the same plasma screening strength, and is reflected in the dynamics of excitation and electron capture processes for the two screened potentials. The TC-AOCC cross sections for total and state-selective electron capture and excitation cross sections with the DHC potential are calculated for a number of representative screening strengths in the 1–300 keV energy range and compared with those for the DH and pure Coulomb potential. The total capture cross sections for a selected number of screening strengths are compared with the available results from classical trajectory Monte Carlo calculations.

  11. Revisiting the Reactivity of Uracil During Collision Induced Dissociation: Tautomerism and Charge-Directed Processes

    NASA Astrophysics Data System (ADS)

    Beach, Daniel G.; Gabryelski, Wojciech

    2012-05-01

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

  12. 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.

  13. Electron capture and ionization processes in high-velocity Cn+ , C-Ar and Cn+ , C-He collisions

    NASA Astrophysics Data System (ADS)

    Labaigt, G.; Jorge, A.; Illescas, C.; Béroff, K.; Dubois, A.; Pons, B.; Chabot, M.

    2015-04-01

    Single-electron and double-electron capture as well as projectile single-ionization and multiple-ionization processes in 125 keV u-1 Cn+-He (n = 1-5) and Cn+-Ar (n=1,2,4) collisions have been studied experimentally and theoretically. Helium target single-ionization and double-ionization cross sections are also reported for Cn+-He (n = 1, 4) collisions in the 100-400 keV u-1 impact energy domain. These results are compared with predictions from the independent atom and electron (IAE) model developed for describing cluster-atom collisions. The ion/atom-atom probabilities required for the IAE simulations have been determined by classical trajectory Monte Carlo (CTMC) and semiclassical atomic orbital close coupling (SCAOCC) calculations for the Ar and He targets, respectively. For comparison, electron capture cross sections were also measured in C-He and C-Ar collisions. In general the agreement between experiment and IAE calculations has been found to be rather good, with the exception of double-electron capture leading to anionic Cn- species.

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

    PubMed

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

    2008-10-24

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

  15. The role of molecular methods in evaluating biological treatment processes.

    PubMed

    Rittmann, Bruce E

    2002-01-01

    Methods derived from molecular biology provide powerful new tools to analyze biological treatment processes. Because molecular methods can be used to directly interrogate genetic information about the microbial community, they can provide the fine detail that is impossible with the blunt, nondiscriminating information usually obtained from more traditional measures such as biochemical oxygen demand and volatile suspended solids. Molecular methods allow tracking of critical groups of microorganisms, such as ammonia oxidizers, that comprise a small fraction of the total biomass. Molecular methods also allow tracking of specific metabolic reactions or other functions that are key to the satisfactory performance of a system. Despite their power, molecular methods do not provide sufficient information when used alone. Aggregated measures and quantitative modeling remain necessary to establish mass balances, quantify the function of the microbial community, and connect the results of molecular assays to practice. Several examples involving nitrifying bacteria in activated sludge illustrate the fine detail available with molecular methods and how they can be linked to traditional and quantitative analyses. Other manuscripts in this special issue also provide examples of the value of using molecular tools in combination with traditional methods.

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

    PubMed

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

    2012-06-01

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

  17. 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

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

    NASA Astrophysics Data System (ADS)

    McQuarrie, Barry Robert

    1998-06-01

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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

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

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

  5. 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.

  6. 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.

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

    SciTech Connect

    Schroeder, W.U.

    1991-01-01

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

  8. 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.

  9. Influence of nuclear exchange on nonadiabatic electron processes in H{sup +}+H{sub 2} collisions

    SciTech Connect

    Errea, L. F.; Illescas, Clara; Macias, A.; Mendez, L.; Rabadan, I.; Riera, A.; Pons, B.

    2010-12-28

    H{sup +}+H{sub 2} collisions are studied by means of a semiclassical approach that explicitly accounts for nuclear rearrangement channels in nonadiabatic electron processes. A set of classical trajectories is used to describe the nuclear motion, while the electronic degrees of freedom are treated quantum mechanically in terms of a three-state expansion of the collision wavefunction. We describe electron capture and vibrational excitation, which can also involve nuclear exchange and dissociation, in the E= 2-1000 eV impact energy range. We compare dynamical results obtained with two parametrizations of the potential energy surface of H{sub 3}{sup +} ground electronic state. Total cross sections for E > 10 eV agree with previous results using a vibronic close-coupling expansion, and with experimental data for E < 10 eV. Additionally, some prototypical features of both nuclear and electron dynamics at low E are discussed.

  10. 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

  11. 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.

  12. 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.

  13. 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).

  14. 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‧.

  15. Phase of molecular ink in nanoscale direct deposition processes

    NASA Astrophysics Data System (ADS)

    Cho, Narae; Ryu, Seol; Kim, Byeongju; Schatz, George C.; Hong, Seunghun

    2006-01-01

    We report the first observation of a phase transition in a nanoscale direct deposition process. This transition involves the melting of molecular ink layers in dip-pen nanolithography, and it is observed by measuring the temperature dependence of the growth rate of the deposited pattern. The results are interpreted using a diffusion equation approach in conjunction with a "double-molecular-layer" model of the adsorbed molecules on the atomic force microscope tip. The theory provides a qualitative explanation for the dependence of the pattern growth rate on solvent and adsorbed water as well as on temperature.

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

    PubMed Central

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

    2016-01-01

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

  17. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors

    PubMed Central

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

    2015-01-01

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed. PMID:25688287

  18. Use of molecularly imprinted polymers in a biotransformation process.

    PubMed

    Ye, L; Ramström, O; Ansell, R J; Månsson, M O; Mosbach, K

    1999-09-20

    Molecularly imprinted polymers are highly stable and can be sterilised, making them ideal for use in biotransformation process. In this communication, we describe a novel application of molecularly imprinted polymers in an enzymatic reaction. The enzymatic condensation of Z-L-aspartic acid with L-phenylalanine methyl ester to give Z-L-Asp-L-Phe-OMe (Z-aspartame) was chosen as a model system to evaluate the applicability of using molecularly imprinted polymers to facilitate product formation. When the product-imprinted polymer is present, a considerable increase (40%) in product yield is obtained. Besides their use to enhance product yields, as demonstrated here, we suggest that imprinted polymers may also find use in the continuous removal of toxic compounds during biochemical reactions.

  19. Positron emission tomography provides molecular imaging of biological processes

    PubMed Central

    Phelps, Michael E.

    2000-01-01

    Diseases are biological processes, and molecular imaging with positron emission tomography (PET) is sensitive to and informative of these processes. This is illustrated by detection of biological abnormalities in neurological disorders with no computed tomography or MRI anatomic changes, as well as even before symptoms are expressed. PET whole body imaging in cancer provides the means to (i) identify early disease, (ii) differentiate benign from malignant lesions, (iii) examine all organs for metastases, and (iv) determine therapeutic effectiveness. Diagnostic accuracy of PET is 8–43% higher than conventional procedures and changes treatment in 20–40% of the patients, depending on the clinical question, in lung and colorectal cancers, melanoma, and lymphoma, with similar findings in breast, ovarian, head and neck, and renal cancers. A microPET scanner for mice, in concert with human PET systems, provides a novel technology for molecular imaging assays of metabolism and signal transduction to gene expression, from mice to patients: e.g., PET reporter gene assays are used to trace the location and temporal level of expression of therapeutic and endogenous genes. PET probes and drugs are being developed together—in low mass amounts, as molecular imaging probes to image the function of targets without disturbing them, and in mass amounts to modify the target's function as a drug. Molecular imaging by PET, optical technologies, magnetic resonance imaging, single photon emission tomography, and other technologies are assisting in moving research findings from in vitro biology to in vivo integrative mammalian biology of disease. PMID:10922074

  20. 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.

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

    PubMed

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

    2014-08-25

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

  2. Experiments with a universe for molecular modelling of biological processes.

    PubMed

    Jedruch, W T; Barski, M

    1990-01-01

    A computer simulation program and results of preliminary simulations of an abstract two-dimensional universe are presented, in which biological and physical processes can be modelled at the molecular level. Two types of permanent elements (atoms) occupy squares of the universe: called 0 and 1. Atoms sharing a common square form a particle, with properties determined by its component atoms. Atoms, particles, and complexes of particles move and collide according to rules like those of classical mechanics. At a higher level of organization, the string of atoms in a particle is viewed as a program, whose execution can affect the space around the particle. The computer program (written in Turbo-Pascal language) can simulate the evolution of the universe starting from any given initial configuration of the particles. Three examples of simulations, showing the development of ordered spatial structures from initial sets of randomly distributed particles, illustrate the universe's potential in modelling various molecular processes.

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

    NASA Astrophysics Data System (ADS)

    Kirby, K. P.

    1983-09-01

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

  4. 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).

  5. 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.

  6. Molecular and dust scattering processes in astrophysical environments

    NASA Astrophysics Data System (ADS)

    Lupu, Roxana-Elena

    2009-06-01

    Understanding the formation and evolution of structure in the universe requires knowledge of the stellar energy output and its processing by gas and dust, evaluating the abundances of atomic and molecular species, and constraining thermodynamic parameters. Molecules, with molecular hydrogen and carbon monoxide being the most abundant, are a major component of the interstellar medium, and play an essential role in structure formation, by participating in gas cooling. Molecular fluorescence studies aim to provide a better interpretation of far-ultraviolet observations, constraining the molecular abundances and their interaction with the radiation field. The fluorescent emission lines offer a set of diagnostics for molecules complementary to absorption line spectroscopy and to observations at infrared and radio wavelengths, but are often poorly reproduced by models. In this work, I have developed and expanded fluorescence models for molecular hydrogen and carbon monoxide, and employed them in determining the spatial distribution of CO in cometary comae, in characterizing the effects of partial frequency redistribution for emission line scattering in planetary atmospheres and reflection nebulae, and in abundance determinations from Bowen fluorescence lines of H 2 in planetary nebulae. Follow-up optical and infrared observations were used in addition to UV data to diagnose molecular excitation, temperature, and spatial distribution in planetary nebula M27. Knowledge of the spectral energy distribution of the exciting stars in the far- ultraviolet is essential in constraining both the fluorescence models and understanding the scattering properties of nebular gas and dust. Sounding rocket observations of the Trifid and Orion nebulae, performed as part of this work, provided the necessary dynamic range and spatial resolution to measure simultaneously the nebular scattered light and the spectral energy distribution of the illuminating stars. These low extinction sight lines

  7. MOLECULAR CLOUDS IN THE TRIFID NEBULA M20: POSSIBLE EVIDENCE FOR A CLOUD-CLOUD COLLISION IN TRIGGERING THE FORMATION OF THE FIRST GENERATION STARS

    SciTech Connect

    Torii, K.; Enokiya, R.; Sano, H.; Yoshiike, S.; Hanaoka, N.; Ohama, A.; Furukawa, N.; Dawson, J. R.; Moribe, N.; Oishi, K.; Nakashima, Y.; Okuda, T.; Yamamoto, H.; Kawamura, A.; Mizuno, N.; Onishi, T.; Fukui, Y.; Maezawa, H.; Mizuno, A.

    2011-09-01

    A large-scale study of the molecular clouds toward the Trifid Nebula, M20, has been made in the J = 2-1 and J = 1-0 transitions of {sup 12}CO and {sup 13}CO. M20 is ionized predominantly by an O7.5 star HD164492. The study has revealed that there are two molecular components at separate velocities peaked toward the center of M20 and that their temperatures-30-50 K as derived by a large velocity gradient analysis-are significantly higher than the 10 K of their surroundings. We identify the two clouds as the parent clouds of the first generation stars in M20. The mass of each cloud is estimated to be {approx}10{sup 3} M{sub sun} and their separation velocity is {approx}8 km s{sup -1} over {approx}1-2 pc. We find that the total mass of stars and molecular gas in M20 is less than {approx}3.2 x 10{sup 3} M{sub sun}, which is too small by an order of magnitude to gravitationally bind the system. We argue that the formation of the first generation stars, including the main ionizing O7.5 star, was triggered by the collision between the two clouds in a short timescale of {approx}1 Myr, a second example alongside Westerlund 2, where a super-star cluster may have been formed due to cloud-cloud collision triggering.

  8. Molecular Clouds in the Trifid Nebula M20: Possible Evidence for a Cloud-Cloud Collision in Triggering the Formation of the First Generation Stars

    NASA Astrophysics Data System (ADS)

    Torii, K.; Enokiya, R.; Sano, H.; Yoshiike, S.; Hanaoka, N.; Ohama, A.; Furukawa, N.; Dawson, J. R.; Moribe, N.; Oishi, K.; Nakashima, Y.; Okuda, T.; Yamamoto, H.; Kawamura, A.; Mizuno, N.; Maezawa, H.; Onishi, T.; Mizuno, A.; Fukui, Y.

    2011-09-01

    A large-scale study of the molecular clouds toward the Trifid Nebula, M20, has been made in the J = 2-1 and J = 1-0 transitions of 12CO and 13CO. M20 is ionized predominantly by an O7.5 star HD164492. The study has revealed that there are two molecular components at separate velocities peaked toward the center of M20 and that their temperatures—30-50 K as derived by a large velocity gradient analysis—are significantly higher than the 10 K of their surroundings. We identify the two clouds as the parent clouds of the first generation stars in M20. The mass of each cloud is estimated to be ~103 M sun and their separation velocity is ~8 km s-1 over ~1-2 pc. We find that the total mass of stars and molecular gas in M20 is less than ~3.2 × 103 M sun, which is too small by an order of magnitude to gravitationally bind the system. We argue that the formation of the first generation stars, including the main ionizing O7.5 star, was triggered by the collision between the two clouds in a short timescale of ~1 Myr, a second example alongside Westerlund 2, where a super-star cluster may have been formed due to cloud-cloud collision triggering.

  9. 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.

  10. Myosin-V stepping kinetics: a molecular model for processivity.

    PubMed

    Rief, M; Rock, R S; Mehta, A D; Mooseker, M S; Cheney, R E; Spudich, J A

    2000-08-15

    Myosin-V is a molecular motor that moves processively along its actin track. We have used a feedback-enhanced optical trap to examine the stepping kinetics of this movement. By analyzing the distribution of time periods separating discrete approximately 36-nm mechanical steps, we characterize the number and duration of rate-limiting biochemical transitions preceding each such step. These data show that myosin-V is a tightly coupled motor whose cycle time is limited by ADP release. On the basis of these results, we propose a model for myosin-V processivity.

  11. 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

  12. A molecular dynamics simulation of rebound, capture and diffusion in collisions at thermal energies between a rare gas atom and an argon cluster ( n=125)

    NASA Astrophysics Data System (ADS)

    de Pujo, P.; Mestdagh, J.-M.; Visticot, J.-P.; Cuvellier, J.; Meynadier, P.; Sublemontier, O.; Lallement, A.; Berlande, J.

    1993-12-01

    Molecular dynamics calculations have been performed to simulate the low energy collision (0.2 eV) of a rare gas atom (He, Ar, Xe) with a cluster of 125 argon atoms. Depending on its relative mass to argon, the projectile is either deflected (He) or captured (Ar, Xe) by the argon cluster. We have determined the deflection function of the He projectile that is scattered, and for Xe we have determined wether it stays near the surface of the cluster or migrates inside. These results have been discussed in the light of very simple models.

  13. 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.

  14. 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.

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

    PubMed

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

    2015-09-01

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

  16. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  18. 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.

  19. 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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  2. 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

  3. 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

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

    SciTech Connect

    Miller, William H.; Orel, Ann E.

    1981-06-01

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

  6. 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)].

  7. THE COLOR DIPOLE APPROACH TO THE DRELL-YAN PROCESS IN PA COLLISIONS

    SciTech Connect

    B. KOPELIOVICH; ET AL

    2001-03-01

    In the target rest frame and at high energies, Drell-Yan (DY) dilepton production looks like bremsstrahlung of massive photons, rather than parton annihilation. The projectile quark is decomposed into a series of Fock states. Configurations with fixed transverse separations are interaction eigenstates for pp scattering. The DY cross section can then be expressed in terms of the same color dipole cross section as DIS. This approach is especially suitable to describe nuclear effects, since it allows to apply Glauber multiple scattering theory. We go beyond the Glauber eikonal approximation by taking into account transitions between interaction eigenstates. We calculate nuclear shadowing at large Feynman-x{sub f} for DY in proton-nucleus collisions, compare to existing data from E772 and make predictions for RHIC. Nuclear effects on the transverse momentum distribution are also investigated.

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

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

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

  9. 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.

  10. Application to processing system using intra-molecular BRET

    NASA Astrophysics Data System (ADS)

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

    2003-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  12. Finding novel molecular connections between developmental processes and disease.

    PubMed

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

    2014-05-01

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

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

    PubMed

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

    2014-08-01

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

  14. 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.

  15. ATOMIC AND MOLECULAR PHYSICS: Influence of Isotope Substitution Helium Atom on Partial Cross Sections in He-HF Collisions

    NASA Astrophysics Data System (ADS)

    Yu, Chun-Ri; Zhang, Jie; Chen, Li; Jiang, Gui-Sheng; Huang, Guo-Dong

    2009-11-01

    Close-coupling equation and anisotropic potential developed in our previous research are applied to HF-3He (4He, 6He, 8He, 10He) collision system, and partial cross sections (PCSs) at the incident energy of 40 meV are calculated. By analyzing the differences of these PCSs, change rules of PCSs with the increase of partial wave number, and with the change of the mass of isotope substitution helium atom are obtained. The results show that excitation PCSs converge faster than elastic PCSs for collision energy and each of systems considered here. Also excitation PCSs converge more rapidly for high-excited states. Tail effect is present only in elastic scattering and low-excited states but not in high-excited states. With the increase of the mass of isotope substitution helium atom, converging speed of elastic, total inelastic, and state-to-state excitation PCS slows down, and the maxima of these PCSs undergoes a regular change.

  16. Classical trajectory study of alignment effects in the capture process: He 2+-Li ∗(2pΣ,2pΠ) collisions

    NASA Astrophysics Data System (ADS)

    Perumal, A. N.; Tripathi, D. N.

    1998-08-01

    A simulation method (CTMC) has been used to investigate the selectivity and alignment effects on the capture process in He 2+-Li ∗(2pΣ,2pΠ) collisions. The anomalous results of the experiment (∼ 50% error) as well as the AO calculation of Gieler et al. in case of capture into He II ( n = 4) from the initial Li ∗ (2pΣ) state are not found in the present work. Relative velocity and spatial overlap together mainly control the capture process in ion-atom collisions. The n-distribution of the final capture state is also presented.

  17. Rubidium-Strontium collisions

    NASA Astrophysics Data System (ADS)

    Kleinert, Michaela; Potter, Garrett; Whitehead, Marc; McEntee, Elyse; Koll, Christopher J.

    2010-03-01

    The invention of the magneto-optical trap (MOT) in 1987 - which was awarded the Noble Price in Physics 10 years later - has enabled many new and exciting experiments. Among them are precision measurements of basic atomic properties, ultracold collisions, Bose-Einstein Condensates, atom lasers, etc.. Recent developments in the field of atomic and molecular physics have included the creation of diatomic (homo- and heteronuclear) molecules. These ultracold molecules promise to revolutionize physical chemistry, few-body physics, precision measurements and quantum information processing, similar to how ultracold atoms revolutionized AMO physics several years ago. We will present our first results of a mixed alkaline (rubidium) and alkaline-earth (strontium) magneto-optical trap.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1980-01-01

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

  7. 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.

  8. 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

  9. 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.

  10. Strategy to improve the quantitative LC-MS analysis of molecular ions resistant to gas-phase collision induced dissociation: application to disulfide-rich cyclic peptides.

    PubMed

    Ciccimaro, Eugene; Ranasinghe, Asoka; D'Arienzo, Celia; Xu, Carrie; Onorato, Joelle; Drexler, Dieter M; Josephs, Jonathan L; Poss, Michael; Olah, Timothy

    2014-12-01

    Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma.

  11. 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

  12. Molecular-level insights into aging processes of skin elastin.

    PubMed

    Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang; Heyroth, Frank; Heinz, Andrea

    2016-01-01

    Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin fibers was characterized by scanning electron microscopy. Mass spectrometric analysis and label-free quantification allowed identifying differences in the cleavage patterns of the elastin samples after enzymatic digestion. Principal component analysis and hierarchical cluster analysis were used to visualize differences between the samples and to determine the contribution of extrinsic and intrinsic aging to the proteolytic susceptibility of elastin. Moreover, the release of potentially bioactive peptides was studied. Skin aging is associated with the decomposition of elastin fibers, which is more pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26. Photoaging makes the N-terminal and central parts of the tropoelastin molecules more susceptible towards enzymatic cleavage and, hence, accelerates the age-related degradation of elastin. PMID:27569260

  13. Collision risk assessment

    NASA Astrophysics Data System (ADS)

    Sánchez Ortiz, N.; Belló Mora, M.; Graziano, M.; Pina Caballero, F.; Sánchez Pérez, J. M.; Klinkrad, H.

    2001-10-01

    Avoidance of near misses or collisions is required for almost all satellites on orbit, but it is of particular interest for manned missions and spacecraft at densely populated regions. In order to avoid these possible collisions, it is needed to determine a possible conjunction and its associated uncertainty. Two main constraints must be taken into account when a tool to forecast the collision risk of an object is being developed: the high number of objects in space and the accuracy of the catalogued object data. The number of objects on Earth orbit makes impossible to propagate all the catalogued objects, thus filtering and parallel processing techniques are presented. The accuracy of the catalogued object data and the propagation of the error over the time identify a position ellipsoid of error, whose behaviour has an important influence on some parameters on the filtering techniques and the way the collision probability is computed. Some collision probability methods are presented.

  14. Molecular Specificity of Multiple Hippocampal Processes Governing Fear Extinction

    PubMed Central

    Radulovic, Jelena; Tronson, Natalie C.

    2010-01-01

    SYNOPSIS Over many years, fear extinction has been conceptualized as one dominant process, new inhibitory learning, which serves to dampen previously acquired fear. Here we present an alternative view, that brain region-specific processing of representations, expectations and emotional attributes of the fear-provoking event, recruits unique mechanisms that interdependently contribute to the conditioning and extinction of fear. The co-occurrence of these mechanisms within the fear circuit can thus be tracked and differentiated at a molecular and cellular level. Among others, the transcriptional regulators cFos, cAMP-dependent response element binding protein (CREB), Zif268, and extracellular signal-regulated kinases (Erk) stand out as hippocampal nuclear markers signaling novelty, arousal, retrieval, and prediction error, respectively. Consistent with evidence from human studies, these findings indicate that, beyond inhibitory learning, fear extinction requires modification of the emotional attributes and expectations that define the threatening context. Given the likely dysregulation of one or more of these processes in anxiety disorders, a key research challenge for the future is the identification and enhancement of individual extinction mechanisms to target the specific components of fear. Environmental stimuli lacking affective properties (conditioned stimuli, CS) rapidly become threatening if presented with stressful events (unconditioned stimuli, US). Consequently, based on a CS-US association, the presentation of the CS triggers species-specific fear responses until the US consistently stops occurring. At that point, new learning takes place and the fear response declines, a phenomenon termed extinction. The view that extinction occurs because a new, inhibitory CS-noUS association gains control over behavior 106, has remained dominant in the field (reviewed by 20,33,35,100). The implications of impaired fear regulation in the development of anxiety disorders

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. An Experimental Investigation of the Droplet Deformation Process Resulting from Binary Collisions of a Viscous Fluid

    NASA Astrophysics Data System (ADS)

    Willis, Keeney; Orme, Melissa

    1997-11-01

    An experimental investigation of the collisional dynamics of equal sized drops of a viscous, silicone based oil, DC 200, has been conducted for head-on impacts in a vacuum. Results show that the range of droplet Weber numbers necessary to describe the boundaries between permanent coalescence and what has been previously described as reflexive separation, is several orders of magnitude higher than has been reported in studies involving water and hydrocarbon fuel droplets. Energy dissipation during the deformation process has been measured, and the results show a wide discrepancy with available theory. Detailed observations of the post-impact deformation process reveals that in this case, the formation of multiple drops is due solely to the growth of Rayleigh instabilities on the extended fluid ligament.

  20. 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

  1. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  3. 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.

  4. 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.

  5. Deviation from a Maxwellian velocity distribution in regions of interstellar molecular hydrogen

    NASA Technical Reports Server (NTRS)

    Gould, R. J.; Levy, M.

    1976-01-01

    The deviation from a Maxwellian velocity distribution caused by excitation of the J = 2 rotational level of parahydrogen (followed by radiative decay) in a molecular hydrogen gas is investigated. It is noted that inelastic collisions deplete the high-velocity tail of the distribution, while elastic collisions tend to refill it; the resulting steady-state distribution has a small depletion in the tail which slightly reduces the cooling rate of the gas. The elastic-collision transport is approximated by a continuous process, a simplified expression is obtained for the inelastic-collision operator, and the Boltzmann equation is then solved analytically. A correction to the inelastic-collision rate is evaluated, and it is found that the relative magnitude of the effect of tail depletion on the inelastic-collision rate is strongly temperature-dependent. The critical molecular density above which the J = 2 level deexcites by superelastic collisions is shown to be a weak function of temperature.

  6. 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.

  7. 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.

  8. 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)

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

    PubMed Central

    Williams, Kevin Jon

    2008-01-01

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

  10. Free-electron laser induced processes in thin molecular ice.

    PubMed

    Siemer, Björn; Roling, Sebastian; Frigge, Robert; Hoger, Tim; Mitzner, Rolf; Zacharias, Helmut

    2014-01-01

    Intermolecular reactions in and on icy films on silicate and carbonaceous grains constitute a major route for the formation of new molecular constituents in interstellar molecular clouds. In more diffuse regions and in protoplanetary discs, energetic radiation can trigger reaction routes far from thermal equilibrium. As an analog of interstellar ice-covered dust grains, highly-oriented pyrolytic graphite (HOPG) covered with D2O, NO, and H atoms is irradiated by ultrashort XUV pulses and the desorbing ionic and neutral products are analysed. The yields of several products show a nonlinear intensity dependence and thus enable the elucidation of reaction dynamics by two-pulse correlated desorption.

  11. 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

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Itoh, Yoh

    2016-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  15. 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.

  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. Long Timestep Molecular Dynamics on the Graphical Processing Unit

    PubMed Central

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

    2013-01-01

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

  18. 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

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

    SciTech Connect

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

    2015-06-10

    We investigate the plausibility of detecting X-ray emission from a stellar jet that impacts a dense molecular cloud, a scenario that may be typical for classical T Tauri stars with jets in dense star-forming complexes. We first model the impact of a jet against a dense cloud using two-dimensional axisymmetric hydrodynamic simulations, exploring different configurations of the ambient environment. Then, we compare our results with XMM-Newton observations of the Herbig–Haro object HH 248, where extended X-ray emission aligned with the optical knots is detected at the edge of the nearby IC 434 cloud. Our simulations show that a jet can produce plasma with temperatures up to 10{sup 7} K, consistent with production of X-ray emission, after impacting a dense cloud. We find that jets denser than the ambient medium but less dense than the cloud produce detectable X-ray emission only at impact with the cloud. From an exploration of the model parameter space, we constrain the physical conditions (jet density and velocity and cloud density) that reproduce the intrinsic luminosity and emission measure of the X-ray source possibly associated with HH 248 well. Thus, we suggest that the extended X-ray source close to HH 248 corresponds to a jet impacting a dense cloud.

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  3. 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.

  4. 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

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  8. 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

  9. 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.

  10. 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.

  11. Thermodynamics of information processing at the molecular scale

    NASA Astrophysics Data System (ADS)

    Gaspard, P.

    2015-07-01

    The thermodynamics of copolymerization processes leading to the formation and replication of copolymers is presented. Copolymers are natural one-dimensional supports of information, which may be coded in the sequence of monomeric units randomly attached or detached during their synthesis. Multivariate fluctuation relations are here established for copolymerization processes synthesizing Bernoulli and first-order Markov chains. Thereof, the thermodynamic entropy production is deduced and shown to depend on quantities characterizing information possibly stored in the copolymer sequence. This article is supplemented with comments by D. Ruelle and Y. Pomeau and a final reply by the author.

  12. Polystannanes: processible molecular metals with defined chemical structures.

    PubMed

    Caseri, Walter

    2016-10-01

    Polystannanes are a unique class of materials as those inorganic polymers (more precisely organometallic polymers) appear to be hitherto the only characterized polymers with a backbone of covalently bound metal atoms. This review reflects the synthesis, spectroscopic characterization (in particular (119)Sn NMR and UV-vis spectroscopy), physical properties and material properties of polystannanes, and their processing into (oriented) films and fiber blends.

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

    PubMed

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

    2010-03-01

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

  14. 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

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Gerya, Taras

    2014-05-01

    On the one hand, the principle of lithostatic pressure is habitually used in metamorphic geology to calculate paleo-depths of metamorphism from mineralogical pressure estimates given by geobarometry. On the other hand, it is obvious that this lithostatic (hydrostatic) pressure principle should only be valid for an ideal case of negligible deviatoric stresses during the long-term development of the entire tectono-metamorphic system - the situation, which newer comes to existence in natural lithospheric processes. The question is therefore not "Do non-lithostatic pressure variations exist?" but " What is the magnitude of long-term non-lithostatic pressure variations in various lithospheric processes, which can be recorded by mineral equilibria of respective metamorphic rocks?". The later question is, in particular, relevant for various types of high-pressure (HP) and ultrahigh-pressure (UHP) rocks, which are often produced in convergent plate boundary settings (e.g., Hacker and Gerya, 2013). This question, can, in particular, be answered with the use of thermo-mechanical models of subduction/collision processes employing realistic P-T-stress-dependent visco-elasto-brittle/plastic rheology of rocks. These models suggest that magnitudes of pressure deviations from lithostatic values can range >50% underpressure to >100% overpressure, mainly in the regions of bending of rheologically strong mantle lithosphere (Burg and Gerya, 2005; Li et al., 2010). In particular, strong undepresures along normal faults forming within outer rise regions of subducting plates can be responsible for downward water suction and deep hydration of oceanic slabs (Faccenda et al., 2009). Weaker HP and UHP rocks of subduction/collision channels are typically subjected to lesser non-lithostatic pressure variations with characteristic magnitudes ranging within 10-20% from the lithostatic values (Burg and Gerya, 2005; Li et al., 2010). The strength of subducted crustal rocks and the degree of

  17. 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.

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Liu, Kun; E906/SeaQuest Collaboration

    2013-10-01

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

  1. Molecular photoionization processes of astrophysical and aeronomical interest

    NASA Technical Reports Server (NTRS)

    Langhoff, P. W.

    1985-01-01

    An account is given of aspects of photoionization processes in molecules, with particular reference to recent theoretical and experimental studies of partial cross sections for production of specific final electronic states and of parent and fragment ions. Such cross sections help provide a basis for specifying the state of excitation of the ionized medium, are useful for estimating the kinetic energy distributions of photoejected electrons and fragment ions, provide parent-and fragment-ion yields, and clarify the possible origins of neutral fragments in highly excited rovibronic states. A descriptive account is given of photoionization phenomena, including tabulation of valence- and inner-shell potentials for some molecules of astrophysical and aeronomical interest. Cross sectional expressions are given. Various approximations currently employed in computational studies are described briefly, threshold laws and high-energy limits are indicated, and distinction is drawn between resonant and direct photoionization phenomena. Recent experimental and theoretical studies of partial photoionization cross sections in selected compounds of astrophysical and aeronomical relevance are described and discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  3. 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

  4. Vibrational origin of the fast relaxation processes in molecular glass formers

    NASA Astrophysics Data System (ADS)

    Mossa, S.; Monaco, G.; Ruocco, G.

    2002-10-01

    We study the interaction of the relaxation processes with the density fluctuations by molecular dynamics simulation of a flexible molecular model for o-terphenyl in the liquid and supercooled phases. We find evidence, besides the structural relaxation, of a secondary vibrational relaxation whose characteristic time, few ps, is slightly temperature dependent. This i) confirms the result by Monaco et al. (Phys. Rev. E, 62 (2000) 7595) of the vibrational nature of the fast relaxation observed in Brillouin Light Scattering experiments in o-terphenyl; and ii) poses a caveat on the interpretation of the BLS spectra of molecular systems in terms of a purely center-of-mass dynamics.

  5. 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

  6. Visually guided collision avoidance and collision achievement.

    PubMed

    Regan; Gray

    2000-03-01

    To survive on today's highways, a driver must have highly developed skills in visually guided collision avoidance. To play such games as cricket, tennis or baseball demands accurate, precise and reliable collision achievement. This review discusses evidence that some of these tasks are performed by predicting where an object will be at some sharply defined instant, several hundred milliseconds in the future, while other tasks are performed by utilizing the fact that some of our motor actions change what we see in ways that obey lawful relationships, and can therefore be learned. Several monocular and binocular visual correlates of the direction of an object's motion relative to the observer's head have been derived theoretically, along with visual correlates of the time to collision with an approaching object. Although laboratory psychophysics can identify putative neural mechanisms by showing which of the known correlates are processed by the human visual system independently of other visual information, it is only field research on, for example, driving, aviation and sport that can show which visual cues are actually used in these activities. This article reviews this research and describes a general psychophysically based rational approach to the design of such field studies.

  7. 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

  8. Geochemical Interpretation of Collision Volcanism

    NASA Astrophysics Data System (ADS)

    Pearce, Julian

    2014-05-01

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

  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. 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.

  11. Photochemical processes in laser ablation of organic solids: Molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yingling, Yaroslava G.

    In this thesis, a comprehensive study of the effect of the photochemical processes on laser ablation mechanisms has been conducted using molecular dynamics simulations. We developed a new concept for modeling photochemical processes in laser ablation of organic films using a mesoscopic coarse-grain breathing sphere model for molecular dynamics simulations. The main advantage of our model is the ability to study the dynamics of the system at the mesoscopic length scale, a regime that is not accessible either with atomistic or continuum computational methods. The photodecomposition of the excited molecules and the chemical reaction patterns in our simulations are based on the photochemistry of chlorobenzene due to ease of its fragmentation and available experimental data. Interpretation of the experimental data is the main objective of our theoretical efforts. Molecular dynamics simulations are used to investigate the effect of photochemical processes on molecular ejection mechanisms in 248-nm laser irradiation of organic solids. Photochemical reactions are found to release additional energy into the irradiated sample and decrease the average cohesive energy, therefore decreasing the value of the ablation threshold. The yield of emitted fragments becomes significant only above the ablation threshold. Below the ablation threshold, only the most volatile photoproduct, HCl, is ejected in very small amounts, whereas the remainder of photoproducts are trapped inside the sample. The presence of photochemical decomposition processes and subsequent chemical reactions changes the temporal and spatial energy deposition profile from pure photothermal ablation. The chemical reactions create an additional local pressure build up and, as a result, generate a strong and broad acoustic pressure wave propagating toward the bottom of the computational cell. The strong pressure wave in conjunction with the temperature increase in the absorbing region causes the ejection of hot massive

  12. Interplay of formulation and process methodology on the extent of nifedipine molecular dispersion in polymers.

    PubMed

    Huang, Jingjun; Li, Ying; Wigent, Rodney J; Malick, Waseem A; Sandhu, Harpreet K; Singhal, Dharmendra; Shah, Navnit H

    2011-11-25

    The aim of this study is to evaluate effects of formulation and process technology on drug molecular dispersibility in solid dispersions (SDs). Nifedipine solid dispersions with ethylcellulose (EC) and/or Eudragit RL (RL) prepared by co-precipitation, co-evaporation, and fusion methods were characterized with FTIR, DSC, and XRPD for the content of nifedipine as molecular dispersion, amorphous and/or crystalline suspensions. A method was developed based on regular solution and Flory-Huggins theories to calculate drug-polymer interaction parameter in solid dispersion systems. A synergic effect of RL and EC on nifedipine molecular dispersibility in solid dispersions was observed. Increasing RL/EC ratio resulted in a higher degree of drug-polymer interaction that thermodynamically favored molecular dispersion, which, however, was counteracted by a corresponding decrease in the matrix glass transition point that kinetically favored phase-separation. Process methodology was found to play an important role in the formation of amorphous SD. The ranking of technologies with respect to the extent of molecular dispersion from high to low is fusion>co-evaporation>co-precipitation, wherein the solidification rate of polymeric solution and non-solvent effects were linked to kinetic entrapment of drug molecules in polymeric networks. Since nifedipine molecular dispersibility in EC/RL polymer(s) is a result of interplay between thermodynamic and kinetic factors, nifedipine molecular dispersions prepared for this study are thermodynamically metastable systems. To explore those supersaturation systems for use in drug delivery of poorly water soluble drugs, it is critical to balance drug-polymer interactions and matrix glass transition point and to consider a process technology with a fast solidification rate during formulation and process development of amorphous SD.

  13. 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.

  14. 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.

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

    PubMed

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

    2016-03-18

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

  16. 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.

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

    PubMed

    Bleiholder, Christian

    2015-10-21

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

  18. Tectonic significance of the Eratosthenes Seamount: a continental fragment in the process of collision with a subduction zone in the eastern Mediterranean (Ocean Drilling Program Leg 160)

    NASA Astrophysics Data System (ADS)

    Robertson, Alastair H. F.

    1998-11-01

    One of the objectives of ODP Leg 160 in the eastern Mediterranean Sea (April-May, 1995) was concerned with the study of processes of genesis and incipient collision of an inferred crustal fragment, the Eratosthenes Seamount, with the active margin of the Eurasian plate to the north, represented by southern Cyprus. The upper part of the Eratosthenes Seamount (i.e. upper several hundred metres) was found to include both shallow- and deep-water carbonates dating back to Early Cretaceous time. Shallow-water platform carbonate deposition, similar to that of the onshore Levant continental margin to the east (i.e. part of the North African plate), was followed by submergence to bathyal depths (>1000 m) in the Late Cretaceous to Middle Eocene, punctuated by depositional and tectonic hiatuses. Tectonic uplift (approximately 1 km) was followed by shallow-water carbonate deposition in the Early Miocene. The platform was exposed during the Messinian desiccation crisis. During the Early Pliocene the platform subsided to bathyal depths associated with localised accumulation of limestone debris flows. Subsidence accelerated in the Late Pliocene-Early Pleistocene, reaching a present-day maximum depth of ca. 2500 m. Deformation of the Eratosthenes Seamount (i.e. subsidence and high-angle faulting) resulted from crustal flexure, induced by southward overthrusting of the Cyprus active margin. Tectonic subsidence of the Eratosthenes Seamount was approximately synchronous with rapid surface uplift of the over-riding plate, the Troodos Ophiolite of southern Cyprus. This uplift is explained in terms of incipient collision of an Eratosthenes continental fragment with a subduction trench, coupled with the effects of diapiric protrusion of serpentinite located within the core of the Troodos Ophiolite. The Eratosthenes drilling, thus, documented a modern analogue of subduction/collisional processes leading to accretion of continental fragments and carbonate platforms in orogenic belts.

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

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2016-03-01

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

  20. In-Line Detection and Measurement of Molecular Contamination in Semiconductor Process Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Jason; West, Michael; Han, Ye; McDonald, Robert C.; Yang, Wenjing; Ormond, Bob; Saini, Harmesh

    2005-09-01

    This paper discusses a fully automated metrology tool for detection and quantitative measurement of contamination, including cationic, anionic, metallic, organic, and molecular species present in semiconductor process solutions. The instrument is based on an electrospray ionization time-of-flight mass spectrometer (ESI-TOF/MS) platform. The tool can be used in diagnostic or analytical modes to understand process problems in addition to enabling routine metrology functions. Metrology functions include in-line contamination measurement with near real-time trend analysis. This paper discusses representative organic and molecular contamination measurement results in production process problem solving efforts. The examples include the analysis and identification of organic compounds in SC-1 pre-gate clean solution; urea, NMP (N-Methyl-2-pyrrolidone) and phosphoric acid contamination in UPW; and plasticizer and an organic sulfur-containing compound found in isopropyl alcohol (IPA). It is expected that these unique analytical and metrology capabilities will improve the understanding of the effect of organic and molecular contamination on device performance and yield. This will permit the development of quantitative correlations between contamination levels and process degradation. It is also expected that the ability to perform routine process chemistry metrology will lead to corresponding improvements in manufacturing process control and yield, the ability to avoid excursions and will improve the overall cost effectiveness of the semiconductor manufacturing process.

  1. 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

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

    SciTech Connect

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

    2014-02-21

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

  3. Molecular diversity and characterization of tetracycline-resistant Staphylococcus aureus isolates from a poultry processing plant.

    PubMed

    Huys, Geert; D'Haene, Klaas; Van Eldere, Johan; von Holy, Alexander; Swings, Jean

    2005-01-01

    DNA fingerprinting and molecular characterization showed that the tetracycline-resistant Staphylococcus aureus population of a South African poultry processing plant comprised one or possibly several tet(K)-containing endemic clones that contaminated chicken and machinery surfaces at all sampled processing stages. The tet(K) gene was transferable by filter mating to S. aureus recipient 80CR5 and was located on a pT181-like plasmid.

  4. Enhanced mechanical properties of graphene/copper nanocomposites using a molecular-level mixing process.

    PubMed

    Hwang, Jaewon; Yoon, Taeshik; Jin, Sung Hwan; Lee, Jinsup; Kim, Taek-Soo; Hong, Soon Hyung; Jeon, Seokwoo

    2013-12-10

    RGO flakes are homogeneously dispersed in a Cu matrix through a molecular-level mixing process. This novel fabrication process prevents the agglomeration of the RGO and enhances adhesion between the RGO and the Cu. The yield strength of the 2.5 vol% RGO/Cu nanocomposite is 1.8 times higher than that of pure Cu. The strengthening mechanism of the RGO is investigated by a double cantilever beam test using the graphene/Cu model structure.

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

    PubMed

    Xie, Ping

    2009-09-16

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

  6. Process for producing high quality, high molecular weight microcrystalline wax derived from undewaxed bright stock

    SciTech Connect

    Miller, S.J.

    1986-08-26

    A process is described for preparing high molecular weight microcrystalline wax from a hydrocracked, undewaxed bright stock, comprising: (a) contacting the bright stock with hydrogen in the presence of a catalyst having hydrodenitrification activity under conditions effective to reduce the nitrogen content of the stock to produce a substantially nitrogen-free product; (b) contacting the substantially nitrogen-free product with hydrogen in the presence of a catalyst having hydrogenation activity under mild conditions to produce a wax-containing oil; and (c) solvent dewaxing the wax-containing oil to produce high molecular weight microcrystalline wax.

  7. 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.

  8. Aerial web-weaving spiders: Linking molecular and organismal processes in evolution.

    PubMed

    Craig, C L

    1992-08-01

    Aerial web-weaving spiders display a wide variety of foraging behaviors that can be tied to the evolution of one family of proteins, the silks. In some cases, the physical structure and mechanical properties of silks alone determine the ecology of spiders: the habitats in which they forage, the prey they capture and their subsequent reproductive success. Future studies that integrate research on the physical structure of silks, the molecular genetics of silk synthesis and the foraging ecology of spiders in primitive and derived phylogenetic groups could reveal how molecular and organismal processes interact in evolution.

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

    PubMed

    Ramlan, Effirul Ikhwan; Zauner, Klaus-Peter

    2013-05-07

    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.

  11. 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

  12. Efficient representations of continuum states for photoionization processes from atomic and molecular targets

    NASA Astrophysics Data System (ADS)

    Yip, Frank L.

    The investigation of single and double photoionization effects in small atoms and molecules provides a means to probe fundamental quantum mechanical phenomena concerning electron correlation and interference effects. To consider these concepts accurately from first principles requires the construction of the exact final continuum states of a many body problem in atomic double photoionization and of the complicated continuum states in molecular single photoionization. Methods designed for incorporating exterior complex scaling (ECS) have proven very successful towards accomplishing these goals, providing a rigorous framework for describing continuum states involving any number of outgoing electrons with numerical exactness. Furthermore, such methods render solutions that can be interrogated to extract the full richness of information about the photoionization process from the wave function. This work aims to demonstrate the use of exterior complex scaling by first exactly solving the three-body breakup problem of the atomic hydride anion. H-- is the simplest atomic system and is most sensitive to electron correlation effects. The application of ECS with an efficient finite-element discrete variable representation proves quite capable and well-suited for this atomic Coulomb breakup problem. The evolution of this framework to treat molecular problems efficiently with exactness is furthered by the design of a hybrid basis method. The incorporation of analytic Gaussian basis sets ubiquitous in bound state molecular descriptions seems natural for considering molecular continuum states. The hybrid method is described in full detail and applied to completely describe photoionization of molecular H+2 and Li+2 . Photoionization of simple molecular systems offers significantly more complexity in the resulting angular distributions of the ejected electron as the target geometry becomes less atomic-like, i.e., as the internuclear separation increases. In this regard

  13. PTtD evolution of continental crust during subduction-collision processes : example of the Briançonnais domain (Western Alps, France).

    NASA Astrophysics Data System (ADS)

    Strzerzynski, P.; Guillot, S.; Leloup, P. H.; Arnaud, N.; Vidal, O.; Ledru, P.; Courrioux, G.; Darmendrail, X.

    2009-04-01

    the significance of the D2 structures in the internal Western Alps. Results indicate that polyphased tectonic occurs during exhumation. The first deformation phase (D1) is characterized by nappe stacking in a context of top to the NW shearing, between 37 and 35 Ma deformation occurs between 1.0 and 0.5 GPa and 360-350°C. Top to the East deformation phase (D2) is associated with decompression up to 0.1 GPa and cooling down to 280°C. D2 deformations end at 31Ma. Following these phases of ductile deformation, two successive brittle deformation phases are evidenced: the first one is characterized by a N-S direction of extension and produce the overall tilting toward the south of the studied zone. The second one is characterized by E-W direction of extension. In the Internal Alps, the transition between Oceanic-continental subduction and continental collision occurred at 32Ma. In this context, D1 deformations that are dated between 37 and 35 Ma are clearly related to continental subduction. In the same way, brittle deformation phases are the expression of continental collision. The D2 tectonic phase took place at the transition between subduction and collision. Its attribution to one of these two processes remains ambiguous and will be discussed at the light of these new results.

  14. 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.

  15. 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

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Tran, H.; Hartmann, J. M.

    2011-06-01

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

  18. 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.

  19. 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.

  20. 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.

  1. Enhanced light-assisted-collision rate via excitation to the long-lived 5S{sub 1/2}-5D{sub 5/2} molecular potential in an {sup 85}Rb magneto-optical trap

    SciTech Connect

    Wilson, Truman M.; Roberts, Jacob L.

    2011-03-15

    We report measurements of a significant increase in the two-body loss rate in an {sup 85}Rb magneto-optic trap (MOT) caused by the addition of light resonant with the 5P{sub 3/2}-to-5D{sub 5/2} transition (776 nm) in Rb. Exposure to the additional light resulted in up to a factor of 5 decrease in the steady-state number of atoms in the MOT. This loss is attributed to more than an order of magnitude increase in the light-assisted collision rate brought about by the 776-nm light. By measuring the intensity dependence of the loss rate, the loss channel was identified to be the relatively long-lived 5S{sub 1/2}-5D{sub 5/2} molecular potential.

  2. Ultrarelativistic quantum molecular dynamics calculations of two-pion Hanbury-Brown-Twiss correlations in central Pb-Pb collisions at sNN=2.76 TeV

    NASA Astrophysics Data System (ADS)

    Li, Qingfeng; Gräf, G.; Bleicher, Marcus

    2012-03-01

    Two-pion Hanbury-Brown-Twiss (HBT) correlations for central Pb-Pb collisions at the Large-Hadron-Collider (LHC) energy of sNN=2.76 TeV are investigated with the microscopic transport model ultrarelativistic quantum molecular dynamics. The transverse momentum dependence of the Pratt-Bertsch HBT radii is extracted from a three-dimensional Gaussian fit to the correlator in the longitudinal comoving system. Qualitative agreement with the ALICE data is obtained, however Rout is overpredicted by nearly 50%. The LHC results are also compared to data from the STAR experiment at RHIC. For both energies we find that the calculated RO:RS ratio is always larger than data, indicating that the emission in the model is less explosive than observed in the data.

  3. Solution-processed ultrathin chemically derived graphene films as soft top contacts for solid-state molecular electronic junctions.

    PubMed

    Li, Tao; Hauptmann, Jonas Rahlf; Wei, Zhongming; Petersen, Søren; Bovet, Nicolas; Vosch, Tom; Nygård, Jesper; Hu, Wenping; Liu, Yunqi; Bjørnholm, Thomas; Nørgaard, Kasper; Laursen, Bo W

    2012-03-01

    A novel method using solution-processed ultrathin chemically derived graphene films as soft top contacts for the non-destructive fabrication of molecular junctions is demonstrated. We believe this protocol will greatly enrich the solid-state test beds for molecular electronics due to its low-cost, easy-processing and flexible nature.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Yano, Ryosuke; Suzuki, Kojiro; Kuroda, Hisayasu

    2007-01-01

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

  11. Simultaneous optical excitation of Na electronic and CF{sub 4} vibrational modes in Na+CF{sub 4} collisions

    SciTech Connect

    Alekseev, V. A.; Grosser, J.; Hoffmann, O.; Rebentrost, F.

    2008-11-28

    We report on the ultraviolet excitation of Na(3s)+CF{sub 4} collision pairs in a crossed molecular beam experiment. We observe Na(3d) collision products originating from the process Na(3s)+CF{sub 4}({nu}{sub 3}=0)+h{nu}{yields}Na(3d)+CF{sub 4}({nu}{sub 3}=1). The spectral intensity distribution of the collision products and the prevailing small angle scattering confirm a previously proposed long range dipole-dipole mechanism. We report velocity-resolved spectra and a comparison to preliminary numerical results based on collisional broadening theory. Polarization experiments suggest future potential for the observation of collision geometries.

  12. 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.

  13. 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?"

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Buchachenko, A. L.

    2014-01-01

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

  16. Role of molecular dynamics on descriptions of shock-front processes

    SciTech Connect

    Karo, A.M.

    1981-07-22

    By means of a computational approach based on classical molecular dynamics, we can begin to form a realistic picture of shock-induced processes occurring at the shock front and resulting from the detailed, violent motion associated with shock motion on an atomic scale. Prototype studies of phase transitions will be discussed. We will also examine the interaction of the shock front with defects, surfaces, voids, and inclusions, and across grain boundaries. We will focus on the critical question of how mechanical energy imparted to a condensed material by shock loading is converted to the activation energy required to overcome some initial energy barrier in an initiation process.

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

    SciTech Connect

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

    2008-03-28

    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(H{sub 2}O){sub 6}{sup 2+/3+} and Ru(H{sub 2}O){sub 6}{sup 2+/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.

  18. 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

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

    PubMed

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

    2014-09-01

    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.

  20. 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

  1. 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.

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

    PubMed

    Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

    2015-07-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2004-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-11-01

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

  5. Measurement of the differential cross section of the photoinitiated reactive collision of O((1)D)+D(2) using only one molecular beam: A study by three dimensional velocity mapping.

    PubMed

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

    2010-06-28

    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

  6. 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

  7. Charge exchange in H^+ + He^+ collision

    NASA Astrophysics Data System (ADS)

    Guevara Leon, Nicolais; Sabin, John R.; Deumens, Erik; Ohrn, Yngve

    2008-05-01

    Charge exchange in H^+ + He^+ collision are investigated theoretically at projectile energies below the ionization threshold at about 100 keV/amu. The electron nuclear dynamics (END) method is used to analyze the collision processes. Total charge exchange cross sections were calculated and compared with other theoretical and experimental data.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  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.

  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 genetic bases of adaptation processes and approaches to their analysis].

    PubMed

    Salmenkova, E A

    2013-01-01

    Great interest in studying the molecular genetic bases of the adaptation processes is explained by their importance in understanding evolutionary changes, in the development ofintraspecific and interspecific genetic diversity, and in the creation of approaches and programs for maintaining and restoring the population. The article examines the sources and conditions for generating adaptive genetic variability and contribution of neutral and adaptive genetic variability to the population structure of the species; methods for identifying the adaptive genetic variability on the genome level are also described. Considerable attention is paid to the potential of new technologies of genome analysis, including next-generation sequencing and some accompanying methods. In conclusion, the important role of the joint use of genomics and proteomics approaches in understanding the molecular genetic bases of adaptation is emphasized.

  15. Molecular Studies on the Ecology of Listeria monocytogenes in the Smoked Fish Processing Industry

    PubMed Central

    Norton, Dawn M.; McCamey, Meghan A.; Gall, Kenneth L.; Scarlett, Janet M.; Boor, Kathryn J.; Wiedmann, Martin

    2001-01-01

    We have applied molecular approaches, including PCR-based detection strategies and DNA fingerprinting methods, to study the ecology of Listeria monocytogenes in food processing environments. A total of 531 samples, including raw fish, fish during the cold-smoking process, finished product, and environmental samples, were collected from three smoked fish processing facilities during five visits to each facility. A total of 95 (17.9%) of the samples tested positive for L. monocytogenes using a commercial PCR system (BAX for Screening/Listeria monocytogenes), including 57 (27.7%) environmental samples (n = 206), 8 (7.8%) raw material samples (n = 102), 23 (18.1%) samples from fish in various stages of processing(n = 127), and 7 (7.3%) finished product samples (n = 96). L. monocytogenes was isolated from 85 samples (16.0%) using culture methods. Used in conjunction with a 48-h enrichment in Listeria Enrichment Broth, the PCR system had a sensitivity of 91.8% and a specificity of 96.2%. To track the origin and spread of L. monocytogenes, isolates were fingerprinted by automated ribotyping. Fifteen different ribotypes were identified among 85 isolates tested. Ribotyping data established possible contamination patterns, implicating raw materials and the processing environment as potential sources of finished product contamination. Analysis of the distribution of ribotypes revealed that each processing facility had a unique contamination pattern and that specific ribotypes persisted in the environments of two facilities over time (P ≤ 0.0006). We conclude that application of molecular approaches can provide critical information on the ecology of different L. monocytogenes strains in food processing environments. This information can be used to develop practical recommendations for improved control of this important food-borne pathogen in the food industry. PMID:11133446

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Collision Broadening Of Line Spectrum In Sonoluminescence

    SciTech Connect

    Li Chaohui; An Yu

    2008-06-24

    The direct measurement of temperature inside a sonoluminescing bubble as it is at its flashing phase is almost impossible due to the smallness of the bubble and the short duration of the flashing. One may estimate the temperature through fitting the continuum spectrum of sonoluminescence by the black body radiation formula, or fitting the shape of atomic or molecular line spectrum (the different temperature, density and pressure result in the different shape of the line spectrum due to the effect of collision broadening). However, the temperature changes in a huge range at short duration as the bubble flashes, therefore, the observed spectra are some kind of average one, so are those fitted results. To evaluate the instantaneous temperature more accurately, we simulate the processes of the bubble motion and the thermodynamics inside the bubble, in which atomic or molecular line spectra with the collision broadening effect and the continuum spectra contributed from the processes of electron-atom bremsstrahlung, electron-ion bremsstrahlung and recombination radiation and radiative attachment of electrons to atoms and molecules are taken into account in calculating the light emission. If both the calculated continuum spectra and the shape of line spectra can well represent the experimental data, we may deduce that the calculation of the temperature, density and pressure is reliable and we indirectly evaluate those quantities inside the bubble. In the present calculation, the line spectra of OH radical at about 310 nm mixing the electron transition with the vibration and rotational bands are considered. The calculation qualitatively consists with the observation, and we expect that with the more precise bubble dynamics model instead of the uniform model employed in the present calculation we may improve the quantitative result.

  1. Dynamics of proton-acetylene collisions at 30 eV

    NASA Astrophysics Data System (ADS)

    Malinovskaya, S. A.; Cabrera-Trujillo, R.; Sabin, John. R.; Deumens, E.; Ohrn, Y.

    2002-07-01

    Collisions of protons with ground state acetylene molecules at 30 eV are studied using the electron nuclear dynamics (END) theory. This time-dependent methodology for the study of molecular processes is a nonadiabatic approach to direct dynamics, which has been successfully applied to ion-atom and ion-molecule reactive collisions. Using the minimal END theory, we calculate the direct and charge-transfer differential cross sections. Different initial conditions lead to diverse product channels, such as charge transfer, proton exchange, and collision induced dissociation. Projectile energy loss is analyzed in terms of transfer into target electronic, translational, and rovibrational excitations. The comparison of the computed results with time-of-flight measurements is discussed.

  2. 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.

  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. Epigenetics and Shared Molecular Processes in the Regeneration of Complex Structures.

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    Xiao, Tiejun; Song, Xueyu

    2013-03-01

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

  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. 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.

  9. MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS

    SciTech Connect

    Andrew W. Wang

    2002-04-01

    Several classes of molecular sieves were investigated as methanol dehydration catalysts for the LPDME{trademark} (liquid-phase dimethyl ether) process. Molecular sieves offer a number of attractive features as potential catalysts for the conversion of methanol to DME. These include (1) a wide range of acid strengths, (2) diverse architectures and channel connectivities that provide latitude for steric control, (3) high active site density, (4) well-investigated syntheses and characterization, and (5) commercial availability in some cases. We directed our work in two areas: (1) a general exploration of the catalytic behavior of various classes of molecular sieves in the LPDME{trademark} system and (2) a focused effort to prepare and test zeolites with predominantly Lewis acidity. In our general exploration, we looked at such diverse materials as chabazites, mordenites, pentasils, SAPOs, and ALPOs. Our work with Lewis acidity sought to exploit the structural advantages of zeolites without the interfering effects of deleterious Broensted sites. We used zeolite Ultrastable Y (USY) as our base material because it possesses a high proportion of Lewis acid sites. This work was extended by modifying the USY through ion exchange to try to neutralize residual Broensted acidity.

  10. 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)

  11. Transport theory beyond binary collisions

    SciTech Connect

    Carrington, Margaret E.; Mrowczynski, Stanislaw

    2005-03-15

    Using the Schwinger-Keldysh technique, we derive the transport equations for a system of quantum scalar fields. We first discuss the general structure of the equations and then their collision terms. Taking into account up to three-loop diagrams in {phi}{sup 3} model and up to four-loop diagrams in {phi}{sup 4} model, we obtain transport equations which include the contributions of multiparticle collisions and particle production processes, in addition to mean-field effects and binary interactions.

  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. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  16. An emerging molecular and cellular framework for memory processing by the hippocampus.

    PubMed

    Wittenberg, Gayle M; Tsien, Joe Z

    2002-10-01

    The hippocampus plays a central role in memory consolidation, a process for converting short-term memory into cortically stored, long-lasting memory in the mammalian brain. Here, we review recent data and discuss the 'synaptic re-entry reinforcement' (SRR) hypothesis, which can account for the role of the hippocampus in memory consolidation at both the molecular and systems levels. The central idea of the SRR hypothesis is that reactivation of neural ensembles in the hippocampus during the consolidation period results in multiple rounds of NMDA-receptor-dependent synaptic reinforcement of the hippocampal memory traces created during initial learning. In addition, such reactivation and reinforcement processes permit the hippocampus to act as a 'coincidence regenerator', providing coordinated input that drives the coherent reactivation of cortical neurons, resulting in the progressive strengthening of cortical memory traces through reactivation of cortical NMDA receptors. PMID:12220877

  17. 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.

  18. 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.

  19. Quasi-classical theory of electronic flux density in electronically adiabatic molecular processes.

    PubMed

    Diestler, D J

    2012-11-26

    The standard Born-Oppenheimer (BO) description of electronically adiabatic molecular processes predicts a vanishing electronic flux density (EFD). A previously proposed "coupled-channels" theory permits the extraction of the EFD from the BO wave function for one-electron diatomic systems, but attempts at generalization to many-electron polyatomic systems are frustrated by technical barriers. An alternative "quasi-classical" approach, which eliminates the explicit quantum dynamics of the electrons within a classical framework, yet retains the quantum character of the nuclear motion, appears capable of yielding EFDs for arbitrarily complex systems. Quasi-classical formulas for the EFD in simple systems agree with corresponding coupled-channels formulas. Results of the application of the new quasi-classical formula for the EFD to a model triatomic system indicate the potential of the quasi-classical scheme to elucidate the dynamical role of electrons in electronically adiabatic processes in more complex multiparticle systems.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. Quantum control of a molecular ionization process by using Fourier-synthesized laser fields

    NASA Astrophysics Data System (ADS)

    Ohmura, Hideki; Saito, Naoaki

    2015-11-01

    In photoexcitation processes, if the motion of excited electrons can be precisely steered by the instantaneous electric field of an arbitrary waveform of a Fourier-synthesized laser field, the resultant matter response can be achieved within one optical cycle, usually within the attosecond (1 as =10-18s) regime. Fourier synthesis of laser fields has been achieved in various ways. However, the general use of Fourier-synthesized laser fields for the control of matter is extremely limited. Here, we report the quantum control of a nonlinear response of a molecular ionization process by using Fourier-synthesized laser fields. The directionally asymmetric molecular tunneling ionization induced by intense (5.0 ×1012W /c m2) Fourier-synthesized laser fields consisting of fundamental, second-, third-, and fourth-harmonic light achieves the orientation-selective ionization; we utilized the orientation-selective ionization for measurement of the relative phase differences between the fundamental and each harmonic light. Our findings impact not only light-wave engineering but also the control of matter, possibly triggering the creation and establishment of a new methodology that uses Fourier-synthesized laser fields.

  6. 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

  7. 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

  8. 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

  9. 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

  10. Probability of satellite collision

    NASA Technical Reports Server (NTRS)

    Mccarter, J. W.

    1972-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  12. 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.

  13. Mechanical properties and biocompatibility of melt processed, self-reinforced ultrahigh molecular weight polyethylene.

    PubMed

    Huang, Yan-Fei; Xu, Jia-Zhuang; Li, Jian-Shu; He, Ben-Xiang; Xu, Ling; Li, Zhong-Ming

    2014-08-01

    The low efficiency of fabrication of ultrahigh molecular weight polyethylene (UHMWPE)-based artificial knee joint implants is a bottleneck problem because of its extremely high melt viscosity. We prepared melt processable UHMWPE (MP-UHMWPE) by addition of 9.8 wt% ultralow molecular weight polyethylene (ULMWPE) as a flow accelerator. More importantly, an intense shear flow was applied during injection molding of MP-UHMWPE, which on one hand, promoted the self-diffusion of UHMWPE chains, thus effectively reducing the structural defects; on the other hand, increased the overall crystallinity and induced the formation of self-reinforcing superstructure, i.e., interlocked shish-kebabs and oriented lamellae. Aside from the good biocompatibility, and the superior fatigue and wear resistance to the compression-molded UHMWPE, the injection-molded MP-UHMWPE exhibits a noteworthy enhancement in tensile properties and impact strength, where the yield strength increases to 46.3 ± 4.4 MPa with an increment of 128.0%, the ultimate tensile strength and Young's modulus rise remarkably up to 65.5 ± 5.0 MPa and 1248.7 ± 45.3 MPa, respectively, and the impact strength reaches 90.6 kJ/m(2). These results suggested such melt processed and self-reinforced UHMWPE parts hold a great application promise for use of knee joint implants, particularly for younger and more active patients. Our work sets up a new method to fabricate high-performance UHMWPE implants by tailoring the superstructure during thermoplastic processing. PMID:24835044

  14. The early molecular processes underlying the neurological manifestations of an animal model of Wilson's disease.

    PubMed

    Lee, Beom Hee; Kim, Joo Hyun; Kim, Jae-Min; Heo, Sun Hee; Kang, Minji; Kim, Gu-Hwan; Choi, Jin-Ho; Yoo, Han-Wook

    2013-05-01

    The Long-Evans Cinnamon (LEC) rat shows age-dependent hepatic manifestations that are similar to those of Wilson's disease (WD). The pathogenic process in the brain has, however, not been evaluated in detail due to the rarity of the neurological symptoms. However, copper accumulation is noted in LEC rat brain tissue from 24 weeks of age, which results in oxidative injuries. The current study investigated the gene expression profiles of LEC rat brains at 24 weeks of age in order to identify the important early molecular changes that underlie the development of neurological symptoms in WD. Biological ontology-based analysis revealed diverse altered expressions of the genes related to copper accumulation. Of particular interest, we found altered expression of genes connected to mitochondrial respiration (Sdhaf2 and Ndufb7), calcineurin-mediated cellular processes (Ppp3ca, Ppp3cb, and Camk2a), amyloid precursor protein (Anks1b and A2m) and alpha-synuclein (Snca). In addition to copper-related changes, compensatory upregulations of Cp and Hamp reflect iron-mediated neurotoxicity. Of note, reciprocal expression of Asmt and Bhmt is an important clue that altered S-adenosylhomocysteine metabolism underlies brain injury in WD, which is directly correlated to the decreased expression of S-adenosylhomocysteine hydrolase in hepatic tissue in LEC rats. In conclusion, our study indicates that diverse molecular changes, both variable and complex, underlie the development of neurological manifestations in WD. Copper-related injuries were found to be the principal pathogenic process, but Fe- or adenosylhomocysteine-related injuries were also implicated. Investigations using other animal models or accessible human samples will be required to confirm our observations.

  15. 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.

  16. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain.

    PubMed

    Russo, Luigi; Palmieri, Maddalena; Caso, Jolanda Valentina; D'Abrosca, Gianluca; Diana, Donatella; Malgieri, Gaetano; Baglivo, Ilaria; Isernia, Carla; Pedone, Paolo V; Fattorusso, Roberto

    2015-02-16

    Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

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

    PubMed

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

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

  3. 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

  4. Molecular genetic testing of uveal melanoma from routinely processed and stained cytology specimens.

    PubMed

    Christopher, Benjamin N; Cebulla, Colleen M; Wakely, Paul E; Davidorf, Frederick H; Abdel-Rahman, Mohamed H

    2011-11-01

    In the following study we investigated the utility of molecular genetic testing of the DNA extracted from routinely stained and processed smears from uveal melanoma (UM). Smears from five uveal melanoma cell lines and 12 primary tumors were prepared and stained with Papanicolaou and Romanowsky stains. Genotyping was carried out utilizing 14 microsatellite markers on chromosomes 3, 6 and 8. Mutational screening for alterations in GNAQ and GNA11 genes was carried out by restriction fragment length polymorphism. The results were compared to those obtained through direct sequencing of frozen tumor tissues. High quality DNA was extracted from the stained slides with no difference in the efficiency of DNA extraction between the two staining techniques. The extracted DNA was of adequate quality for genotyping and mutational screening. DNA extracted from approximately 200 tumor cells is sufficient for reproducible testing of allelic imbalances and for studying the common somatic mutations in GNAQ and GNA11 genes. In conclusion, we presented the feasibility of utilizing routinely stained cytology smears from UM for molecular genetic testing. The DNA obtained is of sufficient quality to carry out genotyping for markers on chromosome 3, 6 and 8, as well as screening for somatic mutations in GNAQ and GNA11 genes.

  5. 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

  6. Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments.

    PubMed

    Pizzarello, Sandra; Davidowski, Stephen K; Holland, Gregory P; Williams, Lynda B

    2013-09-24

    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

  7. 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

  8. Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization

    NASA Astrophysics Data System (ADS)

    Zhao, Xiongce; Rignall, Tauna R.; McCabe, Clare; Adney, William S.; Himmel, Michael E.

    2008-07-01

    We present free energy calculations for the Trichoderma reesei Cel7A (cellobiohydrolase I) linker peptide from molecular dynamics simulations directed towards understanding the linker role in cellulose hydrolysis. The calculations predict an energy storage mechanism of the linker under stretching/compression that is consistent with processive depolymerization. The linker exhibits two stable states at lengths of 2.5 nm and 5.5 nm during extension/compression, with a free energy difference of 10.5 kcal/mol between the two states separated by an energy barrier. The switching between stable states supports the hypothesis that the linker peptide has the capacity to store energy in a manner similar to a spring.

  9. 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.

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

    SciTech Connect

    Chu, S.I.

    1981-01-01

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

  11. 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.

  12. Ionothermal synthesis process for aluminophosphate molecular sieves in the mixed water/ionic liquid system.

    PubMed

    Zhao, Zhenchao; Zhang, Weiping; Xu, Renshun; Han, Xiuwen; Tian, Zhijian; Bao, Xinhe

    2012-01-21

    The synthesis process of aluminophosphate AlPO(4)-11 molecular sieve in the mixed water/1-butyl- 3-methylimidazolium bromide ([bmim]Br) ionic liquid was investigated by XRD, multinuclear solid-state NMR, scanning electron microscopy (SEM) and X-ray energy dispersive spectroscopy (EDS). It was observed that a tablet phase, named SIZ-2, was formed at the early stage of crystallization. During crystallization metastable SIZ-2 with an incompletely condensed framework phosphorus disappeared gradually, and the phosphorous species became fully condensed through hydroxyl reaction with tetrahedral aluminum to form thermodynamically stable AlPO(4)-11 in the final product. It was found that [bmim]Br, acting as the structure-directing agent, was occluded into the AlPO(4)-11 channel.

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

    SciTech Connect

    Otec, Roman

    2006-01-01

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

  15. Combined papillary and mucoepidermoid carcinoma of the thyroid gland: a possible collision tumor diagnosed on fine-needle cytology. Report of a case with immunocytochemical and molecular correlations.

    PubMed

    Fulciniti, Franco; Vuttariello, Emilia; Calise, Celeste; Monaco, Mario; Pezzullo, Luciano; Chiofalo, Maria Grazia; Di Gennaro, Francesca; Malzone, Maria Gabriella; Campanile, Anna Cipolletta; Losito, Nunzia Simona; Botti, Gerardo; Chiappetta, Gennaro

    2015-05-01

    Fine-needle cytology (FNC) is frequently used to diagnose thyroid nodules discovered by palpation or imaging studies. Molecular tests on FNC material may increase its diagnostic accuracy. We report a case of a classic papillary thyroid carcinoma combined with a mucoepidermoid carcinoma correctly identified on FNC. The papillary component had a classic immunophenotype (CK19+, TTF1+), while the mucoepidermoid one was only focally CK19+. Point mutations (BRAF and RAS) and rearrangements (RET/PTC) of the papillary component have been also investigated on FNC samples, with resulting concurrent rearrangements of RET/PTC1 and RET/PTC3, but no point mutations. The histogenesis of combined papillary and mucoepidermoid carcinoma of the thyroid still remains partly unsettled, and further genomic studies are needed to shed some more light on this peculiar neoplasm.

  16. 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

  17. 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.

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

    PubMed

    Herman, Agnieszka

    2011-11-01

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

  19. 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.

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

    PubMed

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

    2014-02-12

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

  1. 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.

  2. COMPLEMENTARY MOLECULAR AND ELEMENTAL DETECTION OF SPECIATED THIOARSENICALS USING ESI-MS IN COMBINATION WITH A XENON-BASED COLLISION-CELL ICP-MS WITH APPLICATION TO FORTIFIED NIST FREEZE-DRIED URINE

    EPA Science Inventory

    The simultaneous detection of arsenic and sulfur in thio-arsenicals was achieved using xenonbased collision cell ICP-MS in combination with HPLC. In an attempt to minimize the 16O16O+ interference at m/z 32, both sample introduction and collision cell experimental parameters were...

  3. 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. 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

  5. The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms.

    PubMed

    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.

  6. 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.

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

    PubMed

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

    2005-01-01

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

  8. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

    PubMed

    Roe, Daniel R; Cheatham, Thomas E

    2013-07-01

    We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ.

  9. Molecular-Scale Structural Controls on Nanoscale Growth Processes: Step-Specific Regulation of Biomineral Morphology

    NASA Astrophysics Data System (ADS)

    Dove, P. M.; Davis, K. J.; De Yoreo, J. J.; Orme, C. A.

    2001-12-01

    Deciphering the complex strategies by which organisms produce nanocrystalline materials with exquisite morphologies is central to understanding biomineralizing systems. One control on the morphology of biogenic nanoparticles is the specific interactions of their surfaces with the organic functional groups provided by the organism and the various inorganic species present in the ambient environment. It is now possible to directly probe the microscopic structural controls on crystal morphology by making quantitative measurements of the dynamic processes occurring at the mineral-water interface. These observations can provide crucial information concerning the actual mechanisms of growth that is otherwise unobtainable through macroscopic techniques. Here we use in situ molecular-scale observations of step dynamics and growth hillock morphology to directly resolve roles of principal impurities in regulating calcite surface morphologies. We show that the interactions of certain inorganic as well as organic impurities with the calcite surface are dependent upon the molecular-scale structures of step-edges. These interactions can assume a primary role in directing crystal morphology. In calcite growth experiments containing magnesium, we show that growth hillock structures become modified owing to the preferential inhibition of step motion along directions approximately parallel to the [010]. Compositional analyses have shown that Mg incorporates at different levels into the two types of nonequivalent steps, which meet at the hillock corner parallel to [010]. A simple calculation of the strain caused by this difference indicates that we should expect a significant retardation at this corner, in agreement with the observed development of [010] steps. If the low-energy step-risers produced by these [010] steps is perpendicular to the c-axis as seems likely from crystallographic considerations, this effect provides a plausible mechanism for the elongated calcite crystal

  10. Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation*

    PubMed Central

    Payne, Christina M.; Bomble, Yannick J.; Taylor, Courtney B.; McCabe, Clare; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.

    2011-01-01

    Proteins employ aromatic residues for carbohydrate binding in a wide range of biological functions. Glycoside hydrolases, which are ubiquitous in nature, typically exhibit tunnels, clefts, or pockets lined with aromatic residues for processing carbohydrates. Mutation of these aromatic residues often results in significant activity differences on insoluble and soluble substrates. However, the thermodynamic basis and molecular level role of these aromatic residues remain unknown. Here, we calculate the relative ligand binding free energy by mutating tryptophans in the Trichoderma reesei family 6 cellulase (Cel6A) to alanine. Removal of aromatic residues near the catalytic site has little impact on the ligand binding free energy, suggesting that aromatic residues immediately upstream of the active site are not directly involved in binding, but play a role in the glucopyranose ring distortion necessary for catalysis. Removal of aromatic residues at the entrance and exit of the Cel6A tunnel, however, dramatically impacts the binding affinity, suggesting that these residues play a role in chain acquisition and product stabilization, respectively. The roles suggested from differences in binding affinity are confirmed by molecular dynamics and normal mode analysis. Surprisingly, our results illustrate that aromatic-carbohydrate interactions vary dramatically depending on the position in the enzyme tunnel. As aromatic-carbohydrate interactions are present in all carbohydrate-active enzymes, these results have implications for understanding protein structure-function relationships in carbohydrate metabolism and recognition, carbon turnover in nature, and protein engineering strategies for biomass utilization. Generally, these results suggest that nature employs aromatic-carbohydrate interactions with a wide range of binding affinities for diverse functions. PMID:21965672

  11. 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

  12. 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

  13. Fast analysis of molecular dynamics trajectories with graphics processing units—Radial distribution function histogramming

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

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

  14. Computational study of alkali-metal-noble gas collisions in the presence of nonresonant lasers - Na + Xe + h/2/pi/omega sub 1 + h/2/pi/omega sub 2 system

    NASA Technical Reports Server (NTRS)

    Devries, P. L.; Chang, C.; George, T. F.; Laskowski, B.; Stallcop, J. R.

    1980-01-01

    The collision of Na with Xe in the presence of both the rhodamine-110 dye laser and the Nd-glass laser is investigated within a quantum-mechanical close-coupled formalism, utilizing ab initio potential curves and transition dipole matrix elements. Both one- and two-photon processes are investigated; the Na + Xe system is not asymptotically resonant with the radiation fields, so that these processes can only occur in the molecular collision region. The one-photon processes are found to have measurable cross sections at relatively low intensities; even the two-photon process has a significant section for field intensities as low as 10 MW/sq cm.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Electron collisions in gas switches

    SciTech Connect

    Christophorou, L.G.

    1989-01-01

    Many technologies rely on the conduction/insulation properties of gaseous matter for their successful operation. Many others (e.g., pulsed power technologies) rely on the rapid change (switching or modulation) of the properties of gaseous matter from an insulator to a conductor and vice versa. Studies of electron collision processes in gases aided the development of pulsed power gas switches, and in this paper we shall briefly illustrate the kind of knowledge on electron collision processes which is needed to optimize the performance of such switching devices. To this end, we shall refer to three types of gas switches: spark gap closing, self-sustained diffuse discharge closing, and externally-sustained diffuse discharge opening. 24 refs., 15 figs., 2 tabs.

  20. Direct monitoring of molecular recognition processes using fluorescence enhancement at colloid-coated microplates.

    PubMed

    Lobmaier, C; Hawa, G; Götzinger, M; Wirth, M; Pittner, F; Gabor, F

    2001-01-01

    Direct monitoring of recognition processes at the molecular level is a valuable tool for studying reaction kinetics to assess affinity constants (e.g. drugs to receptors) and for designing rapid single step immunoassays. Methods currently used to gain information about binding processes predominantly depend on surface plasmon resonance. These systems use excitation with coherent light in attenuated total reflection geometry to obtain discrimination between surface-bound and free molecules in solution. Therefore labeling of the compounds is not necessary, but due to the complexity of the measuring setup the method is rather costly. In this contribution we present a simple method for performing kinetic single step biorecognition assays with fluorophore labeled compounds using the fluorescence enhancement properties of surface bound silver colloids. Silver colloids are bound to standard microplates via silanization of the plastic surface. Fluorophores close to this colloid coated surface show a significant gain in fluorescence compared to fluorophores farther away in the bulk solution. Therefore discrimination between surface bound and free fluorophores is possible and the binding of, for example, fluorophore labeled antibodies to antigens immobilized on the colloid surface results in increasing fluorescence intensity. Utilization of standard microplates makes this method fully compatible with conventional microplate processing and reading devices. Neither excitation with coherent laser light nor ATR geometry is required, the measurement is performed in a standard fluorescence microplate reader in front face geometry with a xenon flash lamp as excitation source. Methods for the preparation of colloid-coated microplates and fluorescence-enhanced biorecognition assays are presented. Additionally the dependence of the system performance on the structure and properties of the metal colloid coated surface is described. A two-component biorecognition model system shows a

  1. 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).

  2. Two-potential approach for electron-molecular collisions at intermediate and high energies - Application to e-N2 scatterings

    NASA Technical Reports Server (NTRS)

    Choi, B. H.; Poe, R. T.; Sun, J. C.; Shan, Y.

    1979-01-01

    A general theoretical approach is proposed for the calculation of elastic, vibrational, and rotational transitions for electron-molecule scattering at intermediate and high-electron-impact energies. In this formulation, contributions to the scattering process come from the incoherent sum of two dominant potentials: a short-range shielded nuclear Coulomb potential from individual atomic centers, and a permanent/induced long-range potential. Application to e-N2 scattering from 50-500 eV incident electron energies has yielded good agreement with absolutely calibrated experiments. Comparisons with other theoretical approaches are made. The physical picture as well as the general features of electron-molecule scattering process are discussed within the framework of the two-potential approach.

  3. Basins in ARC-continental collisions

    USGS Publications Warehouse

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  5. Collisions of ions in gases

    NASA Astrophysics Data System (ADS)

    Bailey, T. L.

    1982-03-01

    This report is a summary description of research carried out under the ONR Project 'Collisions of Ions in Gases'. The work consisted of experimental studies of collisions of low-energy ions (4 < or = E sub L < or = 500 eV) with atoms and molecules, using the ion-beam gas-target technique, and of theoretical and computational studies done in support of the experiments. Three types of experiments were carried out: (a) measurements of relative differential cross-sections for elastic and inelastic (i.e., charge transfer) scattering in collisions of the He(++) ions with Ne, Ar, and Kr atoms, over the ion energy range 8 < or = E sub L < or = 60 eV; (b) kinematical studies of charge transfer in collisions of 30 < or = E sub L < or = 373 eV Ne(+), Ar(+), and Kr(+) ions with H2, D2, O2, and N2 molecules, in which the KE-distributions of the product H2(+), etc., were measured; and (c) measurements of the absolute total cross-sections for the charge transfer process He(++) + R = He(+) + R(+), where R = Ne, Ar, Kr, over the energy range 4 < or = E sub L < or = 500 eV. The experimental results, and their interpretations in terms of appropriate quantum scattering theory (where the latter was feasible) are discussed briefly. The effects of the thermal motions of collision participants (i.e., thermal broadening) in ion-atom and similar scattering experiments were investigated in computational studies, and a new crossed ion-supersonic atom/molecule beams apparatus, designed to remove the thermal broadening effect and to give high resolution in energy and angle, is discussed.

  6. Two-electron excitation in slow ion-atom collisions: Excitation mechanisms and interferences among autoionizing states

    SciTech Connect

    Kimura, M. Rice Univ., Houston, TX . Dept. of Physics)

    1990-01-01

    The two-electron capture or excitation process resulting from collisions of H{sup +} and O{sup 6+} ions with He atoms in the energy range from 0.5 keV/amu to 5 keV/amu is studied within a molecular representation. The collision dynamics for formation of doubly excited O{sup 4+} ions and He** atoms and their (n{ell}, n{prime}{ell}{prime}) populations are analyzed in conjunction with electron correlations. Autoionizing states thus formed decay through the Auger process. An experimental study of an ejected electron energy spectrum shows ample structures in addition to two characteristic peaks that are identified by atomic and molecular autoionizations. These structures are attributable to various interferences among electronic states and trajectories. We examine the dominant sources of the interferences. 12 refs., 5 figs.

  7. Polymorphism of Crystalline Molecular Donors for Solution-Processed Organic Photovoltaics.

    PubMed

    van der Poll, Thomas S; Zhugayevych, Andriy; Chertkov, Eli; Bakus, Ronald C; Coughlin, Jessica E; Teat, Simon J; Bazan, Guillermo C; Tretiak, Sergei

    2014-08-01

    Using ab initio calculations and classical molecular dynamics simulations coupled to complementary experimental characterization, four molecular semiconductors were investigated in vacuum, solution, and crystalline form. Independently, the molecules can be described as nearly isostructural, yet in crystalline form, two distinct crystal systems are observed with characteristic molecular geometries. The minor structural variations provide a platform to investigate the subtlety of simple substitutions, with particular focus on polymorphism and rotational isomerism. Resolved crystal structures offer an exact description of intermolecular ordering in the solid state. This enables evaluation of molecular binding energy in various crystallographic configurations to fully rationalize observed crystal packing on a basis of first-principle calculations of intermolecular interactions.

  8. 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

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

    PubMed

    Lucock, M

    2000-01-01

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

  10. R-matrix Floquet theory of molecular multiphoton processes: II. Multiphoton ionization of H2

    NASA Astrophysics Data System (ADS)

    Colgan, J.; Glass, D. H.; Higgins, K.; Burke, P. G.

    2001-06-01

    Multiphoton ionization rates for H2 immersed in an intense linearly polarized laser field are calculated using the recently developed R-matrix Floquet theory of molecular multiphoton processes. We assume that the H2 molecule is aligned along the laser polarization direction and we adopt the fixed-nuclei approximation, in which the motion of the target electrons is calculated in the laser field and in the field of the nuclei, which are assumed to be fixed in space. An accurate multi-state wavefunction is employed to calculate one-, two- and four-photon ionization rates for H2 at several internuclear separations over a range of frequencies and intensities. Analysis of the ionization rates reveals the important role played both by resonances corresponding to Rydberg bound states converging to the H2+ ion ground state and by doubly excited states converging to the H2+ ion first excited state. These resonances give rise to resonant enhanced multiphoton ionization peaks in many of the ionization rates studied in this paper, and their possible role in controlling the vibrational population of the final H2+ ion is discussed.

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

    PubMed

    Sauvé, Geneviève; Fernando, Roshan

    2015-09-17

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

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

    PubMed

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

    2016-02-18

    Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations.

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

    PubMed

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

    2016-02-18

    Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black-box method that is easily applied, but requires careful set-up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work-protocols developed in our groups for running successful QM/MM calculations. PMID:26696271

  14. 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.

  15. 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

  16. 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.

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

    PubMed

    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.

  18. 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

  19. 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.

  20. In-situ NMR study of molecular and ionic processes inside carbon nanopores

    NASA Astrophysics Data System (ADS)

    Luo, Zhixiang

    Interactions of simple ions with water and interfaces play critical roles in many electrochemical and biological processes. They are especially significant in nanoconfined regions and have a profound impact in many applications, for instance nanofluidics and supercapacitors. This dissertation employs a nuclear magnetic resonance (NMR) technique to study their influence on the ionic processes inside carbon nanopores. To characterize the carbon micropore structure, a convenient NMR method is established by taking a 1H magic angle spinning (MAS) spectrum of the adsorbed water. A density functional theory (DFT) computation of the nucleus-independent chemical shift (NICS) yields a quantitative relationship between the NICS values and the micropore sizes. The carbon micropore size and distribution are derived from the chemical shift and the spectrum lineshape. For aqueous electrolytes inside uncharged carbon nanopores, the measurement of ion concentrations reveals a substantial electroneutrality breakdown. The specific ion effects and ion-ion correlations are shown to play crucial roles in determining the degree of electroneutrality breakdown. The importance of those interactions is further revealed by the asymmetric and nonlinear responses of ion concentrations to the charging of the confining carbon walls. Such information is obtained with a carbon supercapacitor built into the NMR probe. The NMR observations are validated by a numerical calculation of the ion distribution in the nanopores using the generalized Poisson-Boltzmann (PB) equation, demonstrating that the nonelectrostatic interfacial interactions can indeed dominate the electrostatic interactions and lead to the breakdown of electroneutrality inside nanoconfined regions. Interfacial ion hydration is an essential part of the specific ion effects. Using in-situ 23Na and 19F NMR on carbon supercapacitors with different carbon pore sizes, I provide a molecular-scale understanding of the permeation and

  1. 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.

  2. 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.

  3. 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…

  4. 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

  5. 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.

  6. 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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

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

    PubMed

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

    2016-01-01

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

  10. Bubble collision with gravitation

    SciTech Connect

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

    2012-07-01

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

  11. 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.

  12. 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.

  13. 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.

  14. 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...

  15. 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…

  16. Estimating collision efficiencies from contact freezing experiments

    NASA Astrophysics Data System (ADS)

    Nagare, B.; Marcolli, C.; Stetzer, O.; Lohmann, U.

    2015-04-01

    Interactions of atmospheric aerosols with clouds influence cloud properties and modify the aerosol life cycle. Aerosol particles act as cloud condensation nuclei and ice nucleating particles or become incorporated into cloud droplets by scavenging. For an accurate description of aerosol scavenging and ice nucleation in contact mode, collision efficiency between droplets and aerosol particles needs to be known. This study derives the collision rate from experimental contact freezing data obtained with the ETH Collision Ice Nucleation Chamber CLINCH. Freely falling 80 μm water droplets are exposed to an aerosol consisting of 200 nm diameter silver iodide particles of concentrations from 500-5000 cm-3, which act as ice nucleating particles in contact mode. The chamber is kept at ice saturation in the temperature range from 236-261 K leading to slow evaporation of water droplets giving rise to thermophoresis and diffusiophoresis. Droplets and particles bear charges inducing electrophoresis. The experimentally derived collision efficiency of 0.13 is around one order of magnitude higher than theoretical formulations which include Brownian diffusion, impaction, interception, thermophoretic, diffusiophoretic and electric forces. This discrepancy is most probably due to uncertainties and inaccuracies in the description of thermophoretic and diffusiophoretic processes acting together. This is to the authors knowledge the first dataset of collision efficiencies acquired below 273 K. More such experiments with different droplet and particle diameters are needed to improve our understanding of collision processes acting together.

  17. 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.

  18. Collision-spike sputtering of Au nanoparticles

    DOE PAGES

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

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

  19. 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.

  20. 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

  1. Tandem oxidative processes catalyzed by polymer-incarcerated multimetallic nanoclusters with molecular oxygen.

    PubMed

    Miyamura, Hiroyuki; Kobayashi, Shū

    2014-04-15

    alcohols and the following Michael reaction catalyzed by trimetallic PI catalysts containing Au-Pd alloy nanoclusters and tetraalkoxyborates as cross-linkers. All of these heterogeneous catalysts could be recovered by simple operations and reused without significant loss of activity or any leaching of metals. We have demonstrated that the polymer incarceration method enables the simultaneous immobilization of several metals, with which we can achieve one-pot tandem oxidative processes using molecular oxygen as an oxidant within the multifunctional heterogeneous catalysts. Suitable choices of metals and bimetallic structures are crucial for the reactivity and the selection of reaction pathways.

  2. Antimicrobial resistance profiling and molecular subtyping of Campylobacter spp. from processed turkey

    PubMed Central

    2009-01-01

    erythromycin resistance in Campylobacter recovered from processed turkey occurred more frequently among C. coli than C. jejuni. Fla-PFGE types were associated with a particular species, antimicrobial resistance profiles, and a specific plant. Molecular subtyping in this study provided more information about the relationships among antimicrobial-resistant Campylobacter at the processing level. PMID:19772592

  3. Re-accretion Efficiencies in Small Impactor - Large Target Collisions

    NASA Astrophysics Data System (ADS)

    Jankowski, Tim; Wurm, G.; Jens, T.

    2013-10-01

    During the formation process of planets, small dust particles grow to km-sized planetesimals via collisions. While the collision partners are equally sized in early phases, fragmentation, catastrophic destruction and other recycling processes can lead to collisions between partners with various size ranges. The gas in protoplanetary disks exerts size- and mass-dependent drag forces on the dust particles and bodies present which is why the relative velocities between the small particles and larger bodies increase. A field of investigation are the small-impactor large-target collisions where (partial) erosion can occur and small ejected dust particles can be produced. These ejecta can couple to the gas quite rapidly and can then be recaptured by the target and stick to it in secondary collisions. We use a Monte-Carlo code to calculate re-accretion efficiencies under certain conditions i.e. in free molecular flow regime (stream lines end on target body; impactors are completely coupled to the gas). Using experimental data we developed a model for the amount, masses, directions, and velocities of the ejecta depending on the impactor mass and velocity and the position of impact. The amount of re-accreted ejecta as well as the total re-accreted mass can be determined by using the solution of the equation of motion for particles in gaseous environments. Both - the amount dependent efficiency as well as the mass dependent efficiency - are highly dependent on the seven free parameters (impact velocity, impactor size and density, target size and density, gas pressure and temperature) but generally benefit from high gas velocities and a large size difference between target and impactor. Our final intention is to provide an analytical expression for the re-accretion efficiencies in respect to the free parameters and to use this in different disk models for sweeping the free parameters dependent on the distance to the central star. One major advantage of our code is the

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

    PubMed

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

    2012-01-01

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

  5. Collisions of trapped molecules with slow beams

    SciTech Connect

    Tscherbul, T. V.; Dalgarno, A.; Pavlovic, Z.; Sadeghpour, H. R.; Cote, R.

    2010-08-15

    We present a theoretical study of molecular-trap loss induced by collisions with slow atomic beams based on an explicit analysis of collision kinematics in the laboratory frame and a rigorous quantum description of atom-molecule scattering in external fields. The theory is applied to elucidate the effects of nonuniform magnetic and optical trapping fields on low-temperature collisions of OH (J=3/2,M{sub J}=3/2,f) molecules with {sup 4}He atoms. Our calculations quantify the extent to which both elastic and inelastic cross sections are suppressed by external trapping fields, clarify the role of small-angle scattering in trap loss, and may benefit future experiments on collisional cooling of molecules in electromagnetic traps. The calculated cross sections for trap loss in {sup 4}He + OH collisions are consistent with recent experimental observations at low beam energies [B. C. Sawyer et al., Phys. Rev. Lett. 101, 203203 (2008)], demonstrating the importance of including the effects of nonuniform trapping fields in theoretical simulations of cold collision experiments with trapped molecules and slow atomic beams.

  6. Polymorphism of Crystalline Molecular Donors for Solution-Processed Organic Photovoltaics.

    PubMed

    van der Poll, Thomas S; Zhugayevych, Andriy; Chertkov, Eli; Bakus, Ronald C; Coughlin, Jessica E; Teat, Simon J; Bazan, Guillermo C; Tretiak, Sergei

    2014-08-01

    Using ab initio calculations and classical molecular dynamics simulations coupled to complementary experimental characterization, four molecular semiconductors were investigated in vacuum, solution, and crystalline form. Independently, the molecules can be described as nearly isostructural, yet in crystalline form, two distinct crystal systems are observed with characteristic molecular geometries. The minor structural variations provide a platform to investigate the subtlety of simple substitutions, with particular focus on polymorphism and rotational isomerism. Resolved crystal structures offer an exact description of intermolecular ordering in the solid state. This enables evaluation of molecular binding energy in various crystallographic configurations to fully rationalize observed crystal packing on a basis of first-principle calculations of intermolecular interactions. PMID:26277966

  7. 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.

  8. 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.

  9. Cosmic bubble collisions

    NASA Astrophysics Data System (ADS)

    Kleban, Matthew

    2011-10-01

    I briefly review the physics of cosmic bubble collisions in false-vacuum eternal inflation. My purpose is to provide an introduction to the subject for readers unfamiliar with it, focussing on recent work related to the prospects for observing the effects of bubble collisions in cosmology. I will attempt to explain the essential physical points as simply and concisely as possible, leaving most technical details to the references. I make no attempt to be comprehensive or complete. I also present a new solution to Einstein's equations that represents a bubble universe after a collision, containing vacuum energy and ingoing null radiation with an arbitrary density profile.

  10. Chemical activation through super energy transfer collisions.

    PubMed

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

    2014-02-01

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

  11. The interaction of C60 on Si(111) 7x7 studied by Supersonic Molecular Beams: interplay between precursor kinetic energy and substrate temperature in surface activated processes.

    NASA Astrophysics Data System (ADS)

    Aversa, Lucrezia; Taioli, Simone; Nardi, Marco; Tatti, Roberta; Verucchi, Roberto; Iannotta, Salvatore

    2015-06-01

    Buckminsterfullerene (C60) is a molecule fully formed of carbon that can be used, owing to its electronic and mechanical properties, as “clean” precursor for the growth of carbon-based materials, ranging from ?-conjugated systems (graphenes) to synthesized species, e.g. carbides such as silicon carbide (SiC). To this goal, C60 cage rupture is the main physical process that triggers material growth. Cage breaking can be obtained either thermally by heating up the substrate to high temperatures (630°C), after C60 physisorption, or kinetically by using Supersonic Molecular Beam Epitaxy (SuMBE) techniques. In this work, aiming at demonstrating the growth of SiC thin films by C60 supersonic beams, we present the experimental investigation of C60 impacts on Si(111) 7x7 kept at 500°C for translational kinetic energies ranging from 18 to 30 eV. The attained kinetically activated synthesis of SiC submonolayer films is probed by in-situ surface electron spectroscopies (XPS and UPS). Furthermore, in these experimental conditions the C60-Si(111) 7×7 collision has been studied by computer simulations based on a tight-binding approximation to Density Functional Theory, DFT. Our theoretical and experimental findings point towards a kinetically driven growth of SiC on Si, where C60 precursor kinetic energy plays a crucial role, while temperature is relevant only after cage rupture to enhance Si and carbon reactivity. In particular, we observe a counterintuitive effect in which for low kinetic energy (below 22 eV), C60 bounces back without breaking more effectively at high temperature due to energy transfer from excited phonons. At higher kinetic energy (22 < K < 30 eV), for which cage rupture occurs, temperature enhances reactivity without playing a major role in the cage break. These results are in good agreement with ab-initio molecular dynamics simulations. SuMBE is thus a technique able to drive materials growth at low temperature regime.

  12. Icy Collisions - Planet Building beyond the snowline

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    NASA Technical Reports Server (NTRS)

    Hansen, C. Frederick

    1993-01-01

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

  14. Reactive Collisions in Crossed Molecular Beams

    DOE R&D Accomplishments Database

    Herschbach, D. R.

    1962-02-01

    The distribution of velocity vectors of reaction products is discussed with emphasis on the restrictions imposed by the conservation laws. The recoil velocity that carries the products away from the center of mass shows how the energy of reaction is divided between internal excitation and translation. Similarly, the angular distributions, as viewed from the center of mass, reflect the partitioning of the total angular momentum between angular momenta of individual molecules and orbital angular momentum associated with their relative motion. Crossed-beam studies of several reactions of the type M + RI yields R + MI are described, where M = K, Rb, Cs, and R = CH{sub 3}, C{sub 3}H{sub 5}, etc. The results show that most of the energy of reaction goes into internal excitation of the products and that the angular distribution is quite anisotropic, with most of the MI recoiling backward (and R forward) with respect to the incoming K beam. (auth)

  15. Newton's Strange Collisions.

    ERIC Educational Resources Information Center

    Erlichson, Herman

    1995-01-01

    Discusses Newton's apparent oversight of the role of energy considerations in collisions between two spherical bodies related to the third corollary of his "Laws of Motion." Investigates several theories that provide solutions to the mysterious oversight. (LZ)

  16. The Sandbag Collision

    NASA Astrophysics Data System (ADS)

    Zou, Xueli

    2006-10-01

    As physics teachers, we all know that many introductory physics students have difficulties in understanding conservation of energy during inelastic collisions where the difficult-to-visualize concept of internal energy is involved. An interesting approach using a pair of model carts1,2 has been developed to help students visualize and understand the concept of internal thermal energy involved during an inelastic collision. This paper will illustrate a sandbag collision experiment that uses visible deformation of the sandbag to help students visualize where the kinetic energy goes during an inelastic collision. This experiment problem (as shown in Fig. 1) can be broken into three small subparts: 1) The pendulum bob swings down until right before hitting the box—a conservation of energy problem; 2) The bob collides with the box—a conservation of momentum problem; 3) The box slides on the table until it comes to a stop—a conservation of energy problem or a dynamics problem.

  17. Controlling Thermal Collisions with Frequency-Chirped Light

    NASA Astrophysics Data System (ADS)

    Wright, Matthew

    2014-03-01

    We conduct semi-classical monte-carlo simulations of cold collisions utilizing frequency-chirped laser light on the nanosecond timescale. Previous work revealed partial control of light-assisted collisional mechanisms with relatively slow chirp rates (10 GHz/ μs). Collisions induced with positive chirped light enhance the inelastic collisional loss rate of atoms from a magneto-optical trap whereas these trap loss collisions can be blocked when negative chirped light is used. Early quantum and classical simulations show that for negative chirps the laser's frequency continually interacts with the atom-pair during the collision. We investigate how this process depends on the chirp rate and show that by moderately speeding up the chirp (> 50 GHz/ μs), we can significantly enhance the difference in the collisional loss rate induced by the negative and positive chirps, gaining nearly full control of the collision. We also explore extending this model to probe collisions at temperatures exceeding 1 K.

  18. Squeezed States and Particle Production in High Energy Collisions

    NASA Technical Reports Server (NTRS)

    Bambah, Bindu A.

    1996-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Bai, Enjian; Feng, Zhu

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

  20. Survey of atomic processes in edge plasmas

    SciTech Connect

    Janev, R.K.; Post, D.E.; Langer, W.D.; Evans, K.; Heifetz, D.B.; Weisheit, J.C.

    1983-11-01

    A review of the most important reactions of atomic and molecular hydrogen with the fusion edge plasma electrons and ions is presented. An appropriate characterization of the considered collision processes, useful in plasma edge studies (evaluated cross sections, reaction rates, energy gain/loss per collision, etc.) has been performed. While a complete survey of atomic physics of fusion edge plasmas will be given elsewhere shortly, we demonstrate here the relevance of the atomic collision processes for describing the physical state of edge plasmas and understanding the energy balance in cool divertor plasmas. It is found that the excited neutral species play an important role in the low-temperature, high-density plasmas.