Science.gov

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. Formation of cold molecular ions by radiative processes in cold ion-atom collisions

    SciTech Connect

    Rakshit, Arpita; Deb, Bimalendu

    2011-02-15

    We discuss theoretically ion-atom collisions at low energy and predict the possibility of the formation of a cold molecular ion by photoassociation. We present results from radiative homo- and heteronuclear atom-ion cold collisions that reveal threshold behavior of atom-ion systems.

  3. 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}?{sub g}{sup +})-N{sub 2}({sup 1}?{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.

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

    PubMed

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

    2014-12-21

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

  5. Positronium collisions with molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Wilde, R. S.; Fabrikant, I. I.

    2015-09-01

    Positronium (Ps) collisions with molecular hydrogen are investigated theoretically. Elastic and Ps ionization cross sections are calculated. For elastic scattering the pseudopotential method, previously developed for rare-gas atoms, is applied. Ps ionization cross sections are calculated using the binary-encounter approximation. The results agree with swarm measurements at low collision energies and with beam measurements at higher energies. The total Ps-H2 cross section when plotted as a function of collision velocity is close to the e--H2 cross section at velocities above the Ps ionization threshold, confirming earlier observations [Brawley et al., Science 330, 789 (2010), 10.1126/science.1192322]. However, below the threshold the two sets of cross sections are different because of the different nature of the long-range interaction between the projectile and the target, the polarization interaction in the case of e--H2 collisions and the van der Waals interaction in the case of Ps-H2 collisions.

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

    SciTech Connect

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

    1993-04-01

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

  7. The 2011 Dynamics of Molecular Collisions Conference

    SciTech Connect

    Nesbitt, David J.

    2011-07-11

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

  8. Formation of negative hydrogen ions in 7-keV OH+ + Ar and OH+ + acetone collisions: a general process for H-bearing molecular species

    E-print Network

    Juhász, Zoltán; Rangama, Jimmy; Bene, Erika; Sorgunlu-Frankland, Burcu; Frémont, François; Chesnel, Jean-Yves

    2015-01-01

    We demonstrate that the formation of negative hydrogen ions (H-) occurs in a wide class of atomic and molecular collisions. In our experiments, H- emission from hydroxyl cations and acetone molecules was observed in keV-energy collisions. We show that hydride (H-) anions are formed via direct collisional fragmentation of molecules, followed by electron grabbing by fast hydrogen fragments. Such general mechanism in hydrogen-containing molecules may significantly influence reaction networks in planetary atmospheres and astrophysical media and new reaction pathways may have to be added in radiolysis studies.

  9. Inelastic processes in 11000 keV/u collisions of Be q+ (q=24) ions with atomic and molecular

    E-print Network

    , the classical trajectory Monte Carlo (CTMC) technique, to compute cross sections for ionization and state­selective exci­ tation and charge transfer. A large body of work has shown that the CTMC method 1 #12; provides is not readily available, the CTMC results provide a first estimate of the required processes. That is

  10. 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.

  11. 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, Dimitrijevi? & 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.

  12. Molecular Processes in Comets

    NASA Technical Reports Server (NTRS)

    Dalgarno, A.

    1998-01-01

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

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

    PubMed

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

    2015-05-01

    The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan. PMID:26263308

  14. 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.

  15. The "Collisions Cube" Molecular Dynamics Simulator.

    ERIC Educational Resources Information Center

    Nash, John J.; Smith, Paul E.

    1995-01-01

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

  16. FEATURE ARTICLE Surface Processes Induced by Collisions

    E-print Network

    Asscher, Micha

    of the experimental data at low coverage using MD simulations has led to the introduction of a new desorption significantly. The potential importance of this process for inducing novel catalytic routes on surfaces. Introduction Surface phenomena induced by the collisions of energetic gas-phase particles with adsorbates

  17. 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.

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

    PubMed

    Cui, Jie; Krems, Roman V

    2015-08-14

    We show that a Gaussian process model can be combined with a small number (of order 100) of scattering calculations to provide a multidimensional dependence of scattering observables on the experimentally controllable parameters (such as the collision energy or temperature) as well as the potential energy surface (PES) parameters. For the case of Ar-C_{6}H_{6} collisions, we show that 200 classical trajectory calculations are sufficient to provide a ten-dimensional hypersurface, giving the dependence of the collision lifetimes on the collision energy, internal temperature, and eight PES parameters. This can be used for solving the inverse scattering problem, for the efficient calculation of thermally averaged observables, for reducing the error of the molecular dynamics calculations by averaging over the PES variations, and for the analysis of the sensitivity of the observables to individual parameters determining the PES. Trained by a combination of classical and quantum calculations, the model provides an accurate description of the quantum scattering cross sections, even near scattering resonances. PMID:26317721

  19. Gaussian Process Model for Collision Dynamics of Complex Molecules

    NASA Astrophysics Data System (ADS)

    Cui, Jie; Krems, Roman V.

    2015-08-01

    We show that a Gaussian process model can be combined with a small number (of order 100) of scattering calculations to provide a multidimensional dependence of scattering observables on the experimentally controllable parameters (such as the collision energy or temperature) as well as the potential energy surface (PES) parameters. For the case of Ar -C6H6 collisions, we show that 200 classical trajectory calculations are sufficient to provide a ten-dimensional hypersurface, giving the dependence of the collision lifetimes on the collision energy, internal temperature, and eight PES parameters. This can be used for solving the inverse scattering problem, for the efficient calculation of thermally averaged observables, for reducing the error of the molecular dynamics calculations by averaging over the PES variations, and for the analysis of the sensitivity of the observables to individual parameters determining the PES. Trained by a combination of classical and quantum calculations, the model provides an accurate description of the quantum scattering cross sections, even near scattering resonances.

  20. PAMOP: Petascale Atomic, Molecular and Optical Collision Calculations

    E-print Network

    McLaughlin, Brendan M; Pindzola, Michael S; Müller, Alfred

    2015-01-01

    Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schr\\"odinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. In this report, various examples are shown from our theoretical results compared with experimental results obtained from Synchrotron Radiation facilities where the Cray architecture at HLRS is playing an integral part in our computational projects.

  1. 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.

  2. Dynamics of electron removal from helium and molecular hydrogen by collisions with heavy particles

    SciTech Connect

    Meng, L.

    1992-01-01

    Collision systems involving the simplest two-electron targets, helium and molecular hydrogen, have been studied, as part of ongoing research on the effect of electron correlation in ion-atom collisions. Classical phase-space models of the hydrogen molecule and helium are utilized to study electron-capture and ionization processes in collisions of fully stripped ions at intermediate-to-high impact energies (20 keV/u 1 MeV/u) and charge states from 1 to 10. Subshell-capture processes are also studied. A radial correlation between the electrons in helium is implemented in the Classical Trajectory Monte Carlo (CTMC) technique and represents the first theoretical method that yields the dynamics of all four bodies in single and double ionization reactions in the collisions of protons and antiprotons with helium. Good agreement with experimental results are obtained. This work leads to a better understanding of the effect of electron correlation for collisions with two-electron systems.

  3. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

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

  4. Nonadiabatic quantum molecular dynamics with hopping. II. Role of nuclear quantum effects in atomic collisions

    NASA Astrophysics Data System (ADS)

    Fischer, M.; Handt, J.; Schmidt, R.

    2014-07-01

    The role of electron-nuclear correlations, i.e., quantum effects in the nuclear motion in atomic collisions with complex targets, is discussed using the recently developed nonadiabatic quantum molecular dynamics with hopping method [Fischer, Handt, and Schmidt, paper I of this series, Phys. Rev. A 90, 012525 (2014), 10.1103/PhysRevA.90.012525]. It is shown that the excitation process is nearly unaffected by electron-nuclear correlations as long as integral quantities are considered (total kinetic energy loss), whereas the relaxation mechanism of the molecular target is greatly affected (total fragmentation probability). To describe highly differential quantities (kinetic energy loss as a function of the scattering angle), however, the consideration of nuclear quantum effects during the initial excitation process is indispensable, even in collisions where one would expect purely classical behavior of the nuclei due to their small de Broglie wavelength. The calculations reproduce and explain in detail old but still unexplained experimental data of differential energy-loss spectroscopy in He +He and He +H2 collisions.

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

    NASA Astrophysics Data System (ADS)

    Ignjatovi?, Lj M.; Mihajlov, A. A.; Klyucharev, A. N.

    2008-01-01

    The semi-classical method for determining the rate coefficients of the chemi-ionization processes in slow non-symmetric atom-Rydberg atom collisions is applied to the Li*(n) + Na case. Calculated rate coefficients are compared with the existing experimental data from the literature. Obtained results have confirmed that resonant mechanism of non-elastic processes in atom-Rydberg atom collisions are fully applicable to non-symmetric chemi-ionization processes. The rate coefficients of such processes in Li*(n) + Na collisions are determined in the regions of principal quantum number and temperature 4 <= n <= 20 and 700 K <= T <= 1100 K which can be of interest for possible further experiments. Also, the potential curves of several lowest ? states of the molecular ion LiNa+, as well as the values of the square of dipole matrix element for the transition between X2?+- and A2?+-states, are presented in this paper.

  6. Collision Avoidance for Unmanned Aircraft using Markov Decision Processes

    E-print Network

    Lozano-Perez, Tomas

    uncertainty or limited field-of-view constraints, generic MDP/POMDP solvers can be used to generate avoidanceCollision Avoidance for Unmanned Aircraft using Markov Decision Processes Selim Temizer , Mykel J fly safely in civil airspace, robust airborne collision avoid- ance systems must be developed. Instead

  7. Studies of fluctuation processes in nuclear collisions

    SciTech Connect

    Ayik, S.

    1992-02-01

    This report discusses the following topics: Relativistic Boltzmann-Langevin model for heavy-ion collision; K+ production far below free neucleon-nucleon threshold and damping of collective vibrations in a memory-dependent transport model.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

    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 SO2 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 SO2 was found to frequently occur. In contrast, dissociation to O2 was found to be mostly negligible and formation of SO3 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.

  9. 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.

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

    SciTech Connect

    Schlachter, A.S.

    1989-03-01

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

  11. Excitation Mechanism in the Collision-Induced Dissociation of Methane Molecular Ion at Kiloelectronvolt Translational Energy

    E-print Network

    Kim, Myung Soo

    ARTICLES Excitation Mechanism in the Collision-Induced Dissociation of Methane Molecular Ion component arising from vibrational excitation and a large KER component from electronic excitation. CH4 energy content. It has been found that the collision-induced dissociation (CID) via electronic excitation

  12. COLLISIONS OF FAST, HIGHLY STRIPPED CARBON, NIOBIUM, AND LEAD IONS WITH MOLECULAR HYDROGEN

    SciTech Connect

    Schlachter, A. S.; Berkner, K. H.; Graham, W. G.; Pyle, R. V.; Stearns, J. W.; Tanis, J. A.

    1980-11-01

    The range of experimental confirmation of our scaling rule for electron loss from a hydroqen atom in collision with a heavy, highly stripped ion has been considerably broadened by new measurements for carbon, niobium, and lead ions in molecular hydrogen.

  13. Neural processing of imminent collision in humans

    PubMed Central

    Billington, Jac; Wilkie, Richard M.; Field, David T.; Wann, John P.

    2011-01-01

    Detecting a looming object and its imminent collision is imperative to survival. For most humans, it is a fundamental aspect of daily activities such as driving, road crossing and participating in sport, yet little is known about how the brain both detects and responds to such stimuli. Here we use functional magnetic resonance imaging to assess neural response to looming stimuli in comparison with receding stimuli and motion-controlled static stimuli. We demonstrate for the first time that, in the human, the superior colliculus and the pulvinar nucleus of the thalamus respond to looming in addition to cortical regions associated with motor preparation. We also implicate the anterior insula in making timing computations for collision events. PMID:20980303

  14. 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.

  15. 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.

  16. 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.

  17. Cold electron collisions with atomic and molecular ions in merged beams: high-resolution collision spectroscopy in storage rings

    NASA Astrophysics Data System (ADS)

    Wolf, Andreas

    2008-10-01

    Down to the lowest collision energies, free electrons efficiently react with atomic and molecular cations. Atomic ions can bind the colliding electrons by the emission of photons (radiative and dielectronic recombination), while molecular ions are efficiently broken up by slow free electrons without an energy barrier (dissociative recombination). For most atomic and molecular species, the cross sections for recombination and other inelastic cross sections show important resonances reflecting the energetic positions as well as the autoionization and pre-dissociation of quasibound intermediate states formed in the electron collision. High resolution experiments revealing such resonances as well as the underlying atomic and molecular properties and the rich dynamics are performed with merged beams of ions and electrons in ion storage rings, using event-by event counting and imaging methods. Recently, monochromatic electron impact energies down into the few-meV range have been realized by intense and cold merged electron beams from photocathode sources. Ion beam storage controls the internal vibrational and, to some extent, rotational state of the cation. Fast-beam multiparticle imaging is used to reconstruct the molecular fragmentation events and to monitor the initial ionic ro-vibrational state. Examples of recent measurements with multicharged atomic ions and with smaller molecules, from the hydrogen ions to di- and triatomic heavier species (such as CF^+ and CH2^+) are presented.

  18. The Accuracy of Molecular Processes

    NASA Astrophysics Data System (ADS)

    Stavans, Joel

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

  19. Millikelvin Reactive Collisions between Sympathetically Cooled Molecular Ions and Laser-Cooled Atoms in an Ion-Atom Hybrid Trap

    NASA Astrophysics Data System (ADS)

    Hall, Felix H. J.; Willitsch, Stefan

    2012-12-01

    We report on a study of cold reactive collisions between sympathetically cooled molecular ions and laser-cooled atoms in an ion-atom hybrid trap. Chemical reactions were studied at average collision energies ?Ecoll?/kB?20mK, about 2 orders of magnitude lower than has been achieved in previous experiments with molecular ions. Choosing N2++Rb as a prototypical system, we find that the reaction rate is independent of the collision energy within the range studied, but strongly dependent on the internal state of Rb. Highly efficient charge exchange four times faster than the Langevin rate was observed with Rb in the excited (5p) P3/22 state. This observation is rationalized by a capture process dominated by the charge-quadrupole interaction and a near resonance between the entrance and exit channels of the system. Our results provide a test of classical models for reactions of molecular ions at the lowest energies reached thus far.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Super-Penrose process due to collisions inside ergosphere

    E-print Network

    Zaslavskii, O B

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Kirchner, Tom

    2011-05-01

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

  7. Rototranslational collision-induced absorption and collision-induced light scattering spectra of molecular hydrogen using isotropic intermolecular potentials

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Maroulis, G.; Bich, E.

    2012-07-01

    Quantum mechanical lineshapes of collision-induced absorption (CIA) at different temperatures and of collision-induced light scattering (CILS) at room temperature are computed for gaseous molecular hydrogen using theoretical values for induced dipole moments and pair-polarizability trace and anisotropy as input. Comparison with measured spectra of absorption, isotropic and anisotropic light scattering shows satisfactory agreement, for which the uncertainty in measurement of its spectral moments is seen to be large. Empirical models of the dipole moment and pair-polarizability trace and anisotropy which reproduce the experimental spectra and the first three spectral moments more closely than the fundamental theory are also given. Good agreement between computed and experimental lineshapes of both absorption and scattering is obtained when potential models which are constructed from the thermophysical, transport, total scattering cross-section and spectroscopic properties are used. Also, the use of the new potential in lattice dynamic calculations yields good results for several properties of solid hydrogen.

  8. 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.

  9. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K. (Monroeville, PA); Brinker, Charles Jeffrey (Albuquerque, NM)

    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.

  10. 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.

  11. Resource Paper: Molecular Excited State Relaxation Processes.

    ERIC Educational Resources Information Center

    Rhodes, William

    1979-01-01

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

  12. Molecular sieving silica membrane fabrication process

    DOEpatents

    Raman, Narayan K. (400 Maple St. SE., Apartment 112, Albuquerque, NM 87106); Brinker, Charles Jeffrey (14 Eagle Nest Dr., NE., Albuquerque, NM 87122)

    1998-01-01

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

  13. MOLECULAR PROCESSES IN CELLULAR ARSENIC METABOLISM

    EPA Science Inventory

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

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

    NASA Astrophysics Data System (ADS)

    Ati?, Murat; Özdo?an, 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.

  15. Molecular theory of atomic collisions: A generalized perturbed stationary states approach

    NASA Astrophysics Data System (ADS)

    Heil, T. G.; Bottrell, G. J.; Bottcher, C.

    1985-07-01

    The perturbed stationary states equations, which describe low velocity atomic/ionic collisions using continuum states of the aggregate molecule have been generalized to include the effects of electron translation. The generalized nuclear scattering equations reduce to those of the perturbed stationary states method as the electron mass tends to zero. As either nuclear charge tends to zero, the solutions describe the translation of a free atom. The extraction of the proper T-matrices from the nuclear scattering solutions is a major difficulty in the molecular description of atomic collisions since molecular coordinates are not asymptotically appropriate. To this end we have examined asymptotic limits of the Fadeev equations, written in terms of potentials rather than the usual transition operators, to obtain the proper scattering boundary conditions and expressions for the inelastic, rearrangement and ionization T-matrices The theory is to be applied to charge transfer reactions involving low velocity collisions of hydrogen atoms with multiply charged ions.

  16. A CTMC study of collisions between protons and $H_2^+$ molecular ions

    E-print Network

    Fabio Sattin; Luca Salasnich

    1998-07-21

    We study numerically collisions between protons and $H_2^+$ molecular ions at intermediate impact energies by using the Classical Trajectory Monte Carlo method (CTMC). Total and differential cross sections are computed. The results are compared with: a) the standard one electron--two nucleon scattering, and b) the quantum mechanical treatment of the $ H^{+} - H^{+}_{2} $ scattering.

  17. A CTMC study of collisions between protons and $H_{2}^{+}$ molecular ions

    E-print Network

    Sattin, F; Sattin, Fabio; Salasnich, Luca

    1998-01-01

    We study numerically collisions between protons and $H_2^+$ molecular ions at intermediate impact energies by using the Classical Trajectory Monte Carlo method (CTMC). Total and differential cross sections are computed. The results are compared with: a) the standard one electron--two nucleon scattering, and b) the quantum mechanical treatment of the $ H^{+} - H^{+}_{2} $ scattering.

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

    NASA Astrophysics Data System (ADS)

    Oh, Chang-Whan

    2015-04-01

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

  19. 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.

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

    E-print Network

    Youn, Sun-Hyun

    2015-01-01

    By means of adding a collision process between the ball and racket in double pendulum model, we analyzed the tennis stroke. It is possible that the speed of the rebound ball does not simply depend on the angular velocity of the racket, and higher angular velocity sometimes gives lower ball speed. We numerically showed that the proper time lagged racket rotation increases the speed of the rebound ball by 20%. We also showed that the elbow should move in order to add the angular velocity of the racket.

  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. Collision-induced fusion of two C60 fullerenes: Quantum chemical molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jakowski, Jacek; Irle, Stephan; Morokuma, Keiji

    2010-09-01

    We characterize the collision-induced fusion reaction of buckminsterfullerenes by means of direct self-consistent-charge density-functional tight-binding molecular dynamics simulations. In agreement with experimental data, we find that the highest probability of fusion is for collisions with incident energy range of 120-140 eV. In this energy region, fusion occurs by way of the formation of hot, vibrationally excited peanut-shaped structures within 1 ps. These nanopeanuts further undergo relaxation to short carbon nanotubes and are cooling by evaporation of short carbon chains during the next 200 ps. The size of the fusion product after the evaporation agrees well with the average size of carbon clusters experimentally detected after collisions on the microsecond time scale. The average number of sp3 carbons in our simulations is in an excellent correlation with experimental cross sections.

  3. 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.

  4. Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite

    E-print Network

    A. Ito; H. Nakamura

    2006-04-26

    Hydrogen adsorption by graphite is examined by classical molecular dynamics simulation using a modified Brenner REBO potential. Such interactions are typical in chemical sputtering experiments, and knowledge of the fundamental behavior of hydrogen and graphene in collisional conditions is essential for modeling the sputtering mechanism. The hydrogen adsorption rate is found to be dependent on the incident hydrogen energy and not on graphene temperature. Rather than destroying the graphene, hydrogen incidence at energies of less than 100 eV can be classified into three regimes of adsorption, reflection and penetration through one or more graphene layers. Incidence at the lowest energies is shown to distort the graphene structure.

  5. Processing and thermal properties of molecularly oriented polymers

    E-print Network

    Skow, Erik (Erik Dean)

    2007-01-01

    High molecular weight polymers that are linear in molecular construction can be oriented such that some of their physical properties in the oriented direction are enhanced. For over 50 years polymer orientation and processing ...

  6. Molecular processes and turbulent magnetic fields in the solar atmosphere

    NASA Astrophysics Data System (ADS)

    Shapiro, A. I.

    2008-08-01

    Coherent scattering in the solar atmosphere leads to the formation of the linearly polarized solar spectrum, just like Rayleigh scattering leads to the polarization of the blue sky. One of the most prominent features of the linearly polarized solar spectrum is the CN violet system as it is also in the unpolarized spectrum. This thesis is devoted to the modeling and interpretation of this system in both spectra and developing it into a very sensitive tool for studying the magnetic fields and the temperature structure of the solar atmosphere. The understanding of the solar magnetic field structure is very important as it is connected with and even controls most of the solar activity phenomena. Zeeman effect diagnostics allows to measure strong directed magnetic fields which only cover about 1% of the solar atmosphere. The remaining part is occupied by weak entangled magnetic fields with mixed polarity, which might significantly contribute to the overall solar magnetic energy. These fields are invisible to the Zeeman effect due to signal cancellation. Therefore the discovery of the linearly polarized solar spectrum opened a new epoch in solar physics. The polarization due to the scattering processes is modified by weak entangled magnetic fields via the Hanle effect and thus, provides us with a unique possibility to access and study such "hidden" magnetic fields. Molecular lines are very useful for probing magnetic fields as, due to their strong temperature sensitivity, different molecules sample different, narrow layers of the solar atmosphere. Therefore the extension of the atomic Hanle effect to molecular lines can provide the 3D structure of the solar turbulent magnetic field. Moreover, due to the broad range of magnetic sensitivities within narrow spectral regions molecular lines can be used for employing the differential Hanle effect technique, which allows dramatically reduced model dependence of the obtained magnetic field. This thesis consists of two main parts which reflect the two consecutive steps in the modeling of the polarized solar spectrum. First, the physical properties of the molecular scattering process have to be understood. For the CN violet system, it implies taking into account the Paschen-Back effect on the fine structure (which results in a change of intensities and line positions) and interference effects between the fine structure components itself. Both effects influence the Hanle effect and lead to the consequences which are analyzed in detail in the first part of this thesis. Then, to connect the coherent scattering and physical properties of the solar plasma with the emerged solar radiation, which is measured by our detectors, radiative transfer theory has to be applied. The presence of the scattering processes implies the non-equilibrium nature of the problem. Its self-consistent solution is especially complicated for molecular bands as they usually consist of a huge number of transitions which couple the numerous vibrational-rotational molecular levels. This, for example, makes the two-level approximation, often used in atomic calculations unsuitable. Moreover, there is a strong lack of information about the molecular collision rates so they basically enter the calculations as additional free parameter. In the second part of the thesis we present two radiative transfer models with different degrees of complexity and applicability. These models allow us to successfully fit the observations of the CN violet system in both polarized and unpolarized spectra and provide us with a magnetic field estimation. We discuss in detail the model-dependence of our results and general problems of the 1D solar spectrum modeling. The enormous potential of the linearly polarized solar spectrum makes it one of the main tools for studying solar magnetic fields, which becomes very urgent nowadays, as they can affect the Earth's climate and, hence, our life.

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

    PubMed

    Zhang, Dali; Ke, Jiajun; Lu, Lizhu

    2015-10-01

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

  8. Extension of Quantum Molecular Dynamics and its Application to Heavy-Ion Collisions

    E-print Network

    Toshiki Maruyama; Koji Niita; Akira Iwamoto

    1995-09-04

    In order to treat low-energy heavy-ion reactions, we make an extension of quantum molecular dynamics method. A phenomenological Pauli potential is introduced into effective interactions to approximate the nature of the Fermion many-body system. We treat the widths of nucleon wave-packets as time-dependent dynamical variables. With these modifications, our model can well describe the ground-state properties in wide mass range. Improvements due to the extension are also obtained in the nucleus-nucleus collision calculations.

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

    SciTech Connect

    Tasker, Elizabeth J.; Tan, Jonathan C.

    2009-07-20

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

  10. Simultaneous process and molecular design/selection through property integration 

    E-print Network

    Qin, Xiaoyun

    2007-04-25

    The overall purpose of this work is to develop systematic methodology for the simultaneous design and selection of processes and molecules (materials). A propertybased approach is used to develop an interface between process and molecular design...

  11. 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.

  12. Analyzing collision processes with the smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2014-02-01

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

  13. 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.

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

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Managadze, G.

    2010-07-01

    A new concept is proposed, according to which the plasma and collision processes accompanying hypervelocity impacts of meteorites can contribute to the arising of the conditions on early Earth, which are necessary for the appearance of primary forms of living matter. It was shown that the processes necessary for the emergence of living matter could have started in a plasma torch of meteorite impact and have continued in an impact crater in the case of the arising of the simplest life form. It is generally accepted that planets are the optimal place for the origin and evolution of life. In the process of forming the planetary systems the meteorites, space bodies feeding planet growth, appear around stars. In the process of Earth's formation, meteorite sizes ranged from hundreds and thousands of kilometres. These space bodies consisted mostly of the planetesimals and comet nucleus. During acceleration in Earth's gravitational field they reached hypervelocity and, hitting the surface of planet, generated powerful blowouts of hot plasma in the form of a torch. They also created giant-size craters and dense dust clouds. These bodies were composed of all elements needed for the synthesis of organic compounds, with the content of carbon being up to 5%-15%. A new idea of possible synthesis of the complex organic compounds in the hypervelocity impact-generated plasma torch was proposed and experimentally confirmed. A previously unknown and experimentally corroborated feature of the impact-generated plasma torch allowed a new concept of the prehistory of life to be developed. According to this concept the intensive synthesis of complex organic compounds arose during meteoritic bombardment in the first 0.5 billion years at the stage of the planet's formation. This most powerful and destructive action in Earth's history could have played a key role and prepared conditions for the origin of life. In the interstellar gas-dust clouds, the synthesis of simple organic matter could have been explained by an identical process occurring in the plasma torch of hypervelocity collisions between submicron size dust particles. It is assumed that the processes occurred in the highly unbalanced hot plasma simultaneously with the synthesis of simple and complicated organic compounds, thereby ensuring their ordering and assembly. Bona fide experimental evidence presented below indicates that the physical fields generated in the plasma environment in the process of the formation and expansion of the torch meet the main requirements toward “true” local chiral fields. These fields were very likely to be capable to trigger the initial, weak breaking of enantiomer symmetry and determine the “sign” of the asymmetry of the bioorganic world. These fields could have worked as “trapping” fields influencing spontaneous processes occurring in highly overheated and nonequilibrium plasma in the state that is far from the thermodynamical branch of equilibrium and may have contributed to the formation of an environment needed for the synthesis of homochiral molecular structures, which, in turn, were needed for the emergence of the primary forms of living matter. It has been shown experimentally that the plasma-chemical processes in the torch have high catalytic properties and assure the rise of the chemical reaction rates by 10-100 million times. In the process of the plasma flyaway this in turn can assure the fast formation of simple and complicated organic compounds, including hyper-branched polymers. It is possible to assume that predominantly inorganic substances from meteorites were used for the synthesis of complicated organic compounds on early Earth. A laboratory experiment with hypervelocity impact plasma torch modelling by a laser with a Q-switch mode has shown the possibility of high-molecular organic compound synthesis, with mass of approximately 5000 a.m.u. by meteorite impact with an effective diameter of 100 mkm. The target contained only H, C, N and O elements in inorganic forms. The approximation of the curve received in these experimen

  17. Hybrid Simulation between Molecular Dynamics and Binary Collision Approximation Codes for Hydrogen injection onto Carbon Materials

    E-print Network

    Saito, Seiki; Takayama, Arimichi; Kenmotsu, Takahiro; Nakamura, Hiroaki

    2010-01-01

    Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's size is less than several nm for the performance of a computer. To extend the size of the MD simulation, we develop a hybrid simulation code between MD code using REBO potential and binary collision approximation (BCA) code. Using the BCA code instead of computing all particles with a high kinetic energy for every step in the MD simulation, considerable computation time is saved. By demonstrating a hydrogen atom injection on a graphite by the hybrid simulation code, it is found that the hybrid simulation code works efficiently in a large simulation box.

  18. Hybrid simulation between molecular dynamics and binary collision approximation codes for hydrogen injection into carbon materials

    NASA Astrophysics Data System (ADS)

    Saito, Seiki; Ito, Atsushi M.; Takayama, Arimichi; Kenmotsu, Takahiro; Nakamura, Hiroaki

    2011-08-01

    Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, the size of MD simulation box is generally set less than several nm because of the limits of a computer performance. To extend the size of the MD simulation, we develop a hybrid simulation code between MD code using REBO potential and binary collision approximation (BCA) code. Using the BCA code instead of computing all particles with a high kinetic energy for every step in the MD simulation, considerable computation time is saved. By demonstrating a hydrogen atom injection into a graphite by the hybrid simulation code, it is found that the hybrid simulation code works efficiently in a large simulation box.

  19. Multichannel quantum defect theory for cold molecular collisions with a strongly anisotropic potential energy surface

    NASA Astrophysics Data System (ADS)

    Croft, James F. E.; Hutson, Jeremy M.

    2013-03-01

    We show that multichannel quantum defect theory (MQDT) can be applied successfully as an efficient computational method for cold molecular collisions in Li+NH, which has a deep and strongly anisotropic interaction potential. In this strongly coupled system, closed-channel poles restrict the range over which the MQDT Y can be interpolated. We present an improved procedure to transform the MQDT reference functions so that the poles are removed from the energy range of interest. Effects due to very-long-range spin dipolar couplings are outside the scope of MQDT, but can be added perturbatively. This procedure makes it possible to calculate the elastic and inelastic cross sections, over the entire range of energies and fields needed to evaluate the feasibility of sympathetic cooling of NH by Li, using coupled-channel calculations at only five combinations of energy and field.

  20. 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.

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

    PubMed

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

    2012-09-14

    We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH(2)(X(3)B(1))] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH(2)(X(3)B(1)) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH(2), CHD, and CD(2) molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 ?K-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH(2)(X(3)B(1)) molecules in a magnetic trap. Furthermore, we find that ortho-CH(2) undergoes collision-induced spin relaxation much more slowly than para-CH(2), which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules. PMID:22979854

  2. Process Development Strategies in Plant Molecular Farming.

    PubMed

    Buyel, Johannes F

    2015-01-01

    Protein-based biopharmaceuticals are often produced in mammalian cell cultures, which are more expensive than microbial systems but capable of authentic post-translational modifications. The costs are lower if plants are used as an alternative platform to produce complex proteins such as monoclonal antibodies, vaccines and enzymes. This review highlights recent advances that have been achieved in plant-based biopharmaceutical production platforms in terms of expression strategies, product yields and process development. The first generation of plant-derived pharmaceuticals now entering the market is also discussed. Finally, the review considers the downstream processing of plant-derived pharmaceuticals which can account for up to 80% of the production costs. In this context, recent improvements in clarification and integrated process methods will have a strong impact on the economic feasibility of production, especially if supported by and combined with process analytical technology as part of the quality-by-design initiative. PMID:26343135

  3. Directionality and processivity of molecular motors.

    PubMed

    Higuchi, Hideo; Endow, Sharyn A

    2002-02-01

    Analysis of a mutant with altered directionality has led to new insights into motor directionality. The prediction from current models for processivity of a two-heads-bound state has been confirmed by electron microscopy for myosin V and by unbinding experiments for kinesin. Evidence is emerging that non-processive motors bind their filament with one head, hydrolyze ATP and then release, requiring binding by a second motor to complete a step. PMID:11792544

  4. Ab initio molecular dynamics simulation of the energy-relaxation process of the protonated water dimer.

    PubMed

    Yamauchi, Yusuke; Ozawa, Shiho; Nakai, Hiromi

    2007-03-22

    Relaxation processes of the energy-rich protonated water dimer H+(H2O)2 were investigated by the ab initio molecular dynamics (AIMD) method. At first, the energy-rich H+(H2O)2 was reproduced by simulating a collision reaction between the protonated water monomer H3O+ and H2O. Next it was collided with N2 in order to observe the effects of intramolecular vibration redistribution and intermolecular energy transfer. Forty-eight AIMD simulations of the collision of H+(H2O)2 with N2 were performed by changing the initial orientation and the time interval between two collisions. It was revealed that the amount of energy transferred from H+(H2O)2 to N2 decreased the longer the time interval. The relationship between the intermolecular energy transfer and the vibrational states was examined with the use of an energy-transfer spectrogram (ETS), which is an analysis technique combining energy density analysis and short-time Fourier transform. The ETS demonstrates a characteristic vibrational mode for the energy transfer, which corresponds to the stretching of the hydrogen bond between H+(H2O)2 and N2 in an active complex. PMID:17388294

  5. Multiple electron transfer processes in collisions of N6+ and O7+ with methane

    NASA Astrophysics Data System (ADS)

    Guevara, N. L.; Teixeira, E.; Hall, B.; Deumens, E.; Öhrn, Y.; Sabin, J. R.

    2009-12-01

    Recent experiments on collision processes of O7+ and N6+ ions colliding with methane at the same velocity show unexpected differences in the fragmentation cross sections of the methane. Despite the expected similarity of these two processes, as both projectiles are hydrogenic, the mechanisms of electron transfer are different and lead to different fragmentation cross sections. In the present work, the collisions between N6+ and O7+ ions and methane are investigated theoretically at equal velocities corresponding to projectile energies of 30 and 35 keV, respectively. Electron-nuclear dynamics is used to study multiple electron transfer processes occurring in these collisions. Several multiple charge transfer probabilities are calculated and results, averaged over various orientations of the methane molecule, are reported. The collisions proceed in two stages: a fast stage of electron transfer from methane to the ion, and a much slower stage of breakup of the methane. We find and explain the intuitively unexpected result that the total charge transfer cross section for N6+ is slightly larger, but that the O7+ leaves the methane in a higher charged state with higher probability, leading to more fragmentation in the collisions with O7+ .

  6. Scattering processes in antiprotonic hydrogen - hydrogen atom collisions

    E-print Network

    V. P. Popov; V. N. Pomerantsev

    2006-01-11

    The elastic scattering, Stark transitions and Coulomb deexcitation of excited antiprotonic hydrogen atom in collisions with hydrogenic atom have been studied in the framework of the fully quantum-mechanical close-coupling method for the first time. The total cross sections $\\sigma_{nl \\to n'l'}(E)$ and averaged on the initial angular momentum $l$ cross sections $\\sigma_{n\\to n'}(E)$ have been calculated for the initial states of $(\\bar{p}p)_{n}$ atoms with the principal quantum number $n=3 - 14 $ and at the relative energies $E=0.05 - 50$ eV. The energy shifts of the $ns$ states due to the strong interaction and relativistic effects are taken into account. Some of our results are compared with the semiclassical calculations.

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

    PubMed

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

    2015-11-01

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

  8. 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.

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

    SciTech Connect

    Not Available

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

  10. Observation of hard processes in collisions of two quasi-real photons

    NASA Astrophysics Data System (ADS)

    Althoff, M.; Braunschweig, W.; Kirschfink, F. J.; Lübelsmeyer, K.; Martyn, H.-U.; Peise, G.; Rimkus, J.; Rosskamp, P.; Sander, H. G.; Schmitz, D.; Siebke, H.; Wallraff, W.; Fischer, H. M.; Hartmann, H.; Hillen, W.; Jocksch, A.; Knop, G.; Köpke, L.; Kolanoski, H.; Kück, H.; Mertens, V.; Wedemeyer, R.; Wermes, N.; Wollstadt, M.; Eisenberg, Y.; Gather, K.; Hultschig, H.; Joos, P.; Koch, W.; Kötz, U.; Kowalsi, H.; Ladage, A.; Löhr, B.; Lüke, D.; Mättig, P.; Notz, D.; Nowak, R. J.; Pyrlik, J.; Quarrie, D. R.; Rushton, M.; Schütte, W.; Trines, D.; Wolf, G.; Xiao, Ch.; Fohrmann, R.; Hilger, E.; Kracht, T.; Krasemann, H. L.; Leu, P.; Lohrmann, E.; Pandoulas, D.; Poelz, G.; Wiik, B. H.; Beuselinck, R.; Binnie, D. M.; Campbell, A. L.; Dornan, P. J.; Foster, B.; Garbutt, D. A.; Jenkins, C.; Jones, T. D.; Jones, W. G.; McCardle, J.; Sedgbeer, J. K.; Thomas, J.; Wan Abdullah, W. A. T.; Bell, K. W.; Bowler, M. G.; Bull, P.; Cashmore, R. J.; Clarke, P. E. L.; Devenish, R.; Grossmann, P.; Hawkes, C. M.; Lloyd, S. L.; Salmon, G. L.; Wyatt, T. R.; Youngman, C.; Forden, G. E.; Hart, J. C.; Harvey, J.; Hasell, D. K.; Proudfoot, J.; Saxon, D. H.; Woodworth, P. L.; Barreiro, F.; Dittmar, M.; Holder, M.; Neumann, B.; Duchovni, E.; Karshon, U.; Mikenberg, G.; Mir, R.; Revel, D.; Ronat, E.; Shapira, A.; Yekutieli, G.; Barklow, T.; Caldwell, A.; Cherney, M.; Izen, J. M.; Mermikides, M.; Rudolph, G.; Strom, D.; Venkataramania, H.; Wicklund, E.; Wu, Sau Lan; Zobernig, G.; Tasso Collaboration

    1984-04-01

    Hard processes in photon-photon collisions are studied using high statistics data without requiring an electron tag. A high yield of hadrons with pt in the range 1.5-3.0 GeV/ c is observed. This yield exceeds the expectation of the Born term by a factor of four.

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

    NASA Astrophysics Data System (ADS)

    Youn, Sun-Hyun

    2015-10-01

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

  12. Textual collisions: the writing process and the Modernist experiment 

    E-print Network

    Hollis, Erin Michelle

    2005-08-29

    This dissertation explores textual junctures such as this in the compositional processes of James Joyce, Djuna Barnes, Mina Loy and Ezra Pound that illuminate how these modernists negotiated the fraught position of being an author in the early...

  13. Benford’s law in non-equilibrium processes: Droplet collisions case

    NASA Astrophysics Data System (ADS)

    Kim, Sangrak

    2012-10-01

    Benford’s law is investigated for the simulation results generated from non-equilibrium molecular dynamics. A statistic to measure how closely a set of the numbers follows Benford’s law is defined. The simulation data are from the collisions of two nano droplets with different impact velocities. When a non-equilibrium system returns to its equilibrium state, some physical quantities relevant to the non-equilibrium settings follow Benford’s law more closely. The initial settings for the non-equilibrium state can be interpreted as a data fabrication of its corresponding equilibrium state. A connection with the Shannon entropy for the first digit distribution is also discussed.

  14. 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.

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

    E-print Network

    Hahn, Michael

    2015-01-01

    We demonstrate that a nonthermal distribution of particles described by a kappa distribution can be accurately approximated by a weighted sum of Maxwell-Boltzmann distributions. We apply this method to modeling collision processes in kappa-distribution plasmas, with a particular focus on atomic processes important for solar physics. The relevant collision process rate coefficients are generated by summing appropriately weighted Maxwellian rate coefficients. This method reproduces the rate coefficients for a kappa distribution to an estimated accuracy of better than 5%. 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 ...

  16. 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.

  17. Production of large transverse momentum dileptons and photons in $pp$, $dA$ and $AA$ collisions by photoproduction processes

    E-print Network

    Fu, Yong-Ping

    2011-01-01

    The production of large $P_{T}$ dileptons and photons originating from photoproduction processes in $pp$, $dA$ and $AA$ collisions is calculated. We find that the contribution of dileptons and photons produced by photoproduction processes is not prominent at RHIC energies. However, the numerical results indicate that the modification of photoproduction processes becomes evident in the large $P_{T}$ region for $pp$, $dA$ and $AA$ collisions at LHC energies.

  18. GenEx: A simple generator structure for exclusive processes in high energy collisions

    E-print Network

    Kycia, R A; Staszewski, R; Turnau, J

    2014-01-01

    A simple C++ class structure for construction of a Monte Carlo event generators which can produce unweighted events within relativistic phase space is presented. The generator is self-adapting to the provided matrix element and acceptance cuts. The program is designed specially for exclusive processes and includes, as an example of such an application, implementation of the model for exclusive production of meson pairs $pp \\rightarrow p M^+M^- p $ in high energy proton-proton collisions.

  19. Dipolar degrees of freedom and Isospin equilibration processes in Heavy Ion collisions

    E-print Network

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

    2015-01-05

    Background: In heavy ion collision at the Fermi energies Isospin equilibration processes occur- ring when nuclei with different charge/mass asymmetries interacts have been investigated to get information on the nucleon-nucleon Iso-vectorial effective interaction. Purpose: In this paper, for the system 48Ca +27 Al at 40 MeV/nucleon, we investigate on this process by means of an observable tightly linked to isospin equilibration processes and sensitive in exclusive way to the dynamical stage of the collision. From the comparison with dynamical model calculations we want also to obtain information on the Iso-vectorial effective microscopic interaction. Method: The average time derivative of the total dipole associated to the relative motion of all emitted charged particles and fragments has been determined from the measured charges and velocities by using the 4? multi-detector CHIMERA. The average has been determined for semi- peripheral collisions and for different charges Zb of the biggest produced fragment. Experimental evidences collected for the systems 27Al+48Ca and 27Al+40Ca at 40 MeV/nucleon used to support this novel method of investigation are also discussed.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  2. 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.

  3. 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.

  4. 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.

  5. Molecular dynamics simulations for CO2 spectra. III. Permanent and collision-induced tensors contributions to light absorption and scattering

    NASA Astrophysics Data System (ADS)

    Hartmann, J.-M.; Boulet, C.

    2011-05-01

    Classical molecular dynamics simulations have been performed for gaseous CO2 starting from an accurate anisotropic intermolecular potential. Through calculations of the evolutions of the positions and orientations of a large number of molecules, the time evolutions of the permanent and collision-induced electric dipole vector and polarizability tensor are obtained. These are computed from knowledge of static molecular parameters taking only the leading induction terms into account. The Laplace transforms of the auto-correlation functions of these tensors then directly yield the light absorption and scattering spectra. These predictions are, to our knowledge, the first in which the contributions of permanent and collision-induced tensors are simultaneously taken into account for gaseous CO2, without any adjusted parameter. Comparisons between computations and measurements are made for absorption in the region of the ?3 infrared band and for depolarized Rayleigh scattering in the roto-translational band. They demonstrate the quality of the model over spectral ranges from the band center to the far wings where the spectrum varies by several orders of magnitude. The contributions of the permanent and interaction-induced (dipole and polarizability) tensors are analyzed for the first time, through the purely permanent (allowed), purely induced, and cross permanent/induced components of the spectra. It is shown that, while the purely induced contribution is negligible when compared to the collision-broadened allowed component, the cross term due to interferences between permanent and induced tensors significantly participates to the wings of the bands. This successfully clarifies the long lasting, confusing situation for the mechanisms governing the wings of the CO2 spectra considered in this work

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

    SciTech Connect

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

    2011-02-21

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

  7. Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides

    DOEpatents

    Kozyavkin, Sergei A. (Germantown, MD); Malykh, Andrei G. (Germantown, MD); Polouchine, Nikolai N. (Montgomery Village, MD); Slesarev, Alexei I. (Germantown, MD)

    2003-04-15

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

  8. 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.

  9. Study of one- and two-electron processes in slow He{sup 2+}-He collisions

    SciTech Connect

    Fritsch, W.

    1994-12-31

    Electron processes in 4 - 65 keV/u ER He{sup 2+}- He collisions are studied theoretically within the semiclassical close-coupling method. Electron transfer, excitation, transfer excitation, and double-transfer cross sections are determined for final states ranging up to the n=4 shell of target or projectile, from which visible light emission takes place. In slow collisions, the authors find that, surprisingly, the cross section for populating, through single transfer, a given He{sup +} projectile state is about the same as the cross section for populating, through transfer-excitation, the same state in the target ion. A similar relation is found between single-excitation and double-transfer cross sections. This observation is interpreted as arising from the quasimolecular character of the collision, it agrees with recently measured line-emission cross sections. This work is part of a coordinated effort of support for the experimental programme at the European fusion facility JET, Culham, England. It links closely with the experimental work at Groningen, The Netherlands, and CTMC calculations at Rolla, Missouri.

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

    PubMed

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

    2015-12-17

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

  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. 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.

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

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Hahn, M.; Savin, D. W.

    2015-08-01

    We demonstrate that a nonthermal distribution of particles described by a kappa distribution can be accurately approximated by a weighted sum of Maxwell-Boltzmann distributions. We apply this method to modeling collision processes in kappa-distribution plasmas, with a particular focus on atomic processes important for solar physics. The relevant collision process rate coefficients are generated by summing appropriately weighted Maxwellian rate coefficients. This method reproduces the rate coefficients for a kappa distribution to an estimated accuracy of better than 3%. This is equal to or better than the accuracy of rate coefficients generated using “reverse-engineering” methods, which attempt to extract the needed cross sections from the published Maxwellian rate coefficient data and then reconvolve the extracted cross sections with the desired kappa distribution. Our approach of summing Maxwellian rate coefficients is easy to implement using existing spectral analysis software. Moreover, the weights in the sum of the Maxwell-Boltzmann distribution rate coefficients can be found for any value of the parameter ?, thereby enabling one to model plasmas with a time-varying ?. Tabulated Maxwellian fitting parameters are given for specific values of ? 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.

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

    NASA Technical Reports Server (NTRS)

    Hahne, G. E.

    1984-01-01

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

  16. Molecular Tracking, through Processing, of Campylobacter Strains Colonizing Broiler Flocks?

    PubMed Central

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

    2011-01-01

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

  17. 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 ?m 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 ?m 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.

  18. Effect of hyperfine interactions on ultracold molecular collisions: NH(3?-) with Mg(1S) in magnetic fields

    NASA Astrophysics Data System (ADS)

    González-Martínez, Maykel L.; Hutson, Jeremy M.

    2011-11-01

    We investigate the effect of hyperfine interactions on ultracold molecular collisions in magnetic fields, using 24Mg(1S)+14NH(3?-) as a prototype system. We explore the energy and magnetic-field dependence of the cross sections, comparing the results with previous calculations that neglected hyperfine interactions [A.O.G. Wallis and J. M. Hutson, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.103.183201 103, 183201 (2009)]. The main effect of hyperfine interactions for spin relaxation cross sections is that the kinetic energy release of the dominant outgoing channels does not reduce to zero at low fields. This results in reduced centrifugal suppression of the cross sections and increased inelastic cross sections at low energy and low field. We also analyze state-to-state cross sections, for various initial states, and show that hyperfine interactions introduce additional mechanisms for spin relaxation. In particular, there are hyperfine-mediated collisions to outgoing channels that are not centrifugally suppressed. However, for Mg+NH these unsuppressed channels make only small contributions to the total cross sections. We consider the implications of our results for sympathetic cooling of NH by Mg and conclude that the ratio of elastic to inelastic cross sections remains high enough for sympathetic cooling to proceed.

  19. Collision-Dependent Line Areas in the a1?_g? X^3?^-_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^1?_g? X^3?^-_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 ?m we measure line areas with a quality-of-fit QF ? 50,000 using a partially correlated quadratic-speed-dependent Nelkin-Ghatak profile. This spectrometer has achieved this high QF by both suppressing coupled cavity effects and by preserving a high-fidelity frequency axis with absolute frequency accuracy approaching 1 part in 10^9. With this instrument we are also currently exploring collision-induced absorption (CIA) and perturbative line mixing effects in O_2 over the entire 7800-7940 wn spectral range.

  20. 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 characterize both the photoexcitation and subsequent decay processes. These techniques include mass spectrometry, dispersive and threshold photoelectron spectroscopy, laser-induced fluorescence, fluorescence-dip spectroscopy, and laser-induced grating spectroscopy. While the instrumentation is currently available for each of these techniques, two instruments deserve special mention. First, a high-resolution magnetic-bottle electron spectrometer has been developed that is equipped with a pulsed, skimmed molecular beam source. This instrument is capable of {approx}3-4 meV resolution in the electron kinetic energy while providing a collection efficiency of {approx}50%. Second, a time-of-flight mass spectrometer has been constructed with a similar molecular beam source. This instrument is currently being adapted to allow both ion- and electron-imaging studies. A typical experimental study is performed in three steps. First, resonant one-color multiphoton ionization is used to map out the transition between the ground state of the molecule of interest and the low-lying excited state to be used as an intermediate in the double-resonance process. The lasers used in these studies are Nd:YAG-pumped dye lasers with {approx}5 ns pulse durations. In general, this pump transition corresponds to a one- or two-photon process, and the laser output is frequency doubled, tripled, or mixed to generate light in the region of interest. In molecules such as ammonia and aniline, the pump transitions of interest are well characterized, allowing the unambiguous choice of pump transitions that access levels with the rovibronic character of interest. In other cases, the spectroscopy of the pump transition must be analyzed before it can be useful for the double-resonance experiments. In the second step, the pump laser is fixed on the pump transition of interest and a second laser is used to probe transitions from the upper state of the pump transition to the autoionizing or predissociating resonances in the region of interest. The double-resonance spectrum is recorded by scanning the second l

  1. 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.

  2. 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.

  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. 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.

  5. 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

  6. A post-collision internal energy model for O(3P) + SO2(X,1 A1) in DSMC based on Molecular Dynamics computations

    NASA Astrophysics Data System (ADS)

    Parsons, Neal; Levin, Deborah A.

    2014-10-01

    A model is developed for determining molecular internal energies after O(3P) + SO2(X,1 A1) collisions in the Direct Simulation Monte Carlo (DSMC) method in order to improve modeling of the hyperthermal interactions occurring in the upper atmosphere of Io. Molecular Dynamics/Quasi-Classical Trajectory (MD/QCT) studies are conducted to generate post-collision SO2 and post-dissociation SO internal energy distributions as a function of initial SO2 internal energy and relative collision velocity, which are found to be an improvement over the baseline Larsen-Borgnakke (LB) method that often predicts unphysical internal energies above the dissociation energy for non-reacting collisions and under-predicts post-dissociation SO internal energy. An approach for sampling from the MD/QCT-based internal energy distributions in DSMC is developed and DSMC simulations are then conducted for a time-dependent thermal nonequilibrium heat bath using both the MD/QCT-based distributions and the LB model. When only SO2-O collisions are considered, noticeable differences are observed for post-collisional SO2 and SO internal temperatures.

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

    NASA Astrophysics Data System (ADS)

    Yang, Wenbing

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

  8. Dielectronic processes producing radiative stabilization in slow Ne{sup 10+}+He collisions

    SciTech Connect

    Chesnel, J.; Merabet, H.; Fremont, F.; Cremer, G.; Husson, X.; Lecler, D.; Rieger, G.; Spieler, A.; Grether, M.; Stolterfoht, N.

    1996-06-01

    Different contributions to radiative stabilization in Ne{sup 10+}+He collisions at projectile energies of 10 and 150 keV are studied. For both energies, radiative stabilization is found to be equal to {approx_equal}0.3 when referred to the total double capture. In Ne{sup 10+}+He collisions doubly excited states 3{ital lnl}{sup {prime}} and 4{ital lnl}{sup {prime}} ({ital n}{ge}4) are either produced by uncorrelated two-electron transitions or by dielectronic mechanisms due to electron-electron interaction. A strong contribution ({approx_equal}0.15) to the stabilization follows from the decay of near-equivalent electrons 3{ital lnl}{sup {prime}} and 4{ital lnl}{sup {prime}}({ital n}=4,5). Another major contribution (0.10{endash}0.25) to stabilization is due to the decay of configurations 3{ital lnl}{sup {prime}} ({ital n}{ge}6) of nonequivalent electrons produced by the dielectronic process of autoexcitation. A small contribution is found to be due to the configurations 3{ital lnl}{sup {prime}} ({ital n}{approx_gt}9) created by dielectronic phenomena in the postcollisional and asymptotic regions ({approx_equal}0.04). {copyright} {ital 1996 The American Physical Society.}

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Po?evskis, J.; Krasti?š, M.; Kor?ts, 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.

  11. Competition of breakup and dissipative processes in peripheral collisions at Fermi energies

    E-print Network

    T. I. Mikhailova; A. G. Artyukh; M. Colonna; M. Di Toro; B. Erdemchimeg; G. Kaminski; I. N. Mikhailov; Yu. M. Sereda; H. H. Wolter

    2008-11-20

    Heavy ion collisions in the Fermi energy regime may simultaneously show features of direct and dissipative processes. To investigate this behavior in detail, we study isotope and velocity distributions of projectile-like fragments in the reactions $^{18}$O (35 $A\\cdot$MeV) + $^9$Be($^{181}$Ta) at forward angles. We decompose the experimental velocity distributions empirically into two contributions: a direct, `breakup' component centered at beam velocity and a dissipative component at lower velocities leading to a tail of the velocity distributions. The direct component is interpreted in the Goldhaber model, and the widths of the velocity distributions are extracted. The dissipative component is then successfully described by transport calculations. The ratio of the yields of the direct and the dissipative contributions can be understood from the behavior of the deflection functions. The isotope distributions of the dissipative component agree qualitatively with the data, but the modification due to secondary de-excitation needs to be considered. We conclude, that such reactions are of interest to study the equilibration mechanism in heavy ion collisions.

  12. 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

  13. Molecular epidemiology biomarkers-Sample collection and processing considerations

    SciTech Connect

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

    2005-08-07

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Allen, Mark; Kheirkhah, Monireh; Neill, Iain

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  17. IN VIVO OPTICAL MOLECULAR IMAGING: PRINCIPLES AND SIGNAL PROCESSING ISSUES

    E-print Network

    with easily de- tectable bioluminescence and fluorescence labels, optical molecular imaging has emerged developed recently. These have used ei- ther bioluminescence or fluorescence imaging techniques to monitor

  18. Ab Initio Interactive Molecular Dynamics on Graphical Processing Units (GPUs).

    PubMed

    Luehr, Nathan; Jin, Alex G B; Martínez, Todd J

    2015-10-13

    A virtual molecular modeling kit is developed based on GPU-enabled interactive ab initio molecular dynamics (MD). The code uses the TeraChem and VMD programs with a modified IMD interface. Optimization of the GPU accelerated TeraChem program specifically for small molecular systems is discussed, and a robust multiple time step integrator is employed to accurately integrate strong user-supplied pulling forces. Smooth and responsive visualization techniques are developed to allow interactive manipulation at minimum simulation rates below five MD steps per second. Representative calculations at the Hartree-Fock level of theory are demonstrated for molecular systems containing up to a few dozen atoms. PMID:26574246

  19. 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.

  20. Stochastic simulations of cargo transport by processive molecular motors

    E-print Network

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

    2009-12-11

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

  1. 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 rarely noticed that configurational mixing of the lowest energy excited state with other electronic states leads to unique distortions of the lowest energy excited state which result in modifications in the vibronic structure and bandshape of the emission. We have used the emission sideband shapes to evaluate patterns of ground state-excited state and excited state-excited state configurational mixing in some simple series of complexes.

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

    SciTech Connect

    Hong, Woo-Pyo; Jung, Young-Dae

    2014-10-15

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

  3. Young-type interference in collisions between Helium and molecular Hydrogen ions

    NASA Astrophysics Data System (ADS)

    Schmidt, Lothar

    2009-05-01

    The dissociative electron transfer from He into slow diatomic molecular ions was measured in a kinematically complete experiment by using cold target recoil ion momentum spectroscopy (COLTRIMS) in combination with a high resolution molecular fragment imaging technique. The electron transfer leads to neutral molecules in highly excited electronic states which dissociate in a second step of the reaction. With COLTRIMS we determine the energy which is taken from the motion of the projectile and transferred to internal degrees of freedom of the molecule. Furthermore we are able to determine the kinetic energy release (KER) of the dissociation as well as the spatial orientation of the molecular break up. When using H2^+ as projectiles this enables us to select the direct population of the lowest dissociative state of H2 b^3?^+u from the measured data. This reaction channel was analyzed in an inverse kinematics scheme where the molecule is regarded as two closely lying scattering centers at which an incoming He wave scatters. The orientation and the distance of these two scattering centers are obtained by detecting the fragments after the reaction, as the internuclear vector can be determined using the reflection as well as the axial recoil approximation. We find a striking double slit interference pattern in the transverse momentum transfer between the He atom and the molecule which we can modulate by selecting different internuclear distances (i.e. KERs) in our offline analysis. Compared to an optical double slit, the interference's minima and maxima are swapped. The latter is the result of a phase shift in the electronic part of the wave function.

  4. 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.

  5. Electron processes in ion-Rydberg-atom collisions with emphasis on directed linear Stark states

    NASA Astrophysics Data System (ADS)

    Homan, Dean Matthew

    Both classical-trajectory calculations and measurements of electron capture in A+ + B(x) collisions, where the targets are Rydberg atoms, have been performed in the intermediate velocity range. Linear Stark-state targets were created inside a novel device called the Stark barrel. With this new apparatus, off-center atomic states with axial symmetry could be prepared with their axes set at angles 0-360o with respect to the ion beam. Comparison of calculated and measured total-capture cross sections has revealed a new spatial capture mechanism called variously 'three-swap', 'type-two', or 'low- velocity Thomas capture.' In Part I of this Dissertation a classical model of electron capture and ionization by singly charged ions from oriented and aligned elliptic and linear-state Rydberg targets will be introduced to describe the Coulomb three-body dynamics of these processes. Parameter space maps, which correlate initial conditions in the collision system with the final collision channels, are employed to demonstrate that capture events are confined to well-defined regions of phase space. These islands of capture can be characterized by the number of swaps. The number of swaps is defined as the number of times the electron crosses the mid-plane between the passing charge centers during a collision that leads to capture. In Part II measurements of the total electron capture by Li+,/ K+ or Cs+ from a linear-Rydberg target atom are presented as a function of the angle ? between the atom's electric-dipole moment and the ion-beam axis in the reduced-velocity range 0.15/le/tilde v/le 2.4, where /tilde v=Vp/vBohr. The capture cross section versus angle reveals a peak at /theta =180o for /tilde v=0.3 which bifurcates into two distinct peaks at /tilde v=0.7 and then becomes again a single peak near /tilde v=1.0. At /tilde v=1.6 two symmetric shoulders appear near /theta=120o and 240o on a peak at 180o and remain a feature of the capture cross section at higher velocities. Peaks and shoulders are also observed at /tilde v=0.25, 0.5 and 1.0 in the ratio of the capture cross section for electronic charge polarization parallel (/theta=180o) and anti-parallel (0o) to the ion beam direction. The resonance structures seen in these experiments are described classically as overlapping contributions from one-swap, three-swap, and five and greater odd-swap trajectories. Previously unexpected structure seen in the experimental cross sections has been reproduced qualitatively by classical- trajectory and close-coupling models, and in turn the theories have given new insight and direction for experimental work.

  6. Single spin asymmetries in inclusive high energy hadron-hadron collision processes

    E-print Network

    Zuo-tang Liang; C. Boros

    2000-01-31

    It has been realized for quite a long time that single-spin experiments, in which one of the colliding objects is transversely polarized, can be helpful in studying the properties of strong interaction in general and in testing Quantum Chromodynamics (QCD) in particular. Striking effects have been observed in the past few years which deviate drastically from the expectation of the perturbative QCD parton model. These effects have received much attention. New experiments of the similar type are underway and/or planned. Different theoretical attempts have been made to understand these effects. In this review, the special role played by singly polarized high-energy hadron-hadron collisions in High Energy Spin Physics is emphasized. Characteristics of the available data for inclusive hadron productions are briefly summarized. Different theoretical approaches for such processes are reviewed with special attention to a non-perturbative model which explicitly takes the orbital motion of the valence quarks and hadronic surface effects into account. The connection between such asymmetries and hyperon polarization in unpolarized reactions is discussed. An example of the possible application of such experimental results in other processes is given.

  7. Atomic collision effects during PLD processes: nonstoichiometry control in transparent superconductors

    NASA Astrophysics Data System (ADS)

    Hitosugi, Taro; Packwood, D.; Shiraki, S.

    2014-03-01

    The pulsed laser deposition (PLD) growth processes of spinel lithium titanates, Li4Ti5O12 and LiTi2O4, on MgAl2O4 (111) substrates are investigated. Although a Li4Ti5O12 target was used for the depositions, the Li/Ti atomic ratio of the species arriving at the substrate during deposition was only ~0.5, enabling high quality LiTi2O4 films to be prepared with a rocking curve full-width at half-maximum of ~0.05°. The LiTi2O4 epitaxial thin films exhibited high conductivity at room temperature (~3.0 × 103 ?-1cm-1) and a superconducting transition temperature of ~13.3 K. These values are the highest recorded for epitaxial thin films. Moreover, the effect of collisions between the atoms in a plume were studied quantitatively. These results demonstrate the importance of the target composition, providing further insight into Licontaining metal-oxide deposition processes using PLD.

  8. 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.

  9. 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.

  10. Exclusive Higgs boson production through electromagnetic process in p-p and Pb-Pb ultra-peripheral collisions

    NASA Astrophysics Data System (ADS)

    Zhu, Jia-Qing; Ma, Zhi-Lei; Shi, Chao-Yi; Li, Yun-De

    2015-11-01

    The Higgs boson production through electromagnetic process in the exclusive p-p and Pb-Pb ultra-peripheral collisions is calculated. According to the condition of conference, the equivalent photon approximation formulation is used, and the limitations of the variables in the calculations are obtained. Three kinds of the equivalent photon spectrums are considered: the plane wave form, the approximate plane wave forms of Dress et al., and the semi-classical form. For comparison, the gluon-gluon fusion and intrinsic heavy flavors contributions are presented. The numerical results show that, the plane wave photon spectrum with correct limitations of the variables provides more reasonable results for the exclusive p + p ? p + p + H and Pb + Pb ? Pb + Pb + H processes, and the electromagnetic process provides meaningful contributions for the exclusive Higgs production in ultra-peripheral collisions.

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

    NASA Astrophysics Data System (ADS)

    Cheung, Wang K.; Norbury, John W.

    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.

  12. Prediction of Peptide Ion Collision Cross Sections from Topological Molecular Structure and Amino

    E-print Network

    Clemmer, David E.

    monitor the surrounding air are commonly used to detect explosives at airports, chemical warfare agents libraries and protein digests and simultaneously identify the individual constituents. This method has been) Karas, M.; Bachmann, D.; Bahr, U.; Hillenkamp, F. Int. J. Mass Spectrom. Ion Processes 1987, 78, 53

  13. 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.

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

    PubMed

    Beach, Daniel G; Gabryelski, Wojciech

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed

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

    2013-10-25

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

  17. 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.

  18. 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.

  19. Studies of fluctuation processes in nuclear collisions. Progress report, February 15, 1991--February 29, 1992

    SciTech Connect

    Ayik, S.

    1992-02-01

    This report discusses the following topics: Relativistic Boltzmann-Langevin model for heavy-ion collision; K+ production far below free neucleon-nucleon threshold and damping of collective vibrations in a memory-dependent transport model.

  20. Double parton scattering processes in $pp$ collisions and the scale factors

    E-print Network

    A. Del Fabbro

    2001-11-29

    The double parton collisions become increasingly important at high energies. The scale factors are the dimensional parameters which characterize these interactions and are the physical observables that can provide a first quantitative information on the correlations in the hadron structure.

  1. Atomic processes in electron-ion and ion-ion collisions

    SciTech Connect

    Brouillard, F.

    1986-01-01

    This book gives a self-consistent but nonexhaustive account of the current investigations in the field of electronic and ionic collisions. Since the physics of electron-ion and ion-ion collisions is strongly linked to plasmas, it was natural to include lectures on specific collisional problems relevant to astrophysical, Tokamak and dense, laser-produced plasmas. Separate abstracts were prepared for 17 chapters in this book.

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

    SciTech Connect

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

    2005-08-29

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

  4. Cloud-Cloud Collision as a Trigger of the High-mass Star Formation: a Molecular Line Study in RCW120

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  5. 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 ?s/day using implicit solvent models. PMID:24436689

  6. Nonadiabatic molecular collisions. II - A further trajectory-surface-hopping study of the ArH2(+) system

    NASA Astrophysics Data System (ADS)

    Chapman, S.

    1985-05-01

    The nonadiabatic molecular processes of charge exchange and chemical reaction in the species Ar(+) + H2, Ar + H2(+), and Ar + D2(+) are characterized theoretically in three-dimensional space using the trajectory-surface-hopping model of Tully and Preston (1971) and the diatomics-in-molecules hypersurfaces of Kuntz and Roach (1972). The results are presented in tables, graphs, and diagrams and shown to be in good general agreement with experimental data. Findings reported include the direct nature of the reactions, the stripping process involved in the reaction Ar(+) + H2 yields ArH(+) + H, the high rotational temperature of the product ArH(+), and the sensitive dependence of Ar + H2(+) and Ar + D2(+) cross sections on the vibrational state of the reactants.

  7. Symbiotic Nitrogen Fixation (in legumes) Define: The process by which molecular nitrogen (N2) is

    E-print Network

    Constabel, Peter

    Symbiotic Nitrogen Fixation (in legumes) Define: The process by which molecular nitrogen (N2) is reduced ("fixed") directly to NH4 + Reaction: N? - net nitrogen input into soil 5-10 % - model system for plant

  8. 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 Mohorovici? 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

  9. Collision induced absorption in the a1?(v = 2) ? X3?g(-)(v = 0) band of molecular oxygen.

    PubMed

    Spiering, Frans R; van der Zande, Wim J

    2012-07-28

    Using cavity ring-down spectroscopy we measured the collision induced absorption spectrum associated with the a(1)?(v = 2) ?X(3)?(g)(-)(v = 0) band of oxygen near 922 nm both in pure oxygen and in mixtures of oxygen and nitrogen. For pure oxygen, we report for this band an integrated absorption of (1.56 - 0.04/+0.40) × 10(-5) cm(-2) amg(-2). We find that collisions between oxygen and nitrogen do not result in any measurable CIA signal. At 1 bar of oxygen, this collision induced transition is much stronger than the allowed magnetic dipole and electric quadrupole transitions. PMID:22699258

  10. Jet asymmetry and momentum imbalance from 2 ?2 and 2 ?3 partonic processes in relativistic heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Ayala, Alejandro; Dominguez, Isabel; Jalilian-Marian, Jamal; Tejeda-Yeomans, Maria Elena

    2015-10-01

    We study momentum imbalance as a function of jet asymmetry in high-energy heavy-ion collisions. To implement parton production during the collision, we include all leading order (LO) 2 ?2 and 2 ?3 parton processes in pQCD. The produced partons lose energy within the quark gluon plasma and hadronize collinearly when they leave it. The energy and momentum deposited into the plasma is described using linear viscous hydrodynamics with a constant energy loss per unit length and a total energy loss given by a Gaussian probability centered around a mean value E ¯ and a half-width ? E . We argue that the shape of the asymmetry observed by the CERN-CMS Collaboration can indeed be attributed to parton energy loss in the medium and that a good description of data is achieved when one includes a slight enhancement coming from the contribution of 2 ?3 parton processes that modifies the asymmetry distribution of the dijet events. We compare our results to CMS data for the most central collisions and study different values for E ¯ and ? E .

  11. Organic conductors as novel ``molecular rulers`` for advanced manufacturing processes

    SciTech Connect

    Williams, J.M.

    1995-12-31

    Future advanced manufacturing equipment used in high technology programs will require ultra-high precision and associated machining tool operations that require placement accuracy of {approximately} 1--100 nm (1 nm = 10 {angstrom}). There is consensus among engineers that this equipment will be based on STM (Scanning Tunneling Microscope) technology. All such STM-based ``drivers`` must contain a metrology system that requires absolute length standards referenced to atomic spacings for calibration. Properly designed organic conductor substrate crystals have the potential to be molecular rulers for STM-based advanced manufacturing equipment. The major challenges in future organic conductor research aimed at STM metrology application are listed.

  12. 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.

  13. VUV diagnostic of electron impact processes in low temperature molecular hydrogen plasma

    E-print Network

    Komppula, J

    2015-01-01

    Novel methods for diagnostics of molecular hydrogen plasma processes, such as ionization, production of high vibrational levels, dissociation of molecules via excitation to singlet and triplet states and production of metastable states, are presented for molecular hydrogen plasmas in corona equilibrium. The methods are based on comparison of rate coefficients of plasma processes and optical emission spectroscopy of lowest singlet and triplet transitions, i.e. Lyman-band ($B^1\\Sigma^+_u \\rightarrow X^1\\Sigma^+_g$) and molecular continuum ($a^3\\Sigma^+_g \\rightarrow b^3\\Sigma^+_u$), of the hydrogen molecule in VUV wavelength range. Comparison of rate coefficients of spin-allowed and/or spin-forbidden excitations reduces the uncertainty caused by the non-equilibrium distributions of electron energy and molecular vibrational level, which are typically known poorly in plasma sources. The described methods are applied to estimate the rates of various plasma processes in a filament arc discharge.

  14. Hyperon polarization in different inclusive production processes in unpolarized high energy hadron-hadron collisions

    E-print Network

    Hui Dong; Zuo-tang Liang

    2004-06-13

    We apply the picture proposed in a previous Letter, which relates the hyperon polarization in unpolarized hadron-hadron collisions to the left-right asymmetry in singly polarized reactions, to the production of different hyperons in reactions using different projectiles and/or targets. We discuss the different ingredients of the proposed picture in detail and present the results for hyperon polarization in the reactions such as $pp$, $K^-p$, $\\pi^{\\pm}p$, and $\\Sigma^-p$ collisions. We compare the results with the available data and make predictions for future experiments.

  15. 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.

  16. 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

  17. Deformation processes in polycrystalline Zr by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  18. 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.

  19. 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.

  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. Reconstructing the free-energy landscape associated to molecular motors processivity

    E-print Network

    J. Lopez Alamilla; I. Santamaria-Holek

    2012-05-16

    We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ADP. We first reconstruct a continuous free-energy landscape of the cycle catalyst process that allows us to calculate the number of steps given by a single molecular motor. Then, we calculate an analytical expression associated to the translational velocity and the stopping time of the molecular motor in terms of time and ATP concentration. An energetic interpretation of motor processivity is discussed in quantitative form by using experimental data. We also predict a time duration of collective processes that agrees with experimental reports.

  2. Stochastic simulations of cargo transport by processive molecular motors Christian B. Korn,1

    E-print Network

    Schwarz, Ulrich

    Stochastic simulations of cargo transport by processive molecular motors Christian B. Korn,1 Stefan kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic

  3. Post-processing interstitialcy diffusion from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  4. 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

  5. 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

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

    PubMed

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

    2014-03-01

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

  7. Single-electron--removal processes in collisions of positrons and protons with helium at intermediate velocities

    SciTech Connect

    Schultz, D.R.; Olson, R.E.

    1988-08-15

    Total cross sections for single ionization and charge transfer have been calculated using the classical-trajectory Monte Carlo (CTMC) technique for collisions of both positrons and protons with helium. Analysis of the classical trajectories has helped to explain the differences in the collision mechanisms responsible for the observed relative magnitudes of the positron and proton electron-removal cross sections. In the intermediate collision velocity range (1.5 a.u.4.5 a.u.) positrons and protons are found to be equally likely to singly ionize helium, but positrons remain at least half an order of magnitude more likely to remove an electron by charge transfer.

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

    NASA Astrophysics Data System (ADS)

    Kelley, Matthew Thomas

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

  9. Lovastatin production: From molecular basis to industrial process optimization.

    PubMed

    Mulder, Kelly C L; Mulinari, Flávia; Franco, Octávio L; Soares, Maria S F; Magalhães, Beatriz S; Parachin, Nádia S

    2015-11-01

    Lovastatin, composed of secondary metabolites produced by filamentous fungi, is the most frequently used drug for hypercholesterolemia treatment due to the fact that lovastatin is a competitive inhibitor of HMG-CoA reductase. Moreover, recent studies have shown several important applications for lovastatin including antimicrobial agents and treatments for cancers and bone diseases. Studies regarding the lovastatin biosynthetic pathway have also demonstrated that lovastatin is synthesized from two-chain reactions using acetate and malonyl-CoA as a substrate. It is also known that there are two key enzymes involved in the biosynthetic pathway called polyketide synthases (PKS). Those are characterized as multifunctional enzymes and are encoded by specific genes organized in clusters on the fungal genome. Since it is a secondary metabolite, cultivation process optimization for lovastatin biosynthesis has included nitrogen limitation and non-fermentable carbon sources such as lactose and glycerol. Additionally, the influences of temperature, pH, agitation/aeration, and particle and inoculum size on lovastatin production have been also described. Although many reviews have been published covering different aspects of lovastatin production, this review brings, for the first time, complete information about the genetic basis for lovastatin production, detection and quantification, strain screening and cultivation process optimization. Moreover, this review covers all the information available from patent databases covering each protected aspect during lovastatin bio-production. PMID:25868803

  10. 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. PMID:21871546

  11. 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.

  12. Statistical theory of plasma-molecular systems

    NASA Astrophysics Data System (ADS)

    Klimontovich, Iurii L.; Wilhelmsson, Hans; Iakimenko, Ivan P.; Zagorodnii, Anatolii G.

    The fundamental principles of the kinetic theory of combined plasma-molecular systems containing free and bound charged particles are formulated. The collective electromagnetic processes occurring in unbounded and bounded plasma-molecular systems are investigated using a model description of the molecular subsystem. In particular, attention is given to the effect of boundaries on the collision integrals, kinetic coefficients, and particle distributions near the interface. A theory is developed for electromagnetic fluctuations in bounded plasma-molecular systems. The spontaneous emission spectra of plasma-molecular systems of various spatial configurations are analyzed numerically.

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

    PubMed

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

    2015-10-01

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

  14. Photonic, Electronic and Atomic Collisions

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

    Plenary. Electron collisions - past, present and future / J. W. McConkey. Collisions of slow highly charged ions with surfaces / J. Burgdörfer ... [et al.]. Atomic collisions studied with "reaction-microscopes" / R. Moshammer ... [et al.]. Rydberg atoms: a microscale laboratory for studying electron-molecule tnteractions / F. B. Dunning -- Collisions involvintg photons. Quantum control of photochemical reaction dynamics and molecular functions / M. Yamaki ... [et al.]. Manipulating and viewing Rydberg wavepackets / R. R. Jones. Angle-resolved photoelectrons as a probe of strong-field interactions / M. Vrakking. Ultracold Rydberg atoms in a structured environment / I. C. H. Liu and J. M. Rost. Synchrotron-radiation-based recoil ion momentum spectroscopy of laser cooled and trapped cesium atoms / L. H. Coutinho. Reconstruction of attosecond pulse trains / Y. Mairesse ... [et al.]. Selective excitation of metastable atomic states by Femto- and attosecond laser pulses / A. D. Kondorskiy. Accurate calculations of triple differential cross sections for double photoionization of the hygrogen molecule / W. Vanroose ... [et al.]. Double and triple photoionization of Li and Be / J. Colgan, M. S. Pindzola and F. Robicheaux. Few/many body dynamics in strong laser fields / J. Zanghellini and T. Brabec. Rescattering-induced effects in electron-atom scattering in the presence of a circularly polarized laser field / A. V. Flegel ... [et al.]. Multidimensional photoelectron spectroscopy / P. Lablanquie ... [et al.]. Few photon and strongly driven transitions in the XUV and beyond / P. Lambropoulos, L. A. A. Nikolopoulos and S. I. Themelis. Ionization dynamics of atomic clusters in intense laser pulses / U. Saalmann and J. M. Rost. On the second order autocorrelation of an XUV attosecond pulse train / E. P. Benis ... [et al.]. Evidence for rescattering in molecular dissociation / I. D. Williams ... [et al.]. Photoionizing ions using synchrotron radiation / R. Phaneuf. Photo double ionization of fixed in space deuterium molecules / T. Weber ... [et al.]. Coherence and intramolecular scattering in molecular photoionization / U. Becker. Experimental observation of interatomic coulombic decay in neon dimers / T. Jahnke ... [et al.]. Ionization by short UV laser pulses: secondary ATI peaks of the electron spectrum / V. D. Rodríguez, E. Cormier and R. Gayet. Molecular frame photoemission in photoionization of H[symbol] and D[symbol]: the role of dissociation on autoionization of the Q[symbol] and Q[symbol] doubly excited states / D. Dowek, M. Lebech and J. C. Houver. 3p photoemission of 3d transition metals - atoms, molecules and clusters / M. Martins -- Collisions involving electrons. Spin-resolved collisions of electrons with atoms and molecules / G. F. Hanne. Calculation of ionization and excitation processes using the convergent close-coupling method / D. V. Fursa, I. Bray and A. T. Stelbovics. The B-spline R-matrix method for electron and photon collisions with atoms and ions / O. Zatsarinny and K. Bartschat. Absolute angle-differential cross sections for excitation of neon atoms electrons of energy 16.6-19.2 eV / M. Allan ... [et al.]. Studies of QED and nuclear size effects with highly charged ions in an EBIT / J. R. Crespo López-Urrutia ... [et al.]. Recombination of astrophysically relevant ions: Be-like C, N, and O / M. Fogle ... [et al.]. Dissociation and excitation of molecules and molecular ions by electron impact / A. E. Orel and J. Royal state-selective X-ray study of the radiative recombination of U[symbol] ions with cooling electrons / M. Pajek ... [et al.]. Electron collisions with trapped, metastable helium / L. J. Uhlmann ... [et al.]. Non-dipole effects in electron and photon impact ionization / N. L. S. Martin. Electron driven processes in atmospheric behaviour / L. Campbell, M. J. Brunger and P. J. 0. Teubner. Calculation of excitation and ionization for electron-molecule collisions at intermediate energies / J. D. Gorfinkiel. Absolute total cross sections for electron-CH[symbol] scattering at intermediate en

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

    E-print Network

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

    2015-12-26

    In this review we address the dynamics of relativistic heavy-ion reactions and in particular the information obtained from electromagnetic probes that stem from the partonic and hadronic phases. The out-of-equilibrium description of strongly interacting relativistic fields is based on the theory of Kadanoff and Baym. For the modeling of the partonic phase we introduce a dynamical quasiparticle model (DQPM) for QCD in equilibrium. The widths and masses of the quasiparticles are controlled by transport coefficients in comparison to lattice QCD results. The resulting off-shell transport approach - denoted by Parton-Hadron-String Dynamics (PHSD) - also includes covariant dynamical hadronization and keeps track of the hadronic interactions in the final phase. We show that PHSD captures the bulk dynamics of heavy-ion collisions from SPS to LHC energies and provides a basis for the evaluation of the electromagnetic emissivity, using the same dynamical parton propagators as for the system evolution. Direct photon production in elementary processes and heavy-ion reactions at RHIC and LHC energies is investigated and the status of the photon v2 puzzle - a large elliptic flow of the direct photons observed in A+A collisions - is addressed. We discuss the roles of hadronic and partonic sources for the photon spectra and the flow coefficients v2 and v3 and also the possibility to subtract the QGP signal from observables. Furthermore, the production of dilepton pairs is addressed from SIS to LHC energies. The low-mass dilepton yield is enhanced due to the in-medium modification of the rho-meson and at the lowest energy also due to a multiple regeneration of Delta-resonances. In addition, a signal of the partonic degrees-of-freedom is found in the intermediate dilepton mass regime (1.2GeVnature of the very early degrees-of-freedom in nucleus-nucleus collisions.

  16. 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).

  17. Effect of hyperfine interactions on ultracold molecular collisions: NH({sup 3}{Sigma}{sup -}) with Mg({sup 1}S) in magnetic fields

    SciTech Connect

    Gonzalez-Martinez, Maykel L.; Hutson, Jeremy M.

    2011-11-15

    We investigate the effect of hyperfine interactions on ultracold molecular collisions in magnetic fields, using {sup 24}Mg({sup 1}S)+{sup 14}NH({sup 3}{Sigma}{sup -}) as a prototype system. We explore the energy and magnetic-field dependence of the cross sections, comparing the results with previous calculations that neglected hyperfine interactions [A.O.G. Wallis and J. M. Hutson, Phys. Rev. Lett. 103, 183201 (2009)]. The main effect of hyperfine interactions for spin relaxation cross sections is that the kinetic energy release of the dominant outgoing channels does not reduce to zero at low fields. This results in reduced centrifugal suppression of the cross sections and increased inelastic cross sections at low energy and low field. We also analyze state-to-state cross sections, for various initial states, and show that hyperfine interactions introduce additional mechanisms for spin relaxation. In particular, there are hyperfine-mediated collisions to outgoing channels that are not centrifugally suppressed. However, for Mg+NH these unsuppressed channels make only small contributions to the total cross sections. We consider the implications of our results for sympathetic cooling of NH by Mg and conclude that the ratio of elastic to inelastic cross sections remains high enough for sympathetic cooling to proceed.

  18. Molecular Dynamics Study on Synthesis Process of Carbon Nanotubes from Surface Decomposition of SiC

    E-print Network

    Maruyama, Shigeo

    SiC Molecular Dynamics Study on Synthesis Process of Carbon Nanotubes from Surface Decomposition of SiC * Hiroki Yamaguchi , Shigeo Maruyama Dept. of Mech. Eng., The University of Tokyo, 7/or the chirality is a big problem. There is a carbon nanotube synthesis method that the SiC crystal is heated

  19. Electronic processes in molecular dynamics simulations of nanoscale metal tips under electric fields

    E-print Network

    Nordlund, Kai

    Electronic processes in molecular dynamics simulations of nanoscale metal tips under electric dynamics Electronic effects Resistive heating Thermal conduction a b s t r a c t Electronic effects play a crucial role in the temperature evolution of metal parts which have electric cur- rents running through

  20. Symbiotic nitrogen fixation in legumes Define: the process by which molecular nitrogen (N2) is

    E-print Network

    Constabel, Peter

    Symbiotic nitrogen fixation in legumes Define: the process by which molecular nitrogen (N2 input Why is N fixation important? - net nitrogen input into soil 5-10 % - model system for plant-Rhizobium symbiosis: i) formation of nodules ii) plant-bacterium communication iii) biochemistry of nitrogen fixation

  1. C@SZR v *2 Molecular Dynamics of the Formation Process of Fullerene

    E-print Network

    Maruyama, Shigeo

    ·N--²*1 ·C·@SÛZR ­Î·v *2 Molecular Dynamics of the Formation Process of Fullerene (1st Report, Carbon, Cluster 1.·@,Í,¶,ß,É ·@1985 "N,ÉKroto ,ç (1) ,Í·C··"ZZ--¿,ðOE·[U·[,Å·ö"-,³ ,¹·C"¯Zz,É'´¹`¬­c'£,É,æ,Á,Ä--âC C60 ,Ì

  2. MOLECULAR SIMULATIONS OF THE FORMATION PROCESS OF FULLERENE Yasutaka YAMAGUCHI and Shigeo MARUYAMA

    E-print Network

    Maruyama, Shigeo

    MOLECULAR SIMULATIONS OF THE FORMATION PROCESS OF FULLERENE Yasutaka YAMAGUCHI and Shigeo MARUYAMA. The formation mechanism of fullerene, a new type of carbon molecule with hollow caged structure, was studied, yielding the graphitic sheet for Tc fullerene-like caged structure for 2600 K

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

    PubMed

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

    2015-05-28

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

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

    SciTech Connect

    Ayik, S.

    1993-02-01

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

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

    SciTech Connect

    Ayik, S.

    1993-02-01

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

  6. 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.

  7. 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

  8. 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.

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

    SciTech Connect

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

    1996-02-01

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

  10. Section 7.10 An Orbital Overlap or Collision Mechanism of Energy Transfer 411 biphenyl chromophore. The activated process makes up for the large distance of sepa-

    E-print Network

    Turro, Nicholas J.

    Section 7.10 An Orbital Overlap or Collision Mechanism of Energy Transfer 411 biphenyl chromophore. The activated process makes up for the large distance of sepa- ration for the phenanthrene and naphthalene by achieving energy transfer in two steps; that is, step 1 is 3 phenanthrene + biphenyl phenanthrene + 3

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

    SciTech Connect

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

    2011-12-31

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

  12. Detection of molecular processes in the intact retina by ATR-FTIR spectromicroscopy.

    PubMed

    Massaro, Sebastiano; Zlateva, Theodora; Torre, Vincent; Quaroni, Luca

    2008-01-01

    We used Fourier transform infrared spectromicroscopy in the attenuated total reflection configuration to study biochemical events associated with the response to light of an intact retina. We show that the technique is suitable for the detection in real time of molecular processes occurring in rod outer segments induced by light absorption. Two-dimensional correlation analysis was applied to the identification and interpretation of specific spectral changes associated to the evolution of the system. The technique allows us to observe an extensive protein translocation, which we interpret as arising from the release of transducin from the disk membrane and its redistribution from the outer segment towards the inner segment of rod cells. These results are in full agreement with our current understanding of retinal physiology and validate the technique as a useful tool for the study of complex molecular processes in intact tissue. [figure: see text] Spectral changes in the mid infrared region following exposure of an intact retina to light. PMID:17989959

  13. 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.

  14. 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.

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

    E-print Network

    Luca Ciandrini; M. Carmen Romano; A. Parmeggiani

    2014-05-26

    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 biopolymerisation (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 the current 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 co-moving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

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

    NASA Astrophysics Data System (ADS)

    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 biopolymerisation (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 the current 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 co-moving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions.

  17. 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

  18. 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.

  19. Solution processed multilayer polymer light-emitting diodes based on different molecular weight host

    NASA Astrophysics Data System (ADS)

    Al-Attar, Hameed A.; Monkman, Andrew P.

    2011-04-01

    Solution processed multilayer polymer light-emitting diodes (PLEDs) based on different molecular weight host have been investigated. A PLED based on high molecular weight poly (vinyl carbazole) PVKH and low molecular weight poly (vinyl carbazole) PVKL, doped with iridium, tris(2-phenylpyidine) Ir(ppy)3 as a host-guest emitting layer (EML), shows a dramatic increase in device efficiency. When the PVKH was used as a hole transport electron blocking layer (HT-EBL), effective electron blocking was achieved, which leads to an increase exciton population in the phosphorescent zone. The use of low molecular weight PVKL as a host material in the top layer prevents barrier formation for hole transport from the poly(3,4-ethylenedioxy-thiophene) (PEDOT)-EBL to the EML. External quantum efficiency of 11%, current efficiencies of 38 cd/A, power efficiency of 13 lm/W and brightness of 7000 cd/m2, were obtained. The effect of the PVKH layer on the electrical and optical device characteristics was investigated. Simulation of the optical outcoupling using SETFOS 3.1 software is in agreed with the observed results and allowed us to predict the emissive dipole location and distribution in the EML layer. The effect of the PVKH on the exciton quenching by the electrodes was also investigated using time resolved fluorescence photon counting, which indicates weak exciton quenching by the PEDOT layer and the device enhancement predominantly achieved by exciton confinement in the emissive layer.

  20. 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.

  1. 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.

  2. The effect of molecular relaxation processes in air on the rise time of sonic booms

    NASA Technical Reports Server (NTRS)

    Kang, Jongmin; Pierce, Allan D.

    1990-01-01

    A theory is developed to explain the effect of molecular relaxation processes on the rise time of sonic booms. To determine the rise time of sonic booms, both O2 and N2 relaxation processes must be included. The N2 relaxation process delays the shock pressure reaching the maximum pressure, and the O2 relaxation process causes a shock profile to have a gentle slope. The N2 relaxation controls the lower part of overpressure; the O2 relaxation controls the higher part. The constant rise time curves show that the rise times increase as the overpressures and humidity decrease. The present approach gives longer rise times than those acquired by Bass et al. for given shock overpressures.

  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. 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

  5. Molecular studies on the ecology of Listeria monocytogenes in the smoked fish processing industry.

    PubMed

    Norton, D M; McCamey, M A; Gall, K L; Scarlett, J M; Boor, K J; Wiedmann, M

    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 < or = 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

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

    PubMed

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

    2014-12-01

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

  7. Scatter rejection by air gaps in diagnostic radiology. Calculations using a Monte Carlo collision density method and consideration of molecular interference in coherent scattering.

    PubMed

    Persliden, J; Carlsson, G A

    1997-01-01

    The air gap technique is an old method for scatter rejection. It is still used in lung examinations and may be reconsidered for use in digital radiography. Using magnification techniques, for example in mammography, the air gap thereby introduced simultaneously yields scatter rejection. A Monte Carlo collision density method is exploited to investigate the physical parameters relevant to this technique. Radiation quantities of scattered photons at points behind a water slab both on and laterally displaced from the central axis are calculated and their dependence on field area, slab thickness, air gap length and detector type is derived. Values of 'scatter-to-primary' ratios of the plane energy fluence (the energy imparted to a totally absorbing detector) are given for perpendicularly incident 30, 70 and 130 kV energy spectra, slab thicknesses of 0.05 and 0.2 m (30 kV: 0.05 m), air gaps of length 0.002-1.0 m and field areas from 8 x 10(-5) to 0.3 m2. Contrast degradation factors are derived for both totally absorbing and thin detectors. The influence on the scatter-to-primary ratios of using divergent instead of parallel beams and of neglecting molecular interference in coherent scattering is analysed. PMID:9015816

  8. Large transverse momentum dilepton production in heavy ion collisions with two-photon processes

    E-print Network

    Yong-Ping Fu; Yun-De Li

    2015-09-06

    The cold component of large transverse momentum dilepton production via semi-coherent two-photon interaction is calculated. The cold contribution is essential to the dilepton spectra in the soft region for different mass bins. The results are compared with the PHENIX experimental data at RHIC, and we find that the modification of semi-coherent two-photon processes is more evident with the rising dilepton mass bins.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  11. CTMC Investigation of Capture and Ionization Processes in P + H(1s) Collisions in Strong Transverse Magnetic Fields

    NASA Astrophysics Data System (ADS)

    He, Bin; Wang, Jian-Guo; R. K., Janev

    2015-04-01

    The collision processes of proton with H(1s) atoms, which is embedded in strong transverse magnetic fields perpendicular to the initial velocity of the projectile, are studied with the classical trajectory Monte Carlo method in the energy range 25 keV/u-2000 keV/u and B ˜ 104 T. It is found that the charge exchange cross section is decreased while the ionization cross section is increased significantly. The physics of magnetic field effects is analyzed by the time evolution of electron energy and trajectories, and it is found that these effects are induced by the diamagnetic term in the interaction, continuum electron trapping in the target regions and the Lorentz force. The velocity distributions of the ionized electrons, significantly influenced by the applied fields, are also presented. Supported by National Natural Science Foundation of China under Grant Nos. 11104017, 11025417, 11075023, 10974021, 10979007, the Natoinal Basic Research Programm of China under Grant No. 2013CB922200, and the Science and Technology Foundation of Chinese Academy of Engeering Physics under Grant No. 2014B09036

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H ? NaH) and the homonuclear (Na + Na ? Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X1?+) is associated into the molecule in the bound states of the excited state (A1?+) 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.

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

    PubMed

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

    2015-09-01

    The photoassociation processes via the pump-dump scheme for the heternuclear (Na + H ? NaH) and the homonuclear (Na + Na ? Na2) molecular systems are studied, respectively, using the time-dependent quantum wavepacket method. For both systems, the initial atom pair in the continuum of the ground electronic state (X(1)?(+)) is associated into the molecule in the bound states of the excited state (A(1)?(+)) by the pump pulse. Then driven by a time-delayed dumping pulse, the prepared excited-state molecule can be transferred to the bound states of the ground electronic state. It is found that the pump process can induce a superposition of the rovibrational levels |v, j? on the excited state, which can lead to the field-free alignment of the excited-state molecule. The molecular alignment can affect the dumping process by varying the effective coupling intensity between the two electronic states or by varying the population transfer pathways. As a result, the final population transferred to the bound states of the ground electronic state varies periodically with the delay time of the dumping pulse. PMID:26342366

  14. 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

  15. 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

  16. Simulating Picosecond X-ray Diffraction from shocked crystals by Post-processing Molecular Dynamics Calculations

    SciTech Connect

    Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J

    2008-06-19

    Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.

  17. Hydrolysis and oxidation in sub- and supercritical water connecting process engineering science to molecular interactions

    SciTech Connect

    Tester, J.W.; Clime, J.A.

    1999-11-01

    Key engineering issues influencing the development of supercritical water oxidation for waste treatment are reviewed. Major chemical pathways and kinetics for hydrolysis and oxidation reactions of model organic wastes are discussed. In selective examples, results born extensive laboratory-scale measurements are compared with molecular simulations of solvation and reaction effects in supercritical water. Connections between reaction chemistry and observed corrosion in supercritical water oxidation processing equipment are discussed to underscore the importance of understanding electrochemical phenomena over a wide range of temperature and density conditions. Research needs for improved understanding of physical and chemical effects in supercritical fluids are identified.

  18. Remarks on the non-equilibrium effects and collision dynamics in heavy-ion collisions

    E-print Network

    Yogesh K. Vermani; Mandeep Kaur

    2011-12-02

    We study the beam energy dependence of equilibration process and space-time characteristics of participant and spectator matter. For this, we simulated the semi-central collisions of $^{40}Ca+ ^{40}Ca$ at incident energies of 400, 600 and 1000 AMeV within the \\emph{quantum molecular dynamics} (QMD) approach. Our numerical calculations based on the molecular dynamics approach show that incident energy of the projectile influences the reaction observables drastically. The effect is more visible for transverse expansion of the nuclear matter and transparency behavior. The degree of thermalization of participant matter, however, remains independent of the incident energy. The characteristics of the trajectories followed by the nucleons suffering maximal and minimal binary collisions are also analyzed.

  19. Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing.

    PubMed

    Matsumoto, Masakazu; Saito, Shinji; Ohmine, Iwao

    2002-03-28

    Upon cooling, water freezes to ice. This familiar phase transition occurs widely in nature, yet unlike the freezing of simple liquids, it has never been successfully simulated on a computer. The difficulty lies with the fact that hydrogen bonding between individual water molecules yields a disordered three-dimensional hydrogen-bond network whose rugged and complex global potential energy surface permits a large number of possible network configurations. As a result, it is very challenging to reproduce the freezing of 'real' water into a solid with a unique crystalline structure. For systems with a limited number of possible disordered hydrogen-bond network structures, such as confined water, it is relatively easy to locate a pathway from a liquid state to a crystalline structure. For pure and spatially unconfined water, however, molecular dynamics simulations of freezing are severely hampered by the large number of possible network configurations that exist. Here we present a molecular dynamics trajectory that captures the molecular processes involved in the freezing of pure water. We find that ice nucleation occurs once a sufficient number of relatively long-lived hydrogen bonds develop spontaneously at the same location to form a fairly compact initial nucleus. The initial nucleus then slowly changes shape and size until it reaches a stage that allows rapid expansion, resulting in crystallization of the entire system. PMID:11919626

  20. 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.

  1. Evolution and stability of shock waves in dissipative gases characterized by activated inelastic collisions

    E-print Network

    Sirmas, Nick

    2015-01-01

    Previous experiments have revealed that shock waves driven through dissipative gases may become unstable, for example, in granular gases, and in molecular gases undergoing strong relaxation effects. The mechanisms controlling these instabilities are not well understood. We successfully isolated and investigated this instability in the canonical problem of piston driven shock waves propagating into a medium characterized by inelastic collision processes. We treat the standard model of granular gases, where particle collisions are taken as inelastic with constant coefficient of restitution. The inelasticity is activated for sufficiently strong collisions. Molecular dynamic simulations were performed for 30,000 particles. We find that all shock waves investigated become unstable, with density non-uniformities forming in the relaxation region. The wavelength of these fingers is found comparable to the characteristic relaxation thickness. Shock Hugoniot curves for both elastic and inelastic collisions were obtaine...

  2. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

    PubMed Central

    2010-01-01

    Background Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. Results A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. Conclusions MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses. PMID:20650010

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

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang

    2011-11-01

    To date, there is no study on bioethanol processing-induced changes in molecular structural profiles mainly related to lipid biopolymer. The objectives of this study were to: (1) determine molecular structural changes of lipid related functional groups in the co-products that occurred during bioethanol processing; (2) relatively quantify the antisymmetric CH 3 and CH 2 (ca. 2959 and 2928 cm -1, respectively), symmetric CH 3 and CH 2 (ca. 2871 and 2954 cm -1, respectively) functional groups, carbonyl C dbnd O ester (ca. 1745 cm -1) and unsaturated groups (CH attached to C dbnd C) (ca. 3007 cm -1) spectral intensities as well as their ratios of antisymmetric CH 3 to antisymmetric CH 2, and (3) illustrate the molecular spectral analyses as a research tool to detect for the sensitivity of individual moleculars to the bioethanol processing in a complex plant-based feed and food system without spectral parameterization. The hypothesis of this study was that bioethanol processing changed the molecular structure profiles in the co-products as opposed to original cereal grains. These changes could be detected by infrared molecular spectroscopy and will be related to nutrient utilization. The results showed that bioethanol processing had effects on the functional groups spectral profiles in the co-products. It was found that the CH 3-antisymmetric to CH 2-antisymmetric stretching intensity ratio was changed. The spectral features of carbonyl C dbnd O ester group and unsaturated group were also different. Since the different types of cereal grains (wheat vs. corn) had different sensitivity to the bioethanol processing, the spectral patterns and band component profiles differed between their co-products (wheat DDGS vs. corn DDGS). The multivariate molecular spectral analyses, cluster analysis and principal component analysis of original spectra (without spectral parameterization), distinguished the structural differences between the wheat and wheat DDGS and between the corn and corn DDGS in the antisymmetric and symmetric CH 3 and CH 2 spectral region (ca. 2994-2800 cm -1) and unsaturated group band region (3025-2996 cm -1). Further study is needed to quantify molecular structural changes in relation to nutrient utilization of lipid biopolymer.

  4. Competition of coalescence and "fireball" processes in nonequilibrium emission of light charged particles from p+Au collisions

    E-print Network

    A. Budzanowski; M. Fidelus; D. Filges; F. Goldenbaum; H. Hodde; L. Jarczyk; B. Kamys; M. Kistryn; St. Kistryn; St. Kliczewski; A. Kowalczyk; E. Kozik; P. Kulessa; H. Machner; A. Magiera; B. Piskor-Ignatowicz; K. Pysz; Z. Rudy; R. Siudak; M. Wojciechowski

    2008-01-29

    The energy and angular dependence of double differential cross sections was measured for p,d,t,He,Li,Be, and B isotopes produced in collisions of 1.2 and 1.9 GeV protons with Au target. The shape of the spectra and angular distributions almost does not change in the beam energy range from 1.2 to 2.5 GeV, however, the absolute value of the cross sections increases for all ejectiles. A phenomenological model of two emitting, moving sources reproduces very well spectra and angular distributions of intermediate mass fragments. Double differential cross sections for light charged particles (LCP) were analyzed in the frame of the microscopic model of intranuclear cascade (INC) with coalescence of nucleons and statistical model for evaporation of particles from excited residual nuclei. Energy and angular dependencies of data agree satisfactorily neither with predictions of microscopic intranuclear cascade calculations for protons, nor with coalescence calculations for other LCP. Phenomenological inclusion of another reaction mechanism - emission of LCP from a "fireball", i.e., fast and hot moving source - combined with the microscopic model calculations of INC, coalescence and evaporation of particles leads to very good description of the data. It was found that nonequilibrium processes are very important for production of LCP. They exhaust 40-80% of the total cross sections - depending on the emitted particles. Coalescence and "fireball" emission give comparable contributions to the cross sections with exception of 3He data where coalescence clearly dominates. The ratio of sum of all nonequilibrium processes to those proceeding through stage of statistical equilibrium does almost not change in the beam energy range from 1.2 GeV to 2.5 GeV for all light charged particles.

  5. 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.

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

    PubMed

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

    2015-12-17

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

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

    NASA Astrophysics Data System (ADS)

    Chouhan, Lalit Singh; Raina, Avtar K.

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed

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

    2015-09-23

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

  10. 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.

  11. Processing of hydroxyapatite reinforced ultrahigh molecular weight polyethylene for biomedical applications.

    PubMed

    Fang, Liming; Leng, Yang; Gao, Ping

    2005-06-01

    A new method for processing hydroxyapatite/ultrahigh molecular weight polyethylene (HA/UHMWPE) composite has been developed by combining wet ball milling and swelling. Sintered HA particles were ground in ethanol to approximately 50 nm in diameter. The nano-sized HA particles were mechanically mixed with UHMWPE in the ball mill and then compression molded into solid slabs. The slabs were then swollen in a pharmaceutical grade paraffin oil to enhance the UHMWPE chain mobility and HA/UHMWPE interface adhesion before final hot press. The resultant composite exhibits a two-zone network structure formed by a homogeneous HA-rich phase and a UHMWPE-rich phase. This process resulted in a 90% increase in Young's modulus and a 50% increase in the yield strength of HA/UHMWPE composite, comparing with those of unfilled UHMWPE. PMID:15621236

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

    NASA Astrophysics Data System (ADS)

    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.

  13. 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.

  14. Chemi-ionization Processes. Alkali-metal Geocosmical Plasmas

    SciTech Connect

    Klyucharev, Andrey N.; Bezuglov, Nikolay N.; Matveev, Andrey A.; Mihajlov, Anatolij A.; Ignjatovic, Ljubinko M.; Dimitrijevic, Milan S.

    2007-09-28

    Chemi-ionization processes, leading to formation of molecular ions, can play an essential role in the sequence of ion-molecular reactions on surfaces of solid particles or in associative processes of the binary collisions leading to surprising variety of molecular formations in interstellar gas and geocosmical plasmas. The presented results may be recommended for the interpretation of experimental data and for theoretical research of geocosmical plasmas, first of all the the volcanic gases on Io.

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

    PubMed

    Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

    2014-01-01

    For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer. PMID:25384534

  16. Design and synthesis of molecular donors for solution-processed high-efficiency organic solar cells.

    PubMed

    Coughlin, Jessica E; Henson, Zachary B; Welch, Gregory C; Bazan, Guillermo C

    2014-01-21

    Organic semiconductors incorporated into solar cells using a bulk heterojunction (BHJ) construction show promise as a cleaner answer to increasing energy needs throughout the world. Organic solar cells based on the BHJ architecture have steadily increased in their device performance over the past two decades, with power conversion efficiencies reaching 10%. Much of this success has come with conjugated polymer/fullerene combinations, where optimized polymer design strategies, synthetic protocols, device fabrication procedures, and characterization methods have provided significant advancements in the technology. More recently, chemists have been paying particular attention to well-defined molecular donor systems due to their ease of functionalization, amenability to standard organic purification and characterization methods, and reduced batch-to-batch variability compared to polymer counterparts. There are several critical properties for efficient small molecule donors. First, broad optical absorption needs to extend towards the near-IR region to achieve spectral overlap with the solar spectrum. Second, the low lying highest occupied molecular orbital (HOMO) energy levels need to be between -5.2 and -5.5 eV to ensure acceptable device open circuit voltages. Third, the structures need to be relatively planar to ensure close intermolecular contacts and high charge carrier mobilities. And last, the small molecule donors need to be sufficiently soluble in organic solvents (?10 mg/mL) to facilitate solution deposition of thin films of appropriate uniformity and thickness. Ideally, these molecules should be constructed from cost-effective, sustainable building blocks using established, high yielding reactions in as few steps as possible. The structures should also be easy to functionalize to maximize tunability for desired properties. In this Account, we present a chronological description of our thought process and design strategies used in the development of highly efficient molecular donors that achieve power conversion efficiencies greater than 7%. The molecules are based on a modular D(1)-A-D(2)-A-D(1) architecture, where A is an asymmetric electron deficient heterocycle, which allowed us to quickly access a library of compounds and develop structure-property-performance relationships. Modifications to the D1 and D2 units enable spectral coverage throughout the entire visible region and control of HOMO energy levels, while adjustments to the pendant alkyl substituents dictate molecular solubility, thermal transition temperatures, and solid-state organizational tendencies. Additionally, we discuss regiochemical considerations that highlight how individual atom placements can significantly influence molecular and subsequently device characteristics. Our results demonstrate the utility of this architecture for generating promising materials to be integrated into organic photovoltaic devices, call attention to areas for improvement, and provide guiding principles to sustain the steady increases necessary to move this technology forward. PMID:23984626

  17. Transcriptome profile analysis of cell proliferation molecular processes during multicellular trichome formation induced by tomato Wov gene in tobacco

    PubMed Central

    Yang, Changxian; Gao, Yanna; Gao, Shenghua; Yu, Gang; Xiong, Cheng; Chang, Jiang; Li, Hanxia; Ye, Zhibiao

    2015-01-01

    Trichomes, developing from the epidermis of nearly all terrestrial plants, provide good protection from environmental stress. Regulation of trichomes in Rosids has been well characterized. However, little is known about the cell proliferation molecular processes during multicellular trichome formation in Asterids. Ectopic expression of Wov in tobacco and potato induces much more trichome formation than wild type. To gain new insights into the underlying mechanisms during the processes of these trichomes formation, RNA-seq was employed for the young primary leaf tissues in Wov transgenic and wild-type tobacco. We identified differentially expressed genes which are related to various biological processes and molecular functions. Here, we provide details of experimental methods, RNA-seq data (available at Gene Expression Omnibus database under GSE72310). Our data provide new insight into the molecular processes controlling multicellular formation in tobacco. PMID:26697365

  18. Jet asymmetry and momentum imbalance from $2 \\to 2$ and $2 \\to 3$ partonic processes in relativistic heavy-ion collisions

    E-print Network

    Alejandro Ayala; Isabel Dominguez; Jamal Jalilian-Marian; Maria Elena Tejeda-Yeomans

    2015-03-24

    We study momentum imbalance as a function of jet asymmetry in high-energy heavy-ion collisions. To implement parton production during the collision, we include all Leading Order (LO) $2\\to 2$ and $2\\to 3$ parton processes in pQCD. The produced partons lose energy within the quark gluon plasma and hadronize collinearly when they leave it. The energy and momentum deposited into the plasma is described using linear viscous hydrodynamics with a constant energy loss per unit length and a total energy loss given by a Gaussian probability centered around a mean value $\\bar{\\mathcal{E}}$ and a half-width $\\Delta{\\mathcal{E}}$. We argue that the shape of the asymmetry observed by the CERN-CMS Collaboration can indeed be attributed to parton energy loss in the medium and that a good description of data is achieved when one includes a slight enhancement coming from the contribution of $2\\to 3$ parton processes that modifies the asymmetry distribution of the dijet events. We compare our results to CMS data for the most central collisions and study different values for $\\bar{\\mathcal{E}}$ and $\\Delta{\\mathcal{E}}$.

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

    ERIC Educational Resources Information Center

    Mahan, Bruce H.

    1974-01-01

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

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

    PubMed

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

    2015-12-01

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

  1. 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

  2. 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

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

    PubMed

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

    2013-11-12

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

  4. Online monitoring of molecular processes in a plasma air purifying system.

    PubMed

    Schmid, Stefan; Meier, Lukas; Berchtold, Christian; Zenobi, Renato

    2012-04-01

    Plasma air purifying systems present an interesting alternative to filters for purifying air. In this study, molecular processes in a commercially available ac driven plasma air purifier were studied in detail. This air purifier is supposed to reduce all air contaminants to small nontoxic molecules (e.g., H(2)O and CO(2)). However, degradation mechanisms are not yet fully understood. In this study, we investigated the exhaust of the plasma air purifier to determine which degradation products are formed. An interface was designed and constructed to allow the direct coupling of the plasma air purifier's exhaust to a mass spectrometer. The compounds studied, primary and secondary amines, were introduced at a concentration of 1 ppmV. Contrary to our expectations, polymerization instead of degradation was observed. The higher the ac voltage applied (max. 9.0 kV) to the plasma air purifier, the higher the mass of the oligomer distribution. Side chain oxidation products as well as oligomers could be observed for all compounds tested. Starting with amines of low mass (m/z < 200), compounds of molecular masses above 1000 Da were observed in the plasma air purifier. Detailed analysis of the observed mass spectra as well as experiments with deuterated dibutylamine helped to unravel the mechanism taking place in the plasma air purifier. Nitrate anions generated in the plasma air purifier (presumably from N(2)) are proposed to form ionic clusters with protonated amines. PMID:22420672

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

    NASA Astrophysics Data System (ADS)

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

    2007-02-01

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

  6. 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.

  7. The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes

    E-print Network

    Carla Goldman; Elisa T. Sena

    2008-10-07

    We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion processes (ASEP). The model is formulated to account for i) excluded volume interactions, ii) the observed asymmetry of the stochastic movement of individual motors and iii) interactions between motors and cargo. Items (i) and (ii) form the basis of ASEP models and have already been considered in the literature to study the behavior of motor density profile [Parmeggiani 03]. Item (iii) is new. It is introduced here as an attempt to describe explicitly the dependence of cargo movement on the dynamics of motors. The steady-state solutions of the model indicate that the system undergoes a phase transition of condensation type as the motor density varies. We study the consequences of this transition to the properties of cargo velocity.

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

    PubMed

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

    2015-10-20

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

  9. 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.

  10. Ultra-cold Atom CollisionsUltra-cold Atom Collisions and Quantum Dynamics atand Quantum Dynamics at

    E-print Network

    Band, Yehuda B.

    Ultra-cold Atom CollisionsUltra-cold Atom Collisions and Quantum Dynamics atand Quantum Dynamics are available at Ben-Gurion University to carry out research in ultra-cold atomic and molecular physics

  11. 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.

  12. 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

  13. 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) ?-helix:?-sheet ratio (1.015 vs. 0.926), indicating varietal difference in protein secondary structure makeup. All processing applications increased ?-helix:?-sheet ratio, with the largest (P<0.05) increase being observed with roasting and microwaving. The heat-induced changes in ?-helix:?-sheet ratio was strongly correlated to intestinal digestibility of protein within the green (r=-0. 86) and yellow (r=0.81) pea-types. However, across the pea types the correlation was not significant. Principal component and hierarchical cluster analyses on the entire spectral data from the amide region (ca. 1727-1480 cm(-1)) were able to visualize and discriminate the structural difference between pea varieties and processing treatments. This study shows that the molecular spectroscopy can be used as a rapid tool to screen the protein value of raw and heat-treated peas. PMID:26188704

  14. Reconsolidation and Extinction Are Dissociable and Mutually Exclusive Processes: Behavioral and Molecular Evidence

    PubMed Central

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

    2014-01-01

    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. PMID:24523532

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

    SciTech Connect

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

    2011-10-15

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

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

    NASA Astrophysics Data System (ADS)

    Brédas, Jean-Luc

    2007-03-01

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

  17. 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

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

    SciTech Connect

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

    2011-01-01

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

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

    PubMed

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

    2015-08-14

    We propose that information processing can be implemented by measuring the directional components of the macroscopic polarization of an ensemble of molecules subject to a sequence of laser pulses. We describe the logic operation theoretically and demonstrate it by simulations. The measurement of integrated stimulated emission in different phase matching spatial directions provides a logic decomposition of a function that is the discrete analog of an integral transform. The logic operation is reversible and all the possible outputs are computed in parallel for all sets of possible multivalued inputs. The number of logic variables of the function is the number of laser pulses used in sequence. The logic function that is computed depends on the chosen chromophoric molecular complex and on its interactions with the solvent and on the two time intervals between the three pulses and the pulse strengths and polarizations. The outputs are the homodyne detected values of the polarization components that are measured in the allowed phase matching macroscopic directions, kl, kl=?iliki where ki is the propagation direction of the ith pulse and {li} is a set of integers that encodes the multivalued inputs. Parallelism is inherently implemented because all the partial polarizations that define the outputs are processed simultaneously. The outputs, which are read directly on the macroscopic level, can be multivalued because the high dynamical range of partial polarization measurements by nonlinear coherent spectroscopy allows for fine binning of the signals. The outputs are uniquely related to the inputs so that the logic is reversible. PMID:26277126

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  1. Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    SciTech Connect

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

    2011-05-01

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

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

    PubMed Central

    Stone, John E.; Kohlmeyer, Axel

    2011-01-01

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

  3. 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 ?-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

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

    PubMed Central

    Keil, Matthias S.

    2015-01-01

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

  5. Molecular mechanism of the inhibition effect of Lipoxin A4 on corneal dissolving pathology process

    PubMed Central

    Zhou, Hong-Yan; Hao, Ji-Long; Bi, Miao-Miao; Wang, Shuang; Zhang, Hong; Zhang, Wen-Song

    2013-01-01

    AIM Excessive dissolve of corneal tissue induced by MMPs which were activated by cytokins and chemokines will lead to corneal ulcer. The molecular mechanism of Lipoxin A4 (LXA4) on corneal collagen degradation in three dimensions was investigated. METHODS Rabbit corneal fibroblasts were harvested and suspended in serum-free MEM. Type I collagen, DMEM, collagen reconstitution buffer and corneal fibroblast suspension were mixed on ice. The resultant mixture solidified in an incubator, after which test reagents and plasminogen was overlaid and the cultures were returned to the incubator. The supernatants from collagen gel incubations were collected and the amount of hydroxyproline in the hydrolysate was measured. Immunoblot analysis of MMP-1, -3 and TMMP-1,-2 was performed. MMP-2,-9 was detected by the method of Gelatin zymography. Cytotoxicity assay was measured. RESULTS LXA4 inhibited corneal collagen degradation in a dose and time manner. LXA4 inhibited the IL-1? induced increases in the pro-MMP-1, -2, -3, -9 and active MMP-1, -2, -3, -9 in a concentration dependent manner. LXA4 could also inhibit the IL-1? induced increases in TIMP-1, -2. CONCLUSION As a potent anti-inflammation reagent, LXA4 can inhibit corneal collagen degradation induced by IL-1? in corneal fibroblasts thus inhibiting corneal dissolving pathology process. PMID:23550231

  6. Molecular Insights into Plant-Microbial Processes and Carbon Storage in Mangrove Ecosystems

    NASA Astrophysics Data System (ADS)

    Romero, I. C.; Ziegler, S. E.; Fogel, M.; Jacobson, M.; Fuhrman, J. A.; Capone, D. G.

    2009-12-01

    Mangrove forests, in tropical and subtropical coastal zones, are among the most productive ecosystems, representing a significant global carbon sink. We report new molecular insights into the functional relationship among microorganisms, mangrove trees and sediment geochemistry. The interactions among these elements were studied in peat-based mangrove sediments (Twin Cays, Belize) subjected to a long-term fertilization experiment with N and P, providing an analog for eutrophication. The composition and ?13C of bacterial PLFA showed that bacteria and mangrove trees had similar nutrient limitation patterns (N in the fringe mangrove zone, P in the interior zone), and that fertilization with N or P can affect bacterial metabolic processes and bacterial carbon uptake (from diverse mangrove sources including leaf litter, live and dead roots). PCR amplified nifH genes showed a high diversity (26% nifH novel clones) and a remarkable spatial and temporal variability in N-fixing microbial populations in the rhizosphere, varying primarily with the abundance of dead roots, PO4-3 and H2S concentrations in natural and fertilized environments. Our results indicate that eutrophication of mangrove ecosystems has the potential to alter microbial organic matter remineralization and carbon release with important implications for the coastal carbon budget. In addition, we will present preliminary data from a new study exploring the modern calibration of carbon and hydrogen isotopes of plant leaf waxes as a proxy recorder of past environmental change in mangrove ecosystems.

  7. The Molecular Basis of Wound Healing Processes Induced by Lithospermi Radix: A Proteomics and Biochemical Analysis

    PubMed Central

    Hsiao, Chia-Yen; Tsai, Tung-Hu; Chak, Kin-Fu

    2012-01-01

    Lithospermi Radix (LR) is an effective traditional Chinese herb in various types of wound healing; however, its mechanism of action remains unknown. A biochemical and proteomic platform was generated to explore the biological phenomena associated with LR and its active component shikonin. We found that both LR ethanol extracts and shikonin are able to promote cell proliferation by up to 25%. The results of proteomic analysis revealed that twenty-two differentially expressed proteins could be identified when fibroblast cells were treated with LR or shikonin. The functions of those proteins are associated with antioxidant activity, antiapoptosis activity, the regulation of cell mobility, the secretion of collagen, the removal of abnormal proteins, and the promotion of cell proliferation, indicating that the efficacy of LR in wound healing may be derived from a synergistic effect on a number of factors induced by the herbal medicine. Furthermore, an animal model confirmed that LR is able to accelerate wound healing on the flank back of the SD rats. Together these findings help to pinpoint the molecular basis of wound healing process induced by LR. PMID:23024692

  8. 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 of MD simulations of liquid mixture systems car-ried out in this research explain observed experiments and show the details of nanostructural organizations in small solute molecules/IL mixture. Additionally, the research successfully reveals the correct mechanism of graphene exfoliation process in liquid solution. (This will be summarized in Chapter 5.) The research presented in this dissertation enhances our understanding of the microscopic behaviors in complex liquid systems as well as the theoretical method to explore them.

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

    NASA Astrophysics Data System (ADS)

    West, Brantley Andrew

    Conical intersections mediate internal conversion dynamics that compete with even the fastest nuclear motions in molecular systems. Traditional kinetic models do not apply in this regime of commensurate electronic and nuclear motion because the surroundings do not maintain equilibrium throughout the relaxation process. This dissertation focuses on uncovering the physics associated with vibronic interactions at conical intersections. Of particular interest are coherent nuclear motions driven by steep excited state potential energy gradients. Technical advances have only recently made these dynamics accessible in many systems including DNA nucleobases and cyclic polyene molecules. Optical analogues of multidimensional NMR spectroscopies have recently yielded transformative insight in relaxation processes ranging from energy transfer in photosynthesis to bond making and breaking in liquids. Prior to the start of this research, such experiments had only been conducted at infrared and visible wavelengths. Applications in the ultraviolet were motivated by studies of numerous biological systems (e.g., DNA, proteins), but had been challenged by technical issues. The work presented in this dissertation combines pulse generation techniques developed in the optical physics community with spectroscopic techniques largely pioneered by physical chemists to implement two-dimensional ultraviolet spectroscopy (2DUV). This technique is applied at the shortest wavelengths and with the best signal-to-noise ratios reported to date. Sub-picosecond excited state deactivation processes provide photo stability to the DNA double helix. Vibrational energy transfer from the solute to surrounding solvent enables relaxation of the highly non-equilibrium ground state produced by fast internal conversion. In this dissertation, nonlinear spectroscopies carried out at cryogenic temperatures are used to uncover the particular nuclear modes in the solvent that primarily accept vibrational energy from the solute. These measurements additionally expose a competition between internal conversion and vibrational energy transfer onto the DNA backbone. Ring-opening reactions in cycloalkenes are one of the most fundamental reactions in organic chemistry. Traditional textbook understandings of these reactions conveniently hide the intricate physics that occurs prior to bond breaking. Sub-100-femtosecond internal conversion processes precede bond breaking in these systems. This dissertation directly monitors these dynamics in a derivative of cyclohexadiene, alpha-terpinene, and detects coherent wavepacket motions for the first time in solution.

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

    E-print Network

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

    2013-10-17

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

  11. 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 dehydration of ions in voltage-gated carbon nanopores.

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

    SciTech Connect

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

    2013-11-07

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

  13. 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

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

    NASA Astrophysics Data System (ADS)

    Gerya, Taras

    2014-05-01

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

  15. Electron transfer processes in collisions of highly charged energetic (0. 1 to 1. 0 MeV/nucleon) ions with helium atoms

    SciTech Connect

    Datz, S.; Hippler, R.; Andersen, L.H.; Dittner, P.F.; Knudsen, H.; Krause, H.F.; Miller, P.D.; Pepmiller, P.L.; Rosseel, T.; Stolterfoht, N.

    1987-01-01

    We have investigated charge transfer in collisions of energetic (0.1 - 1 MeV/nucleon) highly charged ions with helium atoms with the principal aim clarifying the nature of two-electron processes. The sensitivity of partial charge-changing cross sections (i.e., single- and double-charge transfer, transfer ionization (TI), and single and double ionization) to core configuration and scaling rules for one- and two-electron processes were investigated with iodine ions (q = 5+ ..-->.. 26+) and uranium ions (q = 17+ ..-->.. 44+) using an ion-charge state, recoil-ion coincidence method. Using zero-degree electron spectroscopy in coincidence with charge transfer, we found that at the higher energies, as in the case of 0.1 MeV/nucleon ions previously reported, TI involves the transfer of two electrons to a higher correlated state followed by loss of one electron to the continuum. In addition, we observe very high Rydberg electrons in coincidence with TI, implying a possible up-down correlation in the pair transfer. In addition, we made measurements of VUV photons emitted at the collision in coincidence with He/sup +/ and He/sup 2 +/ recoils. The results show that TI leads to capture into lower n states than single-charge transfer. 15 refs., 10 figs.

  16. From cloud crash to star birth: star formation in cloud collisions

    NASA Astrophysics Data System (ADS)

    Shima, Kazuhiro; Tasker, Elizabeth; Habe, Asao

    2015-08-01

    Much speculation surrounds the role of collisions between giant molecular clouds (GMCs) in the galactic star formation rate.Once thought to be uncommon occurrences, observations and simulation now suggestthese could explain the formation of our most massive stars and super star clusters.To explore the result of such interactions, we simulated idealised GMC collisions with star formation and radiative feedback processes.Our results suggest that the star population formed has a stellar mass function index of -0.1 (compared with -1.4 for the non-collisional population),in good agreement with the observations of the assumed cloud collision case, NGC6334 (Munoz et al. 2007).Radiative feedback has a relatively modest dynamical effect on the collisional gas distribution,but increases the star formation rate post collision as the expanding HII bubbles trigger a subsequent stellar population.

  17. Rotational state-changing cold collisions of hydroxyl ions with helium

    E-print Network

    Hauser, Daniel; Carelli, Fabio; Spieler, Steffen; Lakhmanskaya, Olga; Endres, Eric S; Kumar, Sunil S; Gianturco, Franco; Wester, Roland

    2015-01-01

    Cold molecules are important for many applications, from fundamental precision measurements, quantum information processing, quantum-controlled chemistry, to understanding the cold interstellar medium. Molecular ions are known to be cooled efficiently in sympathetic collisions with cold atoms or ions. However, little knowledge is available on the elementary cooling steps, because the determination of quantum state-to-state collision rates at low temperature is prohibitively challenging for both experiment and theory. Here we present a method to manipulate molecular quantum states by non-resonant photodetachment. Based on this we provide absolute quantum scattering rate coefficients under full quantum state control for the rotationally inelastic collision of hydroxyl anions with helium. Experiment and quantum scattering theory show excellent agreement without adjustable parameters. Very similar rate coefficients are obtained for two different isotopes, which is linked to several quantum scattering resonances a...

  18. 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...

  19. 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…

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

    NASA Astrophysics Data System (ADS)

    Boggavarapu, Sajiv

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

  1. Theory of atomic collisions at ultracold temperatures

    SciTech Connect

    Julienne, P.S.; Heather, R. ); Vigue, J. Laboratoire Associe au Centre National de la Recherche Scientifique et a l'Universite Pierre et Marie Curie )

    1991-08-05

    This paper outlines key problems in the theory of atomic collisions at ultracold temperatures. Features associated with the unusual energy time and distance scales encountered in ultracold collisions are described. The molecular physics of excited plus ground state alkali dimers is examined. A quasistatic model is developed to describe collision rates between normal and ultracold temperatures. Mechanisms are proposed for the very different associative ionization rates observed in an optical trap and in optical molasses. (AIP)

  2. Late Cretaceous-Miocene diachronous onset of back thrusting along the South Caribbean deformed belt and its importance for understanding processes of arc collision and crustal growth

    NASA Astrophysics Data System (ADS)

    Kroehler, Margaret E.; Mann, Paul; Escalona, Alejandro; Christeson, Gail. L.

    2011-12-01

    The Venezuelan basin is obliquely subducted to the east-southeast beneath the continental South American plate at the east-west-trending South Caribbean deformed belt (SCDB), a 50-100-km-wide wedge of accreted sedimentary rocks derived both from offscraping of the 0.5 to 1 km-thick sedimentary cover of the subducting Venezuelan basin and from incorporation of clastic sediments derived from the continental margin of South America. In this paper we describe the structure and sequence stratigraphy of five Late Cretaceous to recent sedimentary sequences overlying a 230,000 km2 area of the southern Venezuelan basin and Beata Ridge. The data set includes 5900 km of 2D seismic reflection data that are tied to lithologic and age data taken from DSDP sites 146/149 and 150 in the central part of the Venezuelan basin. We use observed patterns of wedging in mapped and dated sedimentary sequences adjacent to the SCDB to determine the age of the diachronous west-to-east initiation of thrusting and subduction at the SCDB. The onset of subduction in the SCDB corresponds with the cessation of thrusting from west to east along the zone of collision between the intraoceanic Caribbean arc and the South American continent. This correlation in the age of deformation indicates that collision between the Caribbean arc and the South American continent led to subduction polarity reversal, a process that is commonly observed at various stages of tectonic evolution in other areas of active, arc-continent collision including Japan and Sunda.

  3. Molecular Beam Collisions with a Magnetically Trapped Target Brian C. Sawyer, Benjamin K. Stuhl, Dajun Wang, Mark Yeo, and Jun Ye

    E-print Network

    Jin, Deborah

    at a density of $106 cmÀ3 and temperature of 70 mK. Collision studies between the trapped OH sample pairs [11,12]. Most of these mole- cules are in excited rovibrational states, permitting ultra- cold or Stark decel- eration, but at temperatures typically in the range of 10 mK to 1 K. For example, buffer

  4. ATOMIC AND MOLECULAR PHYSICS: Theoretical Investigation on Excitation, Ionization and Capture in H(1s, 2s) + H(1s, 2s) Collisions

    NASA Astrophysics Data System (ADS)

    Chen, Lan-Fang; Zhu, Xiao-Long; Ma, Xin-Wen; Liu, Ling; He, Bin; Wang, Jian-Guo; Ratko, Janev

    2008-08-01

    Cross sections of electron-loss in H(ls)+ H(ls) collisions and total collisional destruction of H(2s) in H(ls) + H(2s) collisions are calculated by four-body classical-trajectory Monte Carlo (CTMC) method and compared with previous theoretical and experimental data over the energy range of 4-100 keV. For the former a good agreement is obtained within different four-body CTMC calculations, and for the incident energy Ep > 10keV, comparison with the experimental data shows a better agreement than the results calculated by the impact parameter approximation. For the latter, our theory predicts the correct experimental behaviour, and the discrepancies between our results and experimental ones are less than 30%. Based on the successive comparison with experiments, the cross sections for excitation to H(2p), single- and double-ionization and H- formation in H(2s)+H(2s) collisions are calculated in the energy range of 4-100keV for the first time, and compared with those in H(ls)+H(ls) and H(ls)+H(2s) collisions.

  5. Association between Higher Order Visual Processing Abilities and a History of Motor Vehicle Collision Involvement by Drivers Ages 70 and Over

    PubMed Central

    Friedman, Carly; McGwin, Gerald; Ball, Karlene K.; Owsley, Cynthia

    2013-01-01

    Purpose. To examine in a population-based sample of 2000 drivers aged 70 years and older, the independent association between higher order visual processing impairment and motor vehicle collision (MVC) rate during the prior 5 years. Methods. Three higher order visual processing screening tests were administered since previous research found associations between impaired performance on these screens and MVC involvement. They included an estimate of visual processing speed under divided attention conditions (useful field of view [UFOV] subset 2); Trails B, a paper and pencil test of visual processing speed also involving problem solving, executive function, and working memory; and the visual closure subtest of the Motor Free Visual Perception Test (MVPT) examining the ability to recognize objects only partially visible. Potentially confounding variables were also assessed including demographics, general cognitive status, visual acuity, and contrast sensitivity. MVC involvement was determined by accident reports from the Alabama Department of Public Safety, and driving exposure was estimated from the Driving Habits Questionnaire. Results. MVC rates (for at fault and all MVCs) were significantly higher for those older drivers with impairments in any of the three visual processing screening tests. After adjustment for potentially confounding influences, the association between MVC rate and Trails B remained significant, whereas the association with MVPT and UFOV did not. Conclusions. This population-based study of drivers aged 70 years and older suggests that a paper and pencil test assessing higher order visual processing skills is independently associated with a recent history of MVC involvement. PMID:23307969

  6. 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. PMID:21243466

  7. Morphological and molecular processes of polyp formation in Apc(delta716) knockout mice.

    PubMed

    Oshima, H; Oshima, M; Kobayashi, M; Tsutsumi, M; Taketo, M M

    1997-05-01

    Mutations in the human adenomatous polyposis coli (APC) gene are responsible for not only familial adenomatous polyposis but also many sporadic cancers of the digestive tract. Using homologous recombination in embryonic stem cells, we recently constructed Apc gene knockout mice that contained a truncation mutation at codon 716 (Apc(delta716)). The heterozygous mice developed numerous intestinal polyps. All microadenomas dissected from nascent polyps had already lost the wild-type allele, indicating the loss of heterozygosity (M. Oshima et al., Proc. Natl. Acad. Sci. USA, 92: 4482-4486, 1995). We also demonstrated that cyclooxygenase 2 is induced in the polyps at an early stage and plays a key role in polyp development (M. Oshima et al., Cell 87: 803-809, 1996). We have analyzed the process of polyp development in these mice both at morphological and molecular levels. A small intestinal microadenoma is initiated as an outpocketing pouch in a single crypt and develops into the inner (lacteal) side of a neighboring villus forming a double-layer nascent polyp. The microadenoma then enlarges and gets folded inside the villus. When it fills the intravillous space, it expands downward and extends into adjoining villi, rather than rupturing into the intestinal lumen. During this course of development, the basement membrane remains intact, and the labeling index of the microadenoma cells is similar to that of the normal crypt epithelium. As in the crypt cells, neither transforming growth factor beta1 nor its receptor type II is expressed in the microadenoma cells. No hot spot mutations in the K-ras gene are found in the microadenoma tissue during these early stages of polyp development. Essentially, the same results have been obtained for the colonic polyps as well. These results suggest that early adenomas in the Apc(delta716) polyps are very similar to the normal proliferating cells of the crypt except for the lack of directed migration along the crypt-villus axis. PMID:9135000

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

    PubMed Central

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

    1996-01-01

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

  10. Molecular Subtyping and Tracking of Listeria monocytogenes in Latin-Style Fresh-Cheese Processing Plants.

    PubMed

    Kabuki, D Y; Kuaye, A Y; Wiedmann, M; Boor, K J

    2004-09-01

    Latin-style fresh cheeses, which have been linked to at least 2 human listeriosis outbreaks in the United States, are considered to be high-risk foods for Listeria monocytogenes contamination. We evaluated L. monocytogenes contamination patterns in 3 Latin-style fresh-cheese processing plants to gain a better understanding of L. monocytogenes contamination sources in the manufacture of these cheeses. Over a 6-mo period, 246 environmental samples were collected and analyzed for L. monocytogenes using both the Food and Drug Administration (FDA) method and the Biosynth L. monocytogenes detection system (LMDS). Finished cheese samples from the same plants (n = 111) were also analyzed by the FDA method, which was modified to include L. monocytogenes plating medium (LMPM) and the L. monocytogenes confirmatory plating medium (LMCM) used in the LMDS method. Listeria monocytogenes was detected in 6.3% of cheese and 11.0% of environmental samples. Crates, drains, and floor samples showed the highest contamination rates, with 55.6, 30.0, and 20.6% L. monocytogenes positive samples, respectively. Finished products and food contact surfaces were positive in only one plant. The FDA method showed a higher sensitivity than the LMDS method for detection of L. monocytogenes from environmental samples. The addition of LMPM and LMCM media did not further enhance the performance of the FDA method for L. monocytogenes detection from finished products. Molecular subtyping (PCR-based allelic analysis of the virulence genes actA and hly and automated ribotyping) was used to track contamination patterns. Ribotype DUP-1044A, which had previously been linked to a 1998 multistate human listeriosis outbreak in the United States, was the most commonly identified subtype (20/36 isolates) and was isolated from 2 plants. This ribotype was persistent and widespread in one factory, where it was also responsible for the contamination of finished products. We hypothesize that this ribotype may represent a clonal group with a specific ability to persist in food processing environments. While previous listeriosis outbreaks were linked to Latin-style fresh cheeses made from unpasteurized milk, the presence of this organism in pasteurized cheese products illustrates that persistent environmental contamination also represents an important source of finished product contamination. PMID:15375038

  11. Nonadiabatic approach for resonant molecular multiphoton absorption processes in intense infrared laser fields

    E-print Network

    Ho, Tak-San; Chu, Shih-I

    1983-07-14

    A nonperturbative approach for efficient and accurate treatment of the molecular multiphoton absorption (MPA) quantum dynamics in intense infrared (IR) laser fields is presented. The approach is based on the adiabatic separation of the fast...

  12. 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

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

    SciTech Connect

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

    2011-03-21

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

  14. Vibrational energy transfer in shocked molecular crystals.

    PubMed

    Hooper, Joe

    2010-01-01

    We consider the process of establishing thermal equilibrium behind an ideal shock front in molecular crystals and its possible role in initiating chemical reaction at high shock pressures. A new theory of equilibration via multiphonon energy transfer is developed to treat the scattering of shock-induced phonons into internal molecular vibrations. Simple analytic forms are derived for the change in this energy transfer at different Hugoniot end states following shock compression. The total time required for thermal equilibration is found to be an order of magnitude or faster than proposed in previous work; in materials representative of explosive molecular crystals, equilibration is predicted to occur within a few picoseconds following the passage of an ideal shock wave. Recent molecular dynamics calculations are consistent with these time scales. The possibility of defect-induced temperature localization due purely to nonequilibrium phonon processes is studied by means of a simple model of the strain field around an inhomogeneity. The specific case of immobile straight dislocations is studied, and a region of enhanced energy transfer on the order of 5 nm is found. Due to the rapid establishment of thermal equilibrium, these regions are unrelated to the shock sensitivity of a material but may allow temperature localization at high shock pressures. Results also suggest that if any decomposition due to molecular collisions is occurring within the shock front itself, these collisions are not enhanced by any nonequilibrium thermal state. PMID:20078172

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

    NASA Astrophysics Data System (ADS)

    Vagt, Nicole; Braun, Markus

    With the ability to sense gravity plants possess a powerful tool to adapt to a great variety of environmental conditions and to respond to environmental changes in a most beneficial way. Gravity is the only constant factor that provides organisms with reliable information for their orientation since billions of years. Any deviation of the genetically determined set-point angle of the plants organs from the vector of gravity is sensed by specialized cells, the statocytes of roots and shoots in higher plants. Dense particles, so-called statoliths, sediment in the direction of gravity and activate membrane-bound gravireceptors. A physiological signalling-cascade is initiated that eventually results in the gravitropic curvature response, namely, the readjust-ment of the growth direction. Experiments under microgravity conditions have significantly contributed to our understanding of plant gravity-sensing and gravitropic reorientation. For a gravity-sensing lower plant cell type, the rhizoid of the green alga Chara, and for statocytes of higher plant roots, it was shown that the interactions between statoliths and the actomyosin system consisting of the actin cytoskeleton and motor proteins (myosins) are the basis for highly efficient gravity-sensing processes. In Chara rhizoids, the actomyosin represents a guid-ing system that directs sedimenting statoliths to a specific graviperception site. Parabolic flight experiments aboard the airbus A300 Zero-G have provided evidence that lower and higher plant cells use principally the same statolith-mediated gravireceptor-activation mechanism. Graviper-ception is not dependent on mechanical pressure mediated through the weight of the sedimented statoliths, but on direct interactions between the statoliths's surface and yet unknown gravire-ceptor molecules. In contrast to Chara rhizoids, in the gravity-sensing cells of higher plants, the actin cytoskeleton is not essentially involved in the early phases of gravity sensing. Dis-rupting the actomyosin system did not impair the sedimentation of statoliths and did not prevent the activation of gravireceptors. However, experiments in microgravity and inhibitor experiments have demonstrated that the actomyosin system optimizes the statolith-receptor interactions by keeping the sedimented statoliths in motion causing a consistent activation of different gravireceptor molecules. Thereby, a triggered gravitropic signal is created which is the basis for a highly sensitive control and readjustment mechanism. In addition, the results of recent parabolic flight studies on the effects of altered gravity conditions on the gene expres-sion pattern of Arabidopsis seedlings support these findings and provide new insight into the molecular basis of the plants response to different acceleration conditions. The work was financially supported by DLR on behalf of Bundesministerium für Wirtschaft und Technologie (50WB0815).

  16. Excited states structure and processes: Understanding organic light-emitting diodes at the molecular level

    NASA Astrophysics Data System (ADS)

    Shuai, Zhigang; Peng, Qian

    2014-04-01

    Photo- or electro-excited states in polyatomic molecules, aggregates, and conjugated polymers are at the center of organic light-emitting diodes (OLEDs). These can decay radiatively or non-radiatively, determining the luminescence quantum efficiency of molecular materials. According to Kasha’s rule, light-emission is dictated by the lowest-lying excited state. For conjugated polymers, the electron correlation effect can lead the lowest-lying excited state to the even-parity 2Ag state which is non-emissive. To understand the nature of the low-lying excited state structure, we developed the density matrix renormalization group (DMRG) theory and its symmetrization scheme for quantum chemistry applied to calculate the excited states structure. We found there are three types of 1Bu/2Ag crossover behaviors: with electron correlation strength U, with bond length alternation, and with conjugation length. These directly influence the light-emitting property. For the electro-excitation, carriers (electron and hole) are injected independently, forming both singlet and triplet excited bound states with statistically 25% and 75% portions, respectively. We found that the exciton formation rate can depend on spin manifold, and for conjugated polymers, the singlet exciton can have larger formation rate leading to the internal electroluminescence quantum efficiency larger than the 25% spin statistical limit. It is originated from the interchain electron correlation as well as intrachain lattice relaxation. For the dipole allowed emissive state, the radiative decay process via either spontaneous emission or stimulated emission can be computed from electronic structure plus vibronic couplings. The challenging issue lies in the non-radiative decay via non-adiabatic coupling and/or spin-orbit coupling. We developed a unified correlation function formalism for the excited state radiative and non-radiative decay rates. We emphasized the low-frequency mode mixing (Duschinsky rotation) effect on the non-radiative decay. We further combined the non-adiabatic coupling and spin-orbit coupling for the triplet state decay (phosphorescence) quantum efficiency. All the formalisms have been developed analytically, which have been applied to optical spectroscopy, aggregation-induced emission phenomena, and polymer photovoltaic property.

  17. Applications of neural networks to real-time data processing at the Environmental and Molecular Sciences Laboratory (EMSL)

    SciTech Connect

    Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1993-06-01

    Detailed design of the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory (PNL) is nearing completion and construction is scheduled to begin later this year. This facility will assist in the environmental restoration and waste management mission at the Hanford Site. This paper identifies several real-time data processing applications within the EMSL where neural networks can potentially be beneficial. These applications include real-time sensor data acquisition and analysis, spectral analysis, process control, theoretical modeling, and data compression.

  18. Efficient inverted polymer solar cells with thermal-evaporated and solution-processed small molecular electron extraction layer

    NASA Astrophysics Data System (ADS)

    Sun, Fu-Zhou; Shi, Ai-Li; Xu, Zai-Quan; Wei, Huai-Xin; Li, Yan-Qing; Lee, Shuit-Tong; Tang, Jian-Xin

    2013-04-01

    Efficient inverted polymer solar cell is reported upon by integrating with a small molecular 1,3,5-tri(phenyl-2-benzimi-dazolyl)-benzene (TPBi) electron extraction layer (EEL) at low processing temperature with thermal-evaporation and solution-process, resulting in the power conversion efficiencies of 3.70% and 3.47%, respectively. The potential of TPBi as an efficient EEL is associated with its suitable electronic energy level for electron extraction and hole blocking from the active layer to the indium tin oxide cathode.

  19. Process of faceting in nanoparticles of FCC metals: Results of simulation by the molecular-dynamics method

    NASA Astrophysics Data System (ADS)

    Kar'kina, L. E.; Kar'kin, I. N.; Gornostyrev, Yu. N.

    2010-03-01

    The process of formation of facets (faceting) in Ni, Al, and Au nanoparticles has been investigated by the molecular-dynamics method. It has been established that the surface of nanoparticles of fcc metals with attainment of a low-energy habit can be transformed via correlated displacements of atomic groups of the facet in the octahedral plane. It has been shown that such a process is similar to the surface diffusion of atomic n-mers with the activation energy depending on the facet size, and for particles with a diameter d < 3.0 nm the correlated displacement of atomic layers proves to be the dominant mechanism of faceting.

  20. Electrospun fibers from wheat protein: investigation of the interplay between molecular structure and the fluid dynamics of the electrospinning process.

    PubMed

    Woerdeman, Dara L; Ye, Peng; Shenoy, Suresh; Parnas, Richard S; Wnek, Gary E; Trofimova, Olga

    2005-01-01

    In the present work, we demonstrate the ability to electrospin wheat gluten, a polydisperse plant protein polymer that is currently available at roughly 0.50 dollars/lb. A variety of electrospinning experiments were carried out with wheat gluten from two sources, at different solution concentrations, and with native and denatured wheat gluten to illustrate the interplay between protein structure and the fluid dynamics of the electrospinning process. The presence of both cylindrical and flat fibers was observed in the nonwoven mats, which were characterized using both polarized optical microscopy and field emission scanning electron microscopy. Retardance images obtained by polarized optical microscopy exhibited evidence of molecular orientation at the surface of the fibers. We believe that fiber formation by electrospinning is a result of both chain entanglements and the presence of reversible junctions in the protein, in particular, the breaking and re-forming of disulfide bonds that occur via a thiol/disulfide interchange reaction. The presence of the highest molecular weight glutenin polymer chains in the wheat protein appeared to be responsible for the lower threshold concentration for fiber formation, relative to that of a lower molecular weight fraction of wheat protein devoid of the high molecular weight glutenin component. Denaturation of the wheat protein, however, clearly disrupted this delicate balance of properties in the experimental regimes we investigated, as electrospun fibers from the denatured state were not observed. PMID:15762633

  1. 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.

  2. Investigating Students' Ability to Transfer Ideas Learned from Molecular Animations of the Dissolution Process

    ERIC Educational Resources Information Center

    Kelly, Resa M.; Jones, Loretta L.

    2008-01-01

    Animations of the particulate level of matter are widely available for use in chemistry classes and are often the primary means of representing molecular behavior. These animations may also be viewed by individual students using textbook Web sites, although without reinforcement or feedback. It is not known to what extent the material in these…

  3. Teaching the process of molecular phylogeny and systematics: a multi-part inquiry-based exercise.

    PubMed

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

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things. PMID:21123698

  4. Molecular Chaperones of Leishmania: Central Players in Many Stress-Related and -Unrelated Physiological Processes

    PubMed Central

    Requena, Jose M.; Montalvo, Ana M.; Fraga, Jorge

    2015-01-01

    Molecular chaperones are key components in the maintenance of cellular homeostasis and survival, not only during stress but also under optimal growth conditions. Folding of nascent polypeptides is supported by molecular chaperones, which avoid the formation of aggregates by preventing nonspecific interactions and aid, when necessary, the translocation of proteins to their correct intracellular localization. Furthermore, when proteins are damaged, molecular chaperones may also facilitate their refolding or, in the case of irreparable proteins, their removal by the protein degradation machinery of the cell. During their digenetic lifestyle, Leishmania parasites encounter and adapt to harsh environmental conditions, such as nutrient deficiency, hypoxia, oxidative stress, changing pH, and shifts in temperature; all these factors are potential triggers of cellular stress. We summarize here our current knowledge on the main types of molecular chaperones in Leishmania and their functions. Among them, heat shock proteins play important roles in adaptation and survival of this parasite against temperature changes associated with its passage from the poikilothermic insect vector to the warm-blooded vertebrate host. The study of structural features and the function of chaperones in Leishmania biology is providing opportunities (and challenges) for drug discovery and improving of current treatments against leishmaniasis. PMID:26167482

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

    PubMed Central

    Cifuentes, Oscar E.; Carpi, Anthony

    2010-01-01

    Three approaches to molecular phylogenetics are demonstrated to biology students as they explore molecular data from Homo sapiens and four related primates. By analyzing DNA sequences, protein sequences, and chromosomal maps, students are repeatedly challenged to develop hypotheses regarding the ancestry of the five species. Although these exercises were designed to supplement and enhance classroom instruction on phylogeny, cladistics, and systematics in the context of a postsecondary majors-level introductory biology course, the activities themselves require very little prior student exposure to these topics. Thus, they are well suited for students in a wide range of educational levels, including a biology class at the secondary level. In implementing this exercise, we have observed measurable gains, both in student comprehension of molecular phylogeny and in their acceptance of modern evolutionary theory. By engaging students in modern phylogenetic activities, these students better understood how biologists are currently using molecular data to develop a more complete picture of the shared ancestry of all living things. PMID:21123698

  6. Molecular fountain.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

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

  7. Totally asymmetric simple exclusion process simulations of molecular motor transport on random networks with asymmetric exit rates

    NASA Astrophysics Data System (ADS)

    Denisov, D. V.; Miedema, D. M.; Nienhuis, B.; Schall, P.

    2015-11-01

    Using the totally asymmetric simple-exclusion-process and mean-field transport theory, we investigate the transport in closed random networks with simple crossing topology—two incoming, two outgoing segments, as a model for molecular motor motion along biopolymer networks. Inspired by in vitro observation of molecular motor motion, we model the motor behavior at the intersections by introducing different exit rates for the two outgoing segments. Our simulations of this simple network reveal surprisingly rich behavior of the transport current with respect to the global density and exit rate ratio. For asymmetric exit rates, we find a broad current plateau at intermediate motor densities resulting from the competition of two subnetwork populations. This current plateau leads to stabilization of transport properties within such networks.

  8. Escherichia coli ?-galactosidase inhibitors through modifications at the aglyconic moiety: experimental evidence of conformational distortion in the molecular recognition process.

    PubMed

    Calle, Luis; Roldós, Virginia; Cañada, F Javier; Uhrig, María Laura; Cagnoni, Alejandro J; Manzano, Verónica E; Varela, Oscar; Jiménez-Barbero, Jesus

    2013-03-25

    Herein, we describe the use of thioglycosides as glycosidase inhibitors by employing novel modifications at the reducing end of these glycomimetics. The inhibitors display a basic galactopyranosyl unit (1?4)-bonded to a 3-deoxy-4-thiopentopyranose moiety. The molecular basis of the observed inhibition has been studied by using a combination of NMR spectroscopy and molecular modeling techniques. It is demonstrated that these molecules are not recognized by Escherichia coli ?-galactosidase in their ground-state conformation, with a conformational selection process taking place. In fact, the observed conformational distortion depends on the chemical nature of the compounds and results from the rotation around the glycosidic linkage (variation of ? or ?) or from the deformation of the six-membered ring of the pentopyranose. The bound conformations of the ligand are adapted in the enzymatic pocket with a variety of hydrogen-bond, van der Waals, and stacking interactions. PMID:23424005

  9. Molecular surface-free continuum model for electrodiffusion processes Benzhuo Lu a,b,*, J. Andrew McCammon a,b,c,d

    E-print Network

    Lu, Benzhuo

    ; in final form 29 November 2007 Available online 15 December 2007 Abstract Incorporation of van der Waals in molecular computations. In this approach, the van der Waals interactions between biomolecule 0009Molecular surface-free continuum model for electrodiffusion processes Benzhuo Lu a,b,*, J. Andrew

  10. 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 velocities. Using the benchmark system O(D1)+D2 with N2O as the precursor, we demonstrate that the technique is also applicable in a very general sense (i.e., also with a large spread in reactant velocities, products much faster than reactants) and therefore can be used also if such unfortunate conditions cannot be avoided. Since the resulting distribution of velocities in the laboratory frame is not cylindrically symmetric, three dimensional velocity mapping is the method of choice for the detection of the ionized products. For the reconstruction, the distance between the two laser beams is an important parameter. We have measured this distance using the photodissociation of HBr at 193 nm, detecting the H atoms near 243 nm. The collision energy resulting from the 193 nm photodissociation of N2O is 5.2±1.9 kcal/mol. Our results show a preference for backward scattered D atoms with the OH partner fragment in the high vibrational states (v =4-6), in accord with previously published results claiming the growing importance of a linear abstraction mechanism for collision energies higher than 2.4 kcal/mol.

  11. Architecture of a massive parallel processing nano brain operating 100 billion molecular neurons simultaneously

    E-print Network

    Bandyopadhyay, Anirban; Pati, Ranjit

    2008-01-01

    Molecular machines may resolve three distinct bottlenecks of scientific advancement. Nanofactories (Phoenix, 2003) composed of MM may produce atomically perfect products spending negligible amount of energy (Hess, 2004) thus alleviating the energy crisis. Computers made by MM operating thousands of bits at a time may match biological processors mimicking creativity and intelligence (Hall, 2007), thus far considered as the prerogative of nature. State-of-the-art brain surgeries are not yet fatal-less, MMs guided by a nano-brain may execute perfect bloodless surgery (Freitas, 2005). Even though all three bottlenecks converge to a single necessity of nano-brain, futurists and molecular engineers have remained silent on this issue. Our recent invention of 16 bit parallel processor is a first step in this direction (Bandyopadhyay, 2008). However, the device operates inside ultra-high vacuum chamber. For practical application, one needs to design a 3 D standalone architecture. Here, we identify the minimum nano-bra...

  12. Molecular-dynamics Simulation-based Cohesive Zone Representation of Intergranular Fracture Processes in Aluminum

    NASA Technical Reports Server (NTRS)

    Yamakov, Vesselin I.; Saether, Erik; Phillips, Dawn R.; Glaessgen, Edward H.

    2006-01-01

    A traction-displacement relationship that may be embedded into a cohesive zone model for microscale problems of intergranular fracture is extracted from atomistic molecular-dynamics simulations. A molecular-dynamics model for crack propagation under steady-state conditions is developed to analyze intergranular fracture along a flat 99 [1 1 0] symmetric tilt grain boundary in aluminum. Under hydrostatic tensile load, the simulation reveals asymmetric crack propagation in the two opposite directions along the grain boundary. In one direction, the crack propagates in a brittle manner by cleavage with very little or no dislocation emission, and in the other direction, the propagation is ductile through the mechanism of deformation twinning. This behavior is consistent with the Rice criterion for cleavage vs. dislocation blunting transition at the crack tip. The preference for twinning to dislocation slip is in agreement with the predictions of the Tadmor and Hai criterion. A comparison with finite element calculations shows that while the stress field around the brittle crack tip follows the expected elastic solution for the given boundary conditions of the model, the stress field around the twinning crack tip has a strong plastic contribution. Through the definition of a Cohesive-Zone-Volume-Element an atomistic analog to a continuum cohesive zone model element - the results from the molecular-dynamics simulation are recast to obtain an average continuum traction-displacement relationship to represent cohesive zone interaction along a characteristic length of the grain boundary interface for the cases of ductile and brittle decohesion. Keywords: Crack-tip plasticity; Cohesive zone model; Grain boundary decohesion; Intergranular fracture; Molecular-dynamics simulation

  13. Molecular Dynamics Analysis of Elementary Process of Coating by a High-Temperature, High-Speed Droplet

    NASA Astrophysics Data System (ADS)

    Shimizu, Jun; Ohmura, Etsuji; Kobayashi, Yoshifumi; Kiyoshima, Shoichi; Eda, Hiroshi

    Three-dimensional molecular dynamics simulation was conducted to clarify at an atomic level the flattening process of a high-temperature droplet impacting a substrate at high speed. The droplet and the substrate were assumed to consist of pure aluminum, and the Morse potential was postulated between a pair of aluminum atoms. By visualizing the analytical results, the processes of melting and solidification, temperature distribution, deformation velocity, and potential energy of atoms of the droplet were clarified. The following conclusions were obtained: (1) Transfer of the droplet atoms to the horizontal direction in the flattening process increases in proportion to the horizontal distance from the central axis of the droplet. (2) The increase of the flattening ratio of the droplet ends as soon as solidification of the droplet starts from the outside edge of the droplet. This behavior indicates the end of flattening.

  14. Molecular diversity of eukaryotes in municipal wastewater treatment processes as revealed by 18S rRNA gene analysis.

    PubMed

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4-8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes. PMID:25491751

  15. Molecular Diversity of Eukaryotes in Municipal Wastewater Treatment Processes as Revealed by 18S rRNA Gene Analysis

    PubMed Central

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4–8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes. PMID:25491751

  16. Solution-Processed Transistors Using Colloidal Nanocrystals with Composition-Matched Molecular "Solders": Approaching Single Crystal Mobility.

    PubMed

    Jang, Jaeyoung; Dolzhnikov, Dmitriy S; Liu, Wenyong; Nam, Sooji; Shim, Moonsub; Talapin, Dmitri V

    2015-10-14

    Crystalline silicon-based complementary metal-oxide-semiconductor transistors have become a dominant platform for today's electronics. For such devices, expensive and complicated vacuum processes are used in the preparation of active layers. This increases cost and restricts the scope of applications. Here, we demonstrate high-performance solution-processed CdSe nanocrystal (NC) field-effect transistors (FETs) that exhibit very high carrier mobilities (over 400 cm(2)/(V s)). This is comparable to the carrier mobilities of crystalline silicon-based transistors. Furthermore, our NC FETs exhibit high operational stability and MHz switching speeds. These NC FETs are prepared by spin coating colloidal solutions of CdSe NCs capped with molecular solders [Cd2Se3](2-) onto various oxide gate dielectrics followed by thermal annealing. We show that the nature of gate dielectrics plays an important role in soldered CdSe NC FETs. The capacitance of dielectrics and the NC electronic structure near gate dielectric affect the distribution of localized traps and trap filling, determining carrier mobility and operational stability of the NC FETs. We expand the application of the NC soldering process to core-shell NCs consisting of a III-V InAs core and a CdSe shell with composition-matched [Cd2Se3](2-) molecular solders. Soldering CdSe shells forms nanoheterostructured material that combines high electron mobility and near-IR photoresponse. PMID:26280943

  17. Population inversion in a magnetized hydrogen plasma expansion as a consequence of the molecular mutual neutralization process

    SciTech Connect

    Harskamp, W. E. N. van; Brouwer, C. M.; Schram, D. C.; Sanden, M. C. M. van de; Engeln, R.

    2011-03-15

    A weakly magnetized expanding hydrogen plasma, created by a cascaded arc, was investigated using optical emission spectroscopy. The emission of the expanding plasma is dominated by H{sub {alpha}} emission in the first part of the plasma expansion, after which a sharp transition to a blue afterglow is observed. The position of this sharp transition along the expansion axis depends on the magnetic field strength. The blue afterglow emission is associated with population inversion of the electronically excited atomic hydrogen states n=4-6 with respect to n=3. By comparing the measured densities with the densities using an atomic collisional radiative model, we conclude that atomic recombination processes cannot account for the large population densities observed. Therefore, molecular processes must be important for the formation of excited states and for the occurrence of population inversion. This is further corroborated at the transition from red to blue, where a hollow profile of the excited states n=4-6 in the radial direction is observed. This hollow profile is explained by the molecular mutual neutralization process of H{sub 2}{sup +} with H{sup -}, which has a maximum production for excited atomic hydrogen 1-2 cm outside the plasma center.

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

    SciTech Connect

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

    2012-07-15

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

  19. Beyond the Floquet theorem: generalized Floquet formalisms and quasienergy methods for atomic and molecular multiphoton processes in intense laser fields

    NASA Astrophysics Data System (ADS)

    Chu, Shih-I.; Telnov, Dmitry A.

    2004-02-01

    The advancement of high-power and short-pulse laser technology in the past two decades has generated considerable interest in the study of multiphoton and very high-order nonlinear optical processes of atomic and molecular systems in intense and superintense laser fields, leading to the discovery of a host of novel strong-field phenomena which cannot be understood by the conventional perturbation theory. The Floquet theorem and the time-independent Floquet Hamiltonian method are powerful theoretical framework for the study of bound-bound multiphoton transitions driven by periodically time-dependent fields. However, there are a number of significant strong-field processes cannot be directly treated by the conventional Floquet methods. In this review article, we discuss several recent developments of generalized Floquet theorems, formalisms, and quasienergy methods, beyond the conventional Floquet theorem, for accurate nonperturbative treatment of a broad range of strong-field atomic and molecular processes and phenomena of current interests. Topics covered include (a) artificial intelligence (AI)-most-probable-path approach (MPPA) for effective treatment of ultralarge Floquet matrix problem; (b) non-Hermitian Floquet formalisms and complex quasienergy methods for nonperturbative treatment of bound-free and free-free processes such as multiphoton ionization (MPI) and above-threshold ionization (ATI) of atoms and molecules, multiphoton dissociation (MPD) and above-threshold dissociation (ATD) of molecules, chemical bond softening and hardening, charge-resonance enhanced ionization (CREI) of molecular ions, and multiple high-order harmonic generation (HHG), etc.; (c) many-mode Floquet theorem (MMFT) for exact treatment of multiphoton processes in multi-color laser fields with nonperiodic time-dependent Hamiltonian; (d) Floquet-Liouville supermatrix (FLSM) formalism for exact nonperturbative treatment of time-dependent Liouville equation (allowing for relaxations and dephasing mechanisms) and high-order nonlinear optical processes (such as intensity-dependent nonlinear optical susceptibilities and multiphoton resonance fluorescence, etc.); (e) generalized Floquet approaches for the treatment of nonadiabatic and complex geometric phases involving multiphoton transitions; (f) generalized Floquet techniques for the treatment of multiphoton processes in intense laser pulse fields with nonperiodic time-dependent Hamiltonians; (g) Floquet formulations of time-dependent density functional theory (DFT) and time-dependent current DFT for nonperturbative treatment of multiphoton processes of many-electron quantum systems in periodic or polychromatic ( quasiperiodic) laser fields. For each generalized Floquet approach, we present also the corresponding development of new computational techniques for facilitating the study of strong-field processes and phenomena. The advancement of these generalized Floquet formalisms and quasienergy methods provides powerful new theoretical frameworks and accurate computational methods for nonperturbative and ab initio treatment of a wide range of interesting and challenging laser-induced chemical and physical processes and insightful exploration of strong-field atomic and molecular physics.

  20. Identification of light absorbing oligomers from glyoxal and methylglyoxal aqueous processing: a comparative study at the molecular level

    NASA Astrophysics Data System (ADS)

    Finessi, Emanuela; Hamilton, Jacqueline; Rickard, Andrew; Baeza-Romero, Maria; Healy, Robert; Peppe, Salvatore; Adams, Tom; Daniels, Mark; Ball, Stephen; Goodall, Iain; Monks, Paul; Borras, Esther; Munoz, Amalia

    2014-05-01

    Numerous studies point to the reactive uptake of gaseous low molecular weight carbonyls onto atmospheric waters (clouds/fog droplets and wet aerosols) as an important SOA formation route not yet included in current models. However, the evaluation of these processes is challenging because water provides a medium for a complex array of reactions to take place such as self-oligomerization, aldol condensation and Maillard-type browning reactions in the presence of ammonium salts. In addition to adding to SOA mass, aqueous chemistry products have been shown to include light absorbing, surface-active and high molecular weight oligomeric species, and can therefore affect climatically relevant aerosol properties such as light absorption and hygroscopicity. Glyoxal (GLY) and methylglyoxal (MGLY) are the gaseous carbonyls that have perhaps received the most attention to date owing to their ubiquity, abundance and reactivity in water, with the majority of studies focussing on bulk physical properties. However, very little is known at the molecular level, in particular for MGLY, and the relative potential of these species as aqueous SOA precursors in ambient air is still unclear. We have conducted experiments with both laboratory solutions and chamber-generated particles to simulate the aqueous processing of GLY and MGLY with ammonium sulphate (AS) under typical atmospheric conditions and investigated their respective aging products. Both high performance liquid chromatography coupled with UV-Vis detection and ion trap mass spectrometry (HPLC-DAD-MSn) and high resolution mass spectrometry (FTICRMS) have been used for molecular identification purposes. Comprehensive gas chromatography with nitrogen chemiluminescence detection (GCxGC-NCD) has been applied for the first time to these systems, revealing a surprisingly high number of nitrogen-containing organics (ONs), with a large extent of polarities. GCxGC-NCD proved to be a valuable tool to determine overall amount and rates of formation of the light absorbing species. Data obtained from laboratory solutions were merged with those from SOA generated in chamber experiments conducted at the European PhotoReactor (EUPHORE) from the uptake of gas-phase GLY and MGLY onto AS seeds. While in general the results confirm previous studies in ranking MGLY as more effective than GLY in brown carbon formation, the link between overall optical properties and the identified molecular species is reported here for the first time for both systems.

  1. ATOMIC AND MOLECULAR PHYSICS: Interference Angle on Quantum Rotational Energy Transfer in Na + Na2 (A1 ?+u, v = 8 ~ b3?0u, 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 ?+u, v = 8 ~ b3?0u, 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.

  2. 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.

  3. MOLECULAR CHARACTERIZATION OF LISTERIA MONOCYTOGENES ISOLATED FROM A POULTRY FURTHER PROCESSING FACILITY AND FULLY COOKED PRODUCT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was undertaken to explore environmental sources of L. monocytogenes in a commercial chicken further processing facility and to compare those isolates found to others detected on fully cooked product. A survey was conducted in the processing facility whereby forty environmental sites repr...

  4. Molecular Characterization and Serotyping of Salmonella Isolated from the Shell Egg Processing Environment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ABSTRACT BODY: Introduction: Salmonellosis may be contracted by the consumption of raw or undercooked eggs. In order to develop effective sanitation practices it is helpful to understand the location of Salmonella reservoirs in processing environments. Shell egg processing reservoirs for Salmonella...

  5. Molecular dynamics study on the mechanism of AFM-based nanoscratching process with water-layer lubrication

    NASA Astrophysics Data System (ADS)

    Ren, Jiaqi; Zhao, Jinsheng; Dong, Zeguang; Liu, Pinkuan

    2015-08-01

    The atomic force microscopy (AFM) based direct nanoscratching has been thoroughly studied but the mechanism of nanoscratching with water-layer lubrication is yet to be well understood. In current study, three-dimensional molecular dynamics (MD) simulations are conducted to evaluate the effects of the water-layer lubrication on the AFM-based nanoscratching process on monocrystalline copper. Comparisons of workpiece deformation, scratching forces, and friction coefficients are made between the water-lubricated and dry scratching under various thickness of water layer, scratching depth and scratching velocity. Simulation results reveal that the water layer has positive impact on the surface quality and significant influence on the scratching forces (normal forces and tangential forces). The friction coefficients of the tip in water-lubricated nanoscratching are significantly bigger than those in the dry process. Our simulation results shed lights on a promising AFM-based nanofabrication method, which can assist to get nanoscale surface morphologies with higher quality than traditional approaches.

  6. Molecular Dynamics Simulation of Flattening Process of a High-Temperature, High-Speed Droplet—Influence of Impact Parameters

    NASA Astrophysics Data System (ADS)

    Shimizu, J.; Ohmura, E.; Kobayashi, Y.; Kiyoshima, S.; Eda, H.

    2007-12-01

    Three-dimensional molecular dynamics simulation was conducted to clarify at an atomic level the flattening process of a high-temperature droplet impacting a substrate at high speed. The droplet and the substrate were assumed to consist of pure aluminum, and the Morse potential was postulated between a pair of aluminum atoms. In this report, the influence of the impact parameters such as the droplet velocity and the droplet diameter on flattening behavior were analyzed. As a result, the following representative conclusions were obtained: (a) the flattening ratio increases in proportion to the droplet velocity and the droplet diameter; (b) the flattening ratio for nanosized droplet can be reorganized by the same dimensionless parameters of the proper physical properties, such as the viscosity and the surface tension, as those used in the macroscopic flattening process.

  7. Averaging and large deviation principles for fully-coupled piecewise deterministic Markov processes and applications to molecular motors

    E-print Network

    A. Faggionato; D. Gabrielli; M. Ribezzi Crivellari

    2008-09-16

    We consider Piecewise Deterministic Markov Processes (PDMPs) with a finite set of discrete states. In the regime of fast jumps between discrete states, we prove a law of large number and a large deviation principle. In the regime of fast and slow jumps, we analyze a coarse-grained process associated to the original one and prove its convergence to a new PDMP with effective force fields and jump rates. In all the above cases, the continuous variables evolve slowly according to ODEs. Finally, we discuss some applications related to the mechanochemical cycle of macromolecules, including strained--dependent power--stroke molecular motors. Our analysis covers the case of fully--coupled slow and fast motions.

  8. SKA studies of nearby galaxies: star-formation, accretion processes and molecular gas across all environments

    NASA Astrophysics Data System (ADS)

    Beswick, R.; Brinks, E.; Perez-Torres, M.; Richards, A. M. S.; Aalto, S.; Alberdi, A.; Argo, M. K.; van Bemmel, I.; Conway, J. E.; Dickinson, C.; Fenech, D.; Gray, M. D.; Kloeckner, H. R.; Murphy, E.; Muxlow, T. W. B.; Peel, M. W.; Rushton, A.; Schinnerer, E.

    The SKA will be a transformational instrument in the study of our local Universe. In particular, by virtue of its high sensitivity (both to point sources and diffuse low surface brightness emission), angular resolution and the frequency ranges covered, the SKA will undertake a very wide range of astrophysical research in the field of nearby galaxies. By surveying vast numbers of nearby galaxies of all types with $\\mu$Jy sensitivity and sub-arcsecond angular resolutions at radio wavelengths, the SKA will provide the cornerstone of our understanding of star-formation and accretion activity in the local Universe. In this chapter we outline the key continuum and molecular line science areas where the SKA, both during phase-1 and when it becomes the full SKA, will have a significant scientific impact.

  9. Pyrite oxidation and reduction - Molecular orbital theory considerations. [for geochemical redox processes

    NASA Technical Reports Server (NTRS)

    Luther, George W., III

    1987-01-01

    In this paper, molecular orbital theory is used to explain a heterogeneous reaction mechanism for both pyrite oxidation and reduction. The mechanism demonstrates that the oxidation of FeS2 by Fe(3+) may occur as a result of three important criteria: (1) the presence of a suitable oxidant having a vacant orbital (in case of liquid phase) or site (solid phase) to bind to the FeS2 via sulfur; (2) the initial formation of a persulfido (disulfide) bridge between FeS2 and the oxidant, and (3) an electron transfer from a pi(asterisk) orbital in S2(2-) to a pi or pi(asterisk) orbital of the oxidant.

  10. Importance of pore length and geometry in the adsorption/desorption process: a molecular simulation study

    E-print Network

    M. A. Balderas Altamirano; S. Cordero; R. López-Esparza; E. Pérez; A. Gama Goicochea

    2015-07-05

    Discrete potentials can describe properly the liquid vapor boundary that is necessary to model the adsorption of gas molecules in mesoporous systems with computer simulations. Although there are some works in this subject, the simulations are still highly time - consuming. Here we show that an efficient alternative is to use the three - dimensional Ising model, which allows one to model large systems, with geometries as complex as required that accurately represent the liquid vapor boundary. In particular, we report molecular simulations of cylindrical pores of two different geometry, using a discrete potential. The effect of the length of the pore in the hysteresis loop for a finite pore and infinite one is studied in detail. Lastly, we compare our predictions with experimental results and find excellent agreement between the area of the hysteresis loop predicted for the finite pore and that found in adsorption/desorption experiments.

  11. Electronic processes in fast thermite chemical reactions: A first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya

    2008-06-01

    Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7±0.9ps , and bond-overlap population analysis has been used to calculate reaction rates.

  12. Electronic processes in fast thermite chemical reactions: a first-principles molecular dynamics study.

    PubMed

    Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya

    2008-06-01

    Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7+/-0.9 ps , and bond-overlap population analysis has been used to calculate reaction rates. PMID:18643332

  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. Investigations of the structures and molecular processes in polar Langmuir-Blodgett superlattices

    SciTech Connect

    Walsh, S.P.

    1992-01-01

    The principle focus of this research was to prepare polar ultrathin films using an alternating monolayer adaptation of the traditional Langmuir-Blodgett (LB) technique, and to investigate the role that structure (physical and chemical) plays upon the outward manifestation of this internal polarization: pyroelectricity. A specially designed film trough was prepared such that two separate monolayers could be independently manipulated. Alternating bilayer assemblies were be prepared by translating the deposition substrate above and below the surface of the floating monolayers as needed without disruption of the stability of the Langmuir films. Long chain diacetylenic acid and amine amphiphiles were prepared. The diacetylenic amine compound was thoroughly investigated at the gas-water interface. Common conditions of monolayer stability for the acid/amine amphiphile pairs and the concept of isoelectric deposition were developed. Homogeneous and heterogeneous LB assemblies were prepared. Chemical and structural investigations were performed using a combination of x-ray diffraction and FTIR spectroscopic techniques. The melting temperatures of the unpolymerized structures were dependent on organization and ionization of the individual molecules. Solid state polymerization of the diacetylenic multilayers was found to somewhat disrupt the organization of the assemblies, but to suppress monolayer melting. The pyroelectric response in such structures was molecular, not chemical, in nature with the polarization changing as a result of molecular librations. Electrical characterizations of the assemblies showed the thin films to behave as good dielectrics. Pyroelectric responses of the ionized assemblies containing free counter ions were unexpectedly low. It was felt that the low values were due to either a damping of the librational moments by the presence of the counter ions, or that the mobility of these ions offset the librational dipoles of these polar groups.

  15. Processing Strategies to Inactivate Enteric Viruses in Shellfish: Limitations of Surrogate Viruses and Molecular Methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Noroviruses, hepatitis A and E viruses, sapovirus, astrovirus, rotavirus, Aichi virus, enteric adenoviruses, poliovirus, and other enteroviruses enter shellfish through contaminated seawater or by contamination during handling and processing, resulting in outbreaks ranging from isolated to epidemic....

  16. Study of Higgs boson production and its b-bbar decay in gamma-gamma processes in proton-nucleus collisions at the LHC

    E-print Network

    David d'Enterria; Jean-Philippe Lansberg

    2010-01-11

    We explore for the first time the possibilities to measure an intermediate-mass (mH = 115-140 GeV/c^2) Standard-Model Higgs boson in electromagnetic proton-lead (pPb) interactions at the CERN Large Hadron Collider (LHC) via its b-bbar decay. Using equivalent Weizsaecker-Williams photon fluxes and Higgs effective field theory for the coupling gamma-gamma --> H, we obtain a leading-order cross section of the order of 0.3 pb for exclusive Higgs production in elastic (pPb --> gamma-gamma --> p H Pb) and semielastic (pPb --> gamma-gamma --> Pb H X) processes at sqrt(s) = 8.8 TeV. After applying various kinematics cuts to remove the main backgrounds (gamma-gamma --> b-bbar and misidentified gamma-gamma-->q-qbar events), we find that a Higgs boson with mH = 120 GeV/c^2 could be observed in the b-bbar channel with a 3sigma-significance integrating 300 pb^-1 with an upgraded pA luminosity of 10^31 cm^-2s^-1. We also provide for the first time semielastic Higgs cross sections, along with elastic t-tbar cross sections, for electromagnetic pp, pA and AA collisions at the LHC.

  17. Particle-in-cell/Monte Carlo collision simulation of the ionization process of surface-wave plasma discharges resonantly excited by surface plasmon polaritons

    SciTech Connect

    Chen Zhaoquan; Ye Qiubo; Xia Guangqing; Hong Lingli; Hu Yelin; Zheng Xiaoliang; Li Ping; Zhou Qiyan; Hu Xiwei; Liu Minghai

    2013-03-15

    Although surface-wave plasma (SWP) sources have many industrial applications, the ionization process for SWP discharges is not yet well understood. The resonant excitation of surface plasmon polaritons (SPPs) has recently been proposed to produce SWP efficiently, and this work presents a numerical study of the mechanism to produce SWP sources. Specifically, SWP resonantly excited by SPPs at low pressure (0.25 Torr) are modeled using a two-dimensional in the working space and three-dimensional in the velocity space particle-in-cell with the Monte Carlo collision method. Simulation results are sampled at different time steps, in which the detailed information about the distribution of electrons and electromagnetic fields is obtained. Results show that the mode conversion between surface waves of SPPs and electron plasma waves (EPWs) occurs efficiently at the location where the plasma density is higher than 3.57 Multiplication-Sign 10{sup 17} m{sup -3}. Due to the effect of the locally enhanced electric field of SPPs, the mode conversion between the surface waves of SPPs and EPWs is very strong, which plays a significant role in efficiently heating SWP to the overdense state.

  18. 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

  19. Processive ATP-driven Substrate Disassembly by the N-Ethylmaleimide-sensitive Factor (NSF) Molecular Machine*?

    PubMed Central

    Cipriano, Daniel J.; Jung, Jaemyeong; Vivona, Sandro; Fenn, Timothy D.; Brunger, Axel T.; Bryant, Zev

    2013-01-01

    SNARE proteins promote membrane fusion by forming a four-stranded parallel helical bundle that brings the membranes into close proximity. Post-fusion, the complex is disassembled by an AAA+ ATPase called N-ethylmaleimide-sensitive factor (NSF). We present evidence that NSF uses a processive unwinding mechanism to disassemble SNARE proteins. Using a real-time disassembly assay based on fluorescence dequenching, we correlate NSF-driven disassembly rates with the SNARE-activated ATPase activity of NSF. Neuronal SNAREs activate the ATPase rate of NSF by ?26-fold. One SNARE complex takes an average of ?5 s to disassemble in a process that consumes ?50 ATP. Investigations of substrate requirements show that NSF is capable of disassembling a truncated SNARE substrate consisting of only the core SNARE domain, but not an unrelated four-stranded coiled-coil. NSF can also disassemble an engineered double-length SNARE complex, suggesting a processive unwinding mechanism. We further investigated processivity using single-turnover experiments, which show that SNAREs can be unwound in a single encounter with NSF. We propose a processive helicase-like mechanism for NSF in which ?1 residue is unwound for every hydrolyzed ATP molecule. PMID:23775070

  20. GoSynthetic database tool to analyse natural and engineered molecular processes

    PubMed Central

    Liang, Chunguang; Krüger, Beate; Dandekar, Thomas

    2013-01-01

    An essential topic for synthetic biologists is to understand the structure and function of biological processes and involved proteins and plan experiments accordingly. Remarkable progress has been made in recent years towards this goal. However, efforts to collect and present all information on processes and functions are still cumbersome. The database tool GoSynthetic provides a new, simple and fast way to analyse biological processes applying a hierarchical database. Four different search modes are implemented. Furthermore, protein interaction data, cross-links to organism-specific databases (17 organisms including six model organisms and their interactions), COG/KOG, GO and IntAct are warehoused. The built in connection to technical and engineering terms enables a simple switching between biological concepts and concepts from engineering, electronics and synthetic biology. The current version of GoSynthetic covers more than one million processes, proteins, COGs and GOs. It is illustrated by various application examples probing process differences and designing modifications. Database URL: http://gosyn.bioapps.biozentrum.uni-wuerzburg.de. PMID:23813641

  1. Molecular beams in chemistry.

    NASA Technical Reports Server (NTRS)

    Jordan, J. E.; Mason, E. A.; Amdur, I.

    1972-01-01

    The molecular-beam technique is a means for producing isolated atoms or molecules within a narrow range of speed and solid angle. The phenomena studied with molecular beams can be classified as single-particle interactions, many-particle interactions, and two particle-interactions. The results of scattering experiments fall into two categories including collisions that do not result in atomic rearrangements and collisions that do. Experimental methods are discussed, giving attention to low-energy beams, high-energy beams, and intermediate-energy beams. Examples are presented to illustrate the information that can be obtained from elastic, inelastic, and reactive scattering.

  2. 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.

  3. Toward a process-based molecular model of SiC membranes: III. Prediction of transport and separation of binary gaseous mixtures

    E-print Network

    Goddard III, William A.

    Toward a process-based molecular model of SiC membranes: III. Prediction of transport-carbide (SiC) nanopor- ous membranes. By process-based modeling we mean one in which the actual steps hydridopolycarbosilane(HPCS), [SiH2CH2]n, the essential step in the fabrication of SiC nanoporous membranes. In Part II

  4. Root gravitropism: an experimental tool to investigate basic cellular and molecular processes underlying mechanosensing and signal transmission in plants

    NASA Technical Reports Server (NTRS)

    Boonsirichai, K.; Guan, C.; Chen, R.; Masson, P. H.

    2002-01-01

    The ability of plant organs to use gravity as a guide for growth, named gravitropism, has been recognized for over two centuries. This growth response to the environment contributes significantly to the upward growth of shoots and the downward growth of roots commonly observed throughout the plant kingdom. Root gravitropism has received a great deal of attention because there is a physical separation between the primary site for gravity sensing, located in the root cap, and the site of differential growth response, located in the elongation zones (EZs). Hence, this system allows identification and characterization of different phases of gravitropism, including gravity perception, signal transduction, signal transmission, and curvature response. Recent studies support some aspects of an old model for gravity sensing, which postulates that root-cap columellar amyloplasts constitute the susceptors for gravity perception. Such studies have also allowed the identification of several molecules that appear to function as second messengers in gravity signal transduction and of potential signal transducers. Auxin has been implicated as a probable component of the signal that carries the gravitropic information between the gravity-sensing cap and the gravity-responding EZs. This has allowed the identification and characterization of important molecular processes underlying auxin transport and response in plants. New molecular models can be elaborated to explain how the gravity signal transduction pathway might regulate the polarity of auxin transport in roots. Further studies are required to test these models, as well as to study the molecular mechanisms underlying a poorly characterized phase of gravitropism that is independent of an auxin gradient.

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

    Electron-hydrogen scattering in weakly coupled hot-dense plasmas has been investigated using the convergent-close-coupling method. The Yukawa-type Debye-Hückel 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?2s,2p,3s,3p,3d and 2s?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.

  6. Field-based evidence of sedimentary and tectonic processes related to continental collision: the Early Cenozoic basins of Central Eastern Turkey 

    E-print Network

    Booth, Matthew Graham

    2013-07-01

    Turkey is widely accepted to have formed from a collage of microcontinents that rifted from the northern margin of Gondwana and assembled from the Mesozoic to Mid Cenozoic in response to the closure, collision and suturing ...

  7. Probing ice-nucleation processes on the molecular level using second harmonic generation spectroscopy

    NASA Astrophysics Data System (ADS)

    Abdelmonem, A.; Lützenkirchen, J.; Leisner, T.

    2015-08-01

    We present and characterize a novel setup to apply second harmonic generation (SHG) spectroscopy in total internal reflection geometry (TIR) to heterogeneous freezing research. It allows to monitor the evolution of water structuring at solid surfaces at low temperatures prior to heterogeneous ice nucleation. Apart from the possibility of investigating temperature dependence, a major novelty in our setup is the ability of measuring sheet-like samples in TIR geometry in a direct way. As a main experimental result, we find that our method can discriminate between good and poor ice nucleating surfaces. While at the sapphire basal plane, which is known to be a poor ice nucleator, no structural rearrangement of the water molecules is found prior to freezing, the basal plane surface of mica, an analogue to ice active mineral dust surfaces, exhibits a strong change in the nonlinear optical properties at temperatures well above the freezing transition. This is interpreted as a pre-activation, i.e. an increase in the local ordering of the interfacial water which is expected to facilitate the crystallization of ice at the surface. The results are in line with recent predictions by molecular dynamics simulations on a similar system.

  8. Low molecular weight fucoidan ameliorates diabetic nephropathy via inhibiting epithelial-mesenchymal transition and fibrotic processes

    PubMed Central

    Chen, Jihui; Cui, Wentong; Zhang, Quanbin; Jia, Yingli; Sun, Yi; Weng, Lin; luo, Dali; Zhou, Hong; Yang, Baoxue

    2015-01-01

    Diabetic nephropathy (DN) is one of the most serious microvascular complications of diabetes and may lead to end-stage renal disease (ESRD) and chronic renal failure. The aim of this study was to determine whether low-molecular-weight fucoidan (LMWF) can reduce harmful transforming growth factor-? (TGF-?)-mediated renal fibrosis in DN using in vitro and in vivo experimental models. The experimental results showed that LMWF significantly reversed TGF-?1-induced epithelial-mesenchymal transition and dose-dependently inhibited accumulation of extracellular matrix proteins, including connective tissue growth factor and fibronectin. It was found that LMWF significantly reduced blood urea nitrogen and blood creatinine in both type 1 and type 2 diabetic rat models. H&E, PAS and Masson’s trichrome staining of kidney tissue showed LMWF significantly reduced renal interstitial fibrosis. Treatment with LMWF significantly increased E-cadherin expression and reduced ?-SMA, CTGF and fibronectin expression in both type 1 and type 2 diabetic models. LMWF also decreased the phosphorylation of Akt, ERK1/2, p38 and Smad3 in vitro and in vivo. These data suggest that LMWF may protect kidney from dysfunction and fibrogenesis by inhibiting TGF-? pathway and have the potential benefit to slow down the progression of DN. PMID:26550455

  9. Fluorescent Proteins as Biomarkers and Biosensors: Throwing Color Lights on Molecular and Cellular Processes

    PubMed Central

    Stepanenko, Olesya V.; Verkhusha, Vladislav V.; Kuznetsova, Irina M.; Uversky, Vladimir N.; Turoverov, K.K.

    2010-01-01

    Green fluorescent protein (GFP) from jellyfish Aequorea victoria is the most extensively studied and widely used in cell biology protein. GFP-like proteins constitute a fast growing family as several naturally occurring GFP-like proteins have been discovered and enhanced mutants of Aequorea GFP have been created. These mutants differ from wild-type GFP by conformational stability, quantum yield, spectroscopic properties (positions of absorption and fluorescence spectra) and by photochemical properties. GFP-like proteins are very diverse, as they can be not only green, but also blue, orange-red, far-red, cyan, and yellow. They also can have dual-color fluorescence (e.g., green and red) or be non-fluorescent. Some of them possess kindling property, some are photoactivatable, and some are photoswitchable. This review is an attempt to characterize the main color groups of GFP-like proteins, describe their structure and mechanisms of chromophore formation, systemize data on their conformational stability and summarize the main trends of their utilization as markers and biosensors in cell and molecular biology. PMID:18691124

  10. Physiological approaches to understanding molecular actions on dorsolateral prefrontal cortical neurons underlying higher cognitive processing.

    PubMed

    Wang, Min; Arnsten, Amy F T

    2015-11-18

    Revealing how molecular mechanisms influence higher brain circuits in primates will be essential for understanding how genetic insults lead to increased risk of cognitive disorders. Traditionally, modulatory influences on higher cortical circuits have been examined using lesion techniques, where a brain region is depleted of a particular transmitter to determine how its loss impacts cognitive function. For example, depletion of catecholamines or acetylcholine from the dorsolateral prefrontal cortex produces striking deficits in working memory abilities. More directed techniques have utilized direct infusions of drug into a specific cortical site to try to circumvent compensatory changes that are common following transmitter depletion. The effects of drug on neuronal firing patterns are often studied using iontophoresis, where a minute amount of drug is moved into the brain using a tiny electrical current, thus minimizing the fluid flow that generally disrupts neuronal recordings. All of these approaches can be compared to systemic drug administration, which remains a key arena for the development of effective therapeutics for human cognitive disorders. Most recently, viral techniques are being developed to be able to manipulate proteins for which there is no developed pharmacology, and to allow optogenetic manipulations in primate cortex. As the association cortices greatly expand in brain evolution, research in nonhuman primates is particularly important for understanding the modulatory regulation of our highest order cognitive operations. PMID:26646567

  11. 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.

  12. Using the TAP Component of the Antigen-Processing Machinery as a Molecular Adjuvant

    E-print Network

    Vitalis, Timothy Z.; Zhang, Qian-Jin; Alimonti, Judie; Chen, Susan S.; Basha, Genc; Moise, Alexander R.; Tiong, Jacqueline; Tian, Mei Mei; Bok Choi, Kyung; Waterfield, Douglas; Jeffries, Andy; Jefferies, Wilfred A.

    2005-12-30

    surface expression and the cross-presentation mechanism in spleen-derived dendritic cells was augmented by over-expression of TAP. Furthermore, VV-hTAP1,2 increases splenic TAP transport activity and endogenous antigen processing, thus rendering infected...

  13. Odd-even effect in heavy-ion collisions at intermediate energies

    SciTech Connect

    Su Jun; Zhang Fengshou; Bian Baoan

    2011-01-15

    Heavy-ion collisions at intermediate energies are studied by the isospin-dependent quantum molecular dynamics model in the company of the GEMINI model. The isospin-dependent quantum molecular dynamics model is applied to describe the violent stage of the collisions, while the GEMINI model is applied to simulate the decays of the prefragments. The present study mainly focuses on the odd-even effect in the yields of the final fragments. We find that the odd-even effect appears in the deexcitation process of the excited prefragments, and is affected by the excitation energies and the isotope distributions of the prefragments. Both the projectile-isospin-dependent odd-even effect in the region of -4{<=}T{sub Z}{<=}1 and the role of the symmetry energy on the odd-even effect are studied. We find that the odd-even effect depends sensitively on the symmetry energy.

  14. Molecular Mechanism of the Adsorption Process of an Iodide Anion into Liquid-Vapor Interfaces of Water-Methanol Mixtures

    SciTech Connect

    Annapureddy, Harsha V.; Dang, Liem X.

    2012-12-07

    To enhance our understanding of the molecular mechanism of ion adsorption to the interface of mixtures, we systematically carried out a free energy calculations study involving the transport of an iodide anion across the interface of a water-methanol mixture. Many body affects are taken into account to describe the interactions among the species. The surface propensities of I- at interfaces of pure water and methanol are well understood. In contrast, detailed knowledge of the molecular level adsorption process of I- at aqueous mixture interfaces has not been reported. In this paper, we explore how this phenomenon will be affected for mixed solvents with varying compositions of water and methanol. Our potential of mean force study as function of varying compositions indicated that I- adsorption free energies decrease from pure water to pure methanol but not linearly with the concentration of methanol. We analyze the computed density profiles and hydration numbers as a function of concentrations and ion positions with respect to the interface to further explain the observed phenomenon. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences, and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle. The calculations were carried out using computer resources provided by BES.

  15. Molecular Process Producing Oncogene Fusion in Lung Cancer Cells by Illegitimate Repair of DNA Double-Strand Breaks

    PubMed Central

    Seki, Yoshitaka; Mizukami, Tatsuji; Kohno, Takashi

    2015-01-01

    Constitutive activation of oncogenes by fusion to partner genes, caused by chromosome translocation and inversion, is a critical genetic event driving lung carcinogenesis. Fusions of the tyrosine kinase genes ALK (anaplastic lymphoma kinase), ROS1 (c-ros oncogene 1), or RET (rearranged during transfection) occur in 1%–5% of lung adenocarcinomas (LADCs) and their products constitute therapeutic targets for kinase inhibitory drugs. Interestingly, ALK, RET, and ROS1 fusions occur preferentially in LADCs of never- and light-smokers, suggesting that the molecular mechanisms that cause these rearrangements are smoking-independent. In this study, using previously reported next generation LADC genome sequencing data of the breakpoint junction structures of chromosome rearrangements that cause oncogenic fusions in human cancer cells, we employed the structures of breakpoint junctions of ALK, RET, and ROS1 fusions in 41 LADC cases as “traces” to deduce the molecular processes of chromosome rearrangements caused by DNA double-strand breaks (DSBs) and illegitimate joining. We found that gene fusion was produced by illegitimate repair of DSBs at unspecified sites in genomic regions of a few kb through DNA synthesis-dependent or -independent end-joining pathways, according to DSB type. This information will assist in the understanding of how oncogene fusions are generated and which etiological factors trigger them. PMID:26437441

  16. Secondary Ion Mass Spectrometry Imaging of Molecular Distributions in Cultured Neurons and Their Processes: Comparative Analysis of Sample Preparation

    NASA Astrophysics Data System (ADS)

    Tucker, Kevin R.; Li, Zhen; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-11-01

    Neurons often exhibit a complex chemical distribution and topography; therefore, sample preparation protocols that preserve structures ranging from relatively large cell somata to small neurites and growth cones are important factors in secondary ion mass spectrometry (SIMS) imaging studies. Here, SIMS was used to investigate the subcellular localization of lipids and lipophilic species in neurons from Aplysia californica. Using individual neurons cultured on silicon wafers, we compared and optimized several SIMS sampling approaches. After an initial step to remove the high salt culturing media, formaldehyde, paraformaldehyde, and glycerol, and various combinations thereof, were tested for their ability to achieve cell stabilization during and after the removal of extracellular media. These treatments improved the preservation of cellular morphology as visualized with SIMS imaging. For analytes >250 Da, coating the cell surface with a 3.2 nm-thick gold layer increased the ion intensity; multiple analytes previously not observed or observed at low abundance were detected, including intact cholesterol and vitamin E molecular ions. However, once a sample was coated, many of the lower molecular mass (<200 Da) analyte signals were suppressed. The optimum approach depended on the analyte being studied; the approaches evaluated included rinsing with water and cell stabilization with glycerol and 4 % paraformaldehyde. The sample preparation methods described here enhance SIMS imaging of processes of individual cultured neurons over a broad mass range with enhanced image contrast.

  17. Molecular Process Producing Oncogene Fusion in Lung Cancer Cells by Illegitimate Repair of DNA Double-Strand Breaks.

    PubMed

    Seki, Yoshitaka; Mizukami, Tatsuji; Kohno, Takashi

    2015-01-01

    Constitutive activation of oncogenes by fusion to partner genes, caused by chromosome translocation and inversion, is a critical genetic event driving lung carcinogenesis. Fusions of the tyrosine kinase genes ALK (anaplastic lymphoma kinase), ROS1 (c-ros oncogene 1), or RET (rearranged during transfection) occur in 1%-5% of lung adenocarcinomas (LADCs) and their products constitute therapeutic targets for kinase inhibitory drugs. Interestingly, ALK, RET, and ROS1 fusions occur preferentially in LADCs of never- and light-smokers, suggesting that the molecular mechanisms that cause these rearrangements are smoking-independent. In this study, using previously reported next generation LADC genome sequencing data of the breakpoint junction structures of chromosome rearrangements that cause oncogenic fusions in human cancer cells, we employed the structures of breakpoint junctions of ALK, RET, and ROS1 fusions in 41 LADC cases as "traces" to deduce the molecular processes of chromosome rearrangements caused by DNA double-strand breaks (DSBs) and illegitimate joining. We found that gene fusion was produced by illegitimate repair of DSBs at unspecified sites in genomic regions of a few kb through DNA synthesis-dependent or -independent end-joining pathways, according to DSB type. This information will assist in the understanding of how oncogene fusions are generated and which etiological factors trigger them. PMID:26437441

  18. Molecular mechanism of the adsorption process of an iodide anion into liquid-vapor interfaces of water-methanol mixtures

    NASA Astrophysics Data System (ADS)

    Annapureddy, Harsha V. R.; Dang, Liem X.

    2012-12-01

    To enhance our understanding of the molecular mechanism of ion adsorption to the interface of mixtures, we systematically carried out a free energy calculations study involving the transport of an iodide anion across the interface of a water-methanol mixture. Many body affects are taken into account to describe the interactions among the species. The surface propensities of I- at interfaces of pure water and methanol are well understood. In contrast, detailed knowledge of the molecular level adsorption process of I- at aqueous mixture interfaces has not been reported. In this paper, we explore how this phenomenon will be affected for mixed solvents with varying compositions of water and methanol. Our potential of mean force study as function of varying compositions indicated that I- adsorption free energies decrease from pure water to pure methanol but not linearly with the concentration of methanol. We analyze the computed density profiles and hydration numbers as a function of concentrations and ion positions with respect to the interface to further explain the observed phenomenon.

  19. A qualitative inquiry into the effects of visualization on high school chemistry students' learning process of molecular structure

    NASA Astrophysics Data System (ADS)

    Deratzou, Susan

    This research studies the process of high school chemistry students visualizing chemical structures and its role in learning chemical bonding and molecular structure. Minimal research exists with high school chemistry students and more research is necessary (Gabel & Sherwood, 1980; Seddon & Moore, 1986; Seddon, Tariq, & Dos Santos Veiga, 1984). Using visualization tests (Ekstrom, French, Harman, & Dermen, 1990a), a learning style inventory (Brown & Cooper, 1999), and observations through a case study design, this study found visual learners performed better, but needed more practice and training. Statistically, all five pre- and post-test visualization test comparisons were highly significant in the two-tailed t-test (p > .01). The research findings are: (1) Students who tested high in the Visual (Language and/or Numerical) and Tactile Learning Styles (and Social Learning) had an advantage. Students who learned the chemistry concepts more effectively were better at visualizing structures and using molecular models to enhance their knowledge. (2) Students showed improvement in learning after visualization practice. Training in visualization would improve students' visualization abilities and provide them with a way to think about these concepts. (3) Conceptualization of concepts indicated that visualizing ability was critical and that it could be acquired. Support for this finding was provided by pre- and post-Visualization Test data with a highly significant t-test. (4) Various molecular animation programs and websites were found to be effective. (5) Visualization and modeling of structures encompassed both two- and three-dimensional space. The Visualization Test findings suggested that the students performed better with basic rotation of structures as compared to two- and three-dimensional objects. (6) Data from observations suggest that teaching style was an important factor in student learning of molecular structure. (7) Students did learn the chemistry concepts. Based on the Visualization Test results, which showed that most of the students performed better on the post-test, the visualization experience and the abstract nature of the content allowed them to transfer some of their chemical understanding and practice to non-chemical structures. Finally, implications for teaching of chemistry, students learning chemistry, curriculum, and research for the field of chemical education were discussed.

  20. The Sarcomeric M-Region: A Molecular Command Center for Diverse Cellular Processes

    PubMed Central

    Hu, Li-Yen R.; Ackermann, Maegen A.; Kontrogianni-Konstantopoulos, Aikaterini

    2015-01-01

    The sarcomeric M-region anchors thick filaments and withstands the mechanical stress of contractions by deformation, thus enabling distribution of physiological forces along the length of thick filaments. While the role of the M-region in supporting myofibrillar structure and contractility is well established, its role in mediating additional cellular processes has only recently started to emerge. As such, M-region is the hub of key protein players contributing to cytoskeletal remodeling, signal transduction, mechanosensing, metabolism, and proteasomal degradation. Mutations in genes encoding M-region related proteins lead to development of severe and lethal cardiac and skeletal myopathies affecting mankind. Herein, we describe the main cellular processes taking place at the M-region, other than thick filament assembly, and discuss human myopathies associated with mutant or truncated M-region proteins. PMID:25961035

  1. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    SciTech Connect

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule

    2015-05-15

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

  2. Simulating ligand receptor binding at a membrane interface with graphics processing accelerated coarse-grained molecular dynamics

    NASA Astrophysics Data System (ADS)

    Loverde, Sharon M.; Lebard, David N.; Ma, Zhengyu; Klein, Michael L.; Discher, Dennis E.

    2012-02-01

    Motivated by a deeper understanding of the immunological synapse, we develop a molecular-based model to understand receptor-polymer/ligand binding at a membrane interface. We examine the case of weak ligand binding in the limit of confined polymer chains as a function of chain length, binding constant, and system size. We utilize a coarse-grained (CG) model of poly(ethylene oxide) and dimyristoylphosphatidylcholine (DMPC) previously developed by the Klein group and mimic weak binding with a sticky potential. This work employs graphics processing units (GPU) to accelerate the CG-MD simulations, where each simulation is run with multiple random-walker replicas to enhance sampling and facilitate statistical convergence of physical observables. Our results demonstrate that such an aggressive combination of GPU acceleration with CG modeling can yield accurate and precise data on polymer-DMPC binding, and, more importantly, hints at the mechanism behind empirical data of polymer binding to a T-cell receptor protein.

  3. Mathematical model and calculation algorithm of micro and meso levels of separation process of gaseous mixtures in molecular sieves

    NASA Astrophysics Data System (ADS)

    Umarova, Zhanat; Botayeva, Saule; Yegenova, Aliya; Usenova, Aisaule

    2015-05-01

    In the given article, the main thermodynamic aspects of the issue of modeling diffusion transfer in molecular sieves have been formulated. Dissipation function is used as a basic notion. The differential equation, connecting volume flow with the change of the concentration of catchable component has been derived. As a result, the expression for changing the concentration of the catchable component and the coefficient of membrane detecting has been received. As well, the system approach to describing the process of gases separation in ultra porous membranes has been realized and micro and meso-levels of mathematical modeling have been distinguished. The non-ideality of the shared system is primarily taken into consideration at the micro-level and the departure from the diffusion law of Fick has been taken into account. The calculation method of selectivity considering fractal structure of membranes has been developed at the meso level. The calculation algorithm and its software implementation have been suggested.

  4. Molecular Mechanisms at the Basis of Plasticity in the Developing Visual Cortex: Epigenetic Processes and Gene Programs

    PubMed Central

    Maya-Vetencourt, José Fernando; Pizzorusso, Tommaso

    2013-01-01

    Neuronal circuitries in the mammalian visual system change as a function of experience. Sensory experience modifies neuronal networks connectivity via the activation of different physiological processes such as excitatory/inhibitory synaptic transmission, neurotrophins, and signaling of extracellular matrix molecules. Long-lasting phenomena of plasticity occur when intracellular signal transduction pathways promote epigenetic alterations of chromatin structure that regulate the induction of transcription factors that in turn drive the expression of downstream targets, the products of which then work via the activation of structural and functional mechanisms that modify synaptic connectivity. Here, we review recent findings in the field of visual cortical plasticity while focusing on how physiological mechanisms associated with experience promote structural changes that determine functional modifications of neural circuitries in V1. We revise the role of microRNAs as molecular transducers of environmental stimuli and the role of immediate early genes that control gene expression programs underlying plasticity in the developing visual cortex. PMID:25157210

  5. Using the TAP Component of the Antigen-Processing Machinery as a Molecular Adjuvant

    PubMed Central

    2005-01-01

    We hypothesize that over-expression of transporters associated with antigen processing (TAP1 and TAP2), components of the major histocompatibility complex (MHC) class I antigen-processing pathway, enhances antigen-specific cytotoxic activity in response to viral infection. An expression system using recombinant vaccinia virus (VV) was used to over-express human TAP1 and TAP2 (VV-hTAP1,2) in normal mice. Mice coinfected with either vesicular stomatitis virus plus VV-hTAP1,2 or Sendai virus plus VV-hTAP1,2 increased cytotoxic lymphocyte (CTL) activity by at least 4-fold when compared to coinfections with a control vector, VV encoding the plasmid PJS-5. Coinfections with VV-hTAP1,2 increased virus-specific CTL precursors compared to control infections without VV-hTAP1,2. In an animal model of lethal viral challenge after vaccination, VV-hTAP1,2 provided protection against a lethal challenge of VV at doses 100-fold lower than control vector alone. Mechanistically, the total MHC class I antigen surface expression and the cross-presentation mechanism in spleen-derived dendritic cells was augmented by over-expression of TAP. Furthermore, VV-hTAP1,2 increases splenic TAP transport activity and endogenous antigen processing, thus rendering infected targets more susceptible to CTL recognition and subsequent killing. This is the first demonstration that over-expression of a component of the antigen-processing machinery increases endogenous antigen presentation and dendritic cell cross-presentation of exogenous antigens and may provide a novel and general approach for increasing immune responses against pathogens at low doses of vaccine inocula. PMID:16389301

  6. Molecular kinetic theory of strongly nonequilibrium processes of mass, momentum, and energy transfer: Local equilibrium criteria

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2015-09-01

    Consequences of the complete system of transfer equations of the properties (momentum, energy, and mass) of particles and their pairs are considered under local equilibrium conditions with regard to the Bogoliubov hierarchy of relaxation times between the first and second distribution functions (DFs) and distinctions in the characteristic relaxation times of particle momentum, energy, and mass. It is found that even under the local equilibrium condition in the Bogoliubov hierarchy of relaxation times between the first and second DFs, pair correlations are maintained between all dynamic variables (velocity, temperature, and density) whose values are proportional to the gradients of transferable properties. A criterion is introduced requiring there be no local equilibrium condition upon reaching the critical value at which the description of the transfer process becomes incorrect in classical nonequilibrium thermodynamics. External forces are considered in the equations for strongly nonequilibrium processes. Along with allowing for intermolecular potentials, it becomes possible to discuss the concept of passive forces (introduced in thermodynamics by Gibbs) from the standpoint of the kinetic theory. It is shown that use of this concept does not reflect modern representations of real processes.

  7. SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene

    SciTech Connect

    Walewski, L.; Krachtus, D; Fischer, S.; Smith, Jeremy C; Bala, P.; Lesyng, B.

    2005-09-01

    Self-consistent charge-density functional tight-binding SCC-DFTB is a computationally efficient method applicable to large (bio)molecular systems in which (bio)chemical reactions may occur. Among these reactions are proton transfer processes. This method, along with more advanced ab initio techniques, is applied in this study to compute intramolecular barriers for single and double proton transfer processes in the model systems, malonaldehyde and porphycene, respectively. SCC-DFTB is compared with experimental data and higher-level ab initio calculations. For malonaldehyde, the SCC-DFTB barrier height is 3.1 kcal/mol in vacuo and 4.2 kcal/mol in water solution. In the case of porphycene, the minimum energy pathways for double intramolecular proton transfer were determined using the conjugate peak refinement (CPR) method. Six isomers of porphycene were ordered according to energy. The only energetically allowed pathway was found to connect two symmetrical trans states via an unstable cis-A isomer. The SCC-DFTB barrier heights are 11.1 kcal/mol for the trans-cis-A process, and 7.4 kcal/mol for the reverse cis-A-trans one with the energy difference of 3.7 kcal/mol between the trans- and cis-A states. The method provides satisfactory energy results when compared with reference ab initio and experimental data.

  8. Synchronization of elastically coupled processive molecular motors and regulation of cargo transport

    NASA Astrophysics Data System (ADS)

    Kohler, Felix; Rohrbach, Alexander

    2015-01-01

    The collective work of motor proteins plays an important role in cellular transport processes. Since measuring intermotor coupling and hence a comparison to theoretical predictions is difficult, we introduce the synchronization as an alternative observable for motor cooperativity. This synchronization can be determined from the ratio of the mean times of motor resting and stepping. Results from a multistate Markov chain model and Brownian dynamics simulations, describing the elastically coupled motors, coincide well. Our model can explain the experimentally observed effect of strongly increased transport velocities and powers by the synchronization and coupling of myosin V and kinesin I.

  9. New Insight into the Colonization Processes of Common Voles: Inferences from Molecular and Fossil Evidence

    PubMed Central

    Tougard, Christelle; Renvoisé, Elodie; Petitjean, Amélie; Quéré, Jean-Pierre

    2008-01-01

    Elucidating the colonization processes associated with Quaternary climatic cycles is important in order to understand the distribution of biodiversity and the evolutionary potential of temperate plant and animal species. In Europe, general evolutionary scenarios have been defined from genetic evidence. Recently, these scenarios have been challenged with genetic as well as fossil data. The origins of the modern distributions of most temperate plant and animal species could predate the Last Glacial Maximum. The glacial survival of such populations may have occurred in either southern (Mediterranean regions) and/or northern (Carpathians) refugia. Here, a phylogeographic analysis of a widespread European small mammal (Microtus arvalis) is conducted with a multidisciplinary approach. Genetic, fossil and ecological traits are used to assess the evolutionary history of this vole. Regardless of whether the European distribution of the five previously identified evolutionary lineages is corroborated, this combined analysis brings to light several colonization processes of M. arvalis. The species' dispersal was relatively gradual with glacial survival in small favourable habitats in Western Europe (from Germany to Spain) while in the rest of Europe, because of periglacial conditions, dispersal was less regular with bottleneck events followed by postglacial expansions. Our study demonstrates that the evolutionary history of European temperate small mammals is indeed much more complex than previously suggested. Species can experience heterogeneous evolutionary histories over their geographic range. Multidisciplinary approaches should therefore be preferentially chosen in prospective studies, the better to understand the impact of climatic change on past and present biodiversity. PMID:18958287

  10. Spatially and temporally coordinated processes of cells at molecular to cellular scales

    NASA Astrophysics Data System (ADS)

    Spatz, Joachim

    2013-03-01

    Our approach to engineer cellular environments is based on self-organizing spatial positioning of single signaling molecules attached to synthetic extracellular matrices, which offers the highest spatial resolution with respect to the position of single signaling molecules. This approach allows tuning tissue with respect to its most relevant properties, i.e., viscoelasticity, peptide composition, nanotopography and spatial nanopatterning of signaling molecule. Such materials are defined as ``nano-digital materials'' since they enable the counting of individual signaling molecules, separated by a biologically inert background. Within these materials, the regulation of cellular responses is based on a biologically inert background which does not initiate any cell activation, which is then patterned with specific signaling molecules such as peptide ligands in well defined nanoscopic geometries. This approach is very powerful, since it enables the testing of cellular responses to individual, specific signaling molecules and their spatial ordering. We found that integrin cluster have a functional packing density which is defined by an integrin-integrin spacing of approximately 68 nanometers. We have also developed methods which allows the light initiated activation of adhesion processes by switching the chemical composition of the extracellular matrix. This enabled us to identify the frequency of leader cell formation in collective cell migration as a matter of initial cell cluster pattern size and geometry. Moreover, ``nano-digital supports'' such as those described herein are clearly capable of involvement in such dynamic cellular processes as protein ordering at the cell's periphery which in turn leads to programming cell responses.

  11. Potential for spin-based information processing in a thin-film molecular semiconductor

    NASA Astrophysics Data System (ADS)

    Warner, Marc; Din, Salahud; Tupitsyn, Igor S.; Morley, Gavin W.; Stoneham, A. Marshall; Gardener, Jules A.; Wu, Zhenlin; Fisher, Andrew J.; Heutz, Sandrine; Kay, Christopher W. M.; Aeppli, Gabriel

    2013-11-01

    Organic semiconductors are studied intensively for applications in electronics and optics, and even spin-based information technology, or spintronics. Fundamental quantities in spintronics are the population relaxation time (T1) and the phase memory time (T2): T1 measures the lifetime of a classical bit, in this case embodied by a spin oriented either parallel or antiparallel to an external magnetic field, and T2 measures the corresponding lifetime of a quantum bit, encoded in the phase of the quantum state. Here we establish that these times are surprisingly long for a common, low-cost and chemically modifiable organic semiconductor, the blue pigment copper phthalocyanine, in easily processed thin-film form of the type used for device fabrication. At 5K, a temperature reachable using inexpensive closed-cycle refrigerators, T1 and T2 are respectively 59ms and 2.6?s, and at 80K, which is just above the boiling point of liquid nitrogen, they are respectively 10?s and 1?s, demonstrating that the performance of thin-film copper phthalocyanine is superior to that of single-molecule magnets over the same temperature range. T2 is more than two orders of magnitude greater than the duration of the spin manipulation pulses, which suggests that copper phthalocyanine holds promise for quantum information processing, and the long T1 indicates possibilities for medium-term storage of classical bits in all-organic devices on plastic substrates.

  12. Potential for spin-based information processing in a thin-film molecular semiconductor.

    PubMed

    Warner, Marc; Din, Salahud; Tupitsyn, Igor S; Morley, Gavin W; Stoneham, A Marshall; Gardener, Jules A; Wu, Zhenlin; Fisher, Andrew J; Heutz, Sandrine; Kay, Christopher W M; Aeppli, Gabriel

    2013-11-28

    Organic semiconductors are studied intensively for applications in electronics and optics, and even spin-based information technology, or spintronics. Fundamental quantities in spintronics are the population relaxation time (T1) and the phase memory time (T2): T1 measures the lifetime of a classical bit, in this case embodied by a spin oriented either parallel or antiparallel to an external magnetic field, and T2 measures the corresponding lifetime of a quantum bit, encoded in the phase of the quantum state. Here we establish that these times are surprisingly long for a common, low-cost and chemically modifiable organic semiconductor, the blue pigment copper phthalocyanine, in easily processed thin-film form of the type used for device fabrication. At 5?K, a temperature reachable using inexpensive closed-cycle refrigerators, T1 and T2 are respectively 59?ms and 2.6??s, and at 80?K, which is just above the boiling point of liquid nitrogen, they are respectively 10??s and 1??s, demonstrating that the performance of thin-film copper phthalocyanine is superior to that of single-molecule magnets over the same temperature range. T2 is more than two orders of magnitude greater than the duration of the spin manipulation pulses, which suggests that copper phthalocyanine holds promise for quantum information processing, and the long T1 indicates possibilities for medium-term storage of classical bits in all-organic devices on plastic substrates. PMID:24162849

  13. The problems of solar-terrestrial coupling and new processes introduced to the physics of the ionosphere from the physics of atomic collisions

    NASA Astrophysics Data System (ADS)

    Avakyan, Sergei

    2010-05-01

    Further progress in research of solar-terrestrial coupling requires better understanding of solar variability influence on the ionosphere. The most powerful manifestations of solar variability are solar flares and geomagnetic storms. During a flare EUV/X-ray irradiations are completely absorbed in the ionosphere producing SID. During geomagnetic storms precipitations of electrons with energy of several keV (and to a lesser extent protons precipitations) from radiation belts and geomagnetosphere produce additional ionization and low latitude auroras. Considering the physics of ionosphere during the last several decades we have been taking into account three novel processes well known in the physics of atomic collisions. These are Auger effect [S. V. Avakyan, The consideration of Auger processes in the upper atmosphere of Earth. In Abstracts of paper presented at the Tenth scien. and techn. Conf. of young specialists of S.I. Vavilov State Optical Institute, 1974, 29-31.], multiple photoionization of upper, valence shell [S.V. Avakyan, The source of O++ ions in the upper atmosphere, 1979, Cosmic Res, 17, 942 - 943] and Rydberg excitation of all the components of upper atmosphere [S.V. Avakyan, The new factor in the physics of solar - terrestrial relations - Rydberg atomic and molecules states. Conf. on Physics of solar-terrestrial relationships, 1994, Almaty, 3 - 5]. In the present paper the results of bringing these new processes in the ionospheric physics are discussed and also its possible role in the physics of solar-terrestrial coupling is considered. Involving these processes to the model estimations allowed us for the first time to come to the following important conclusions: - Auger electrons play the determinant role at the formation of energy spectrum of photoelectrons and secondary auroral electrons at the range above 150 eV; - double photoionization of the outer shell of the oxygen atom (by a single photon) plays a dominant role in the formation of ionospheric doubly charged positive ions, and Auger effect mainly determines the formation of double- and triple charged ions in the low ionosphere of planets and also comets; - transitions in the Rydberg excited ionospheric atoms and molecules play the main role in generation of new type of upper atmospheric emission - microwave characteristic radiation. The ionospheric O++ ions fill the magnetosphere after geomagnetic storms. These ions scatter the solar radiation in one of the most intense lines with a wavelength of 30.4 nm (He+) and also in the 50.7-, 70.3-, 83.3-83.5-nm lines in geocorona to the nocturnal side, giving rise to additional ionization and optical excitation in the F-region. The first calculations of the excitation rate of Rydberg states by photoelectrons and by auroral electrons (including Auger electrons) were carried out. It was shown that such process can generate the microwave ionospheric radioemission. Such emissions were observed during solar flares and in auroras. We suggest that Rydberg microwave radioemissions which take place during ionospheric disturbances produced by the solar flares and geomagnetic storms can be considered as an agent of influence of solar-geomagnetic activity on the biosphere and also as a factor of Sun-weather-climate links All these results obtained experimental confirmation in space investigations and in some ground-based measurements carried out with radiophysical and optical methods. The new processes which we introduced to the physics of upper atmosphere and ionosphere are now widely used in the ionospheric science for interpretation of spacecraft measurement data (the spacecrafts ISIS, GEOS-1, IMAGE, the satellites DE-1,-B, EXOS-D (AKEBOHO), FAST, Intercosmos-19, -24, -25, the orbital stations "Salut", "Mir"). There is a Russian patent on the method of remote registration of radioactive atmospheric clouds and nuclear weapon tests over the atmosphere by means of optical fluorescence which is based on Auger processes.

  14. N-linked glycan recognition and processing: the molecular basis of endoplasmic reticulum quality control.

    PubMed

    Moremen, Kelley W; Molinari, Maurizio

    2006-10-01

    Nascent polypeptides emerging into the lumen of the endoplasmic reticulum (ER) are N-glycosylated on asparagines in Asn-Xxx-Ser/Thr motifs. Processing of the core oligosaccharide eventually determines the fate of the associated polypeptide by regulating entry into and retention by the calnexin chaperone system, or extraction from the ER folding environment for disposal. Recent advances have shown that at least two N-glycans are necessary for protein access to the calnexin chaperone system and that polypeptide cycling in the system is a rather rare event, which, for folding-defective polypeptides, is activated only upon persistent misfolding. Additionally, dismantling of the polypeptide-bound N-glycan interrupts futile folding attempts, and elicits preparation of the misfolded chain for dislocation into the cytosol and degradation. PMID:16938451

  15. Molecular insights into cold active polygalacturonase enzyme for its potential application in food processing.

    PubMed

    Ramya, L N; Pulicherla, K K

    2015-09-01

    Pectin is a complex structural heteropolysaccharide that require numerous pectinolytic enzymes for its complete degradation. Polygalacturonase from mesophilic or thermophilic origin are being widely used in fruit and vegetable processing in the recent decades to degrade pectic substances. Recently cold active pectinases are finding added advantages over meso and thermophilic counterparts, to use in industrial scale particularly in food processing industry. They facilitate in conservation of several properties of foods so that the end product retains its naturality and also generates economic benefits. In the present study, Pseudoalteromonas haloplanktis, a well reported marine psychrophile is taken as a model organism for cold active polygalacturonase and is evaluated in comparision to the routinely used mesophilic and thermophilic enzymes by insicio approach. Polygalacturonase sequences from industrially important microbial sources were subjected to MEME and Pfam wherein motifs and domains involved in the conservation were analyzed. Dendrogram revealed sequence level similarity and motifs showed uniform distribution of conserved regions that are involved in important functions. It was also observed through clustalW analysis that the amount of arginine content of psychrophiles is less when compared with thermophiles. Finally, all the modeled enzyme structures were subjected to docking studies using Autodock 4.2 with the substrate polygalacturonic acid and binding energies were found to be -5.73, -6.22 and -7.27 KCals/mole for meso, thermo and psychrophiles respectively which indicates the efficiency of psychrophilic enzymes when compared with its counterparts giving scope for further experimentation to find their better usage in various food industry applications. PMID:26344963

  16. Pomegranate juice and specific components inhibit cell and molecular processes critical for metastasis of breast cancer.

    PubMed

    Rocha, Ana; Wang, Lei; Penichet, Manuel; Martins-Green, Manuela

    2012-12-01

    Breast cancer is the most common cancer and the second leading cause of cancer death and morbidity among women in the western world. Pomegranate juice (PJ) and three of its specific components have been shown to inhibit processes involved in prostate cancer metastasis. If this also proves to be true for breast cancer, these natural treatments will be promising agents against breast cancer that can serve as potentially effective and nontoxic alternatives or adjuncts to the use of conventional selective estrogen receptor modulators for breast cancer prevention and treatment. To test this possibility, we have used two breast cancer cell lines, MDA-MB-231 cells (ER(-)) and MCF7 (ER(+)), and the non-neoplastic cell line MCF10A. We show that, in addition to inhibiting growth of the breast cancer cells, PJ or a combination of its components luteolin (L) + ellagic acid (E) + punicic acid (P) increase cancer cell adhesion and decrease cancer cell migration but do not affect normal cells. These treatments also inhibit chemotaxis of the cancer cells to SDF1?, a chemokine that attracts breast cancer cells to the bone. We hypothesized that PJ and L + E + P stimulate expression of genes that increase adhesion and inhibit genes that stimulate cell migration and inhibit chemotaxis to SDF1?. Using qPCR, we confirmed these proposed effects on gene expression and in addition we found that a gene important in epithelial-to-meshenchymal transitions is decreased. We also found that pro-inflammatory cytokines/chemokines are significantly reduced by these treatments, thereby having the potential to decrease inflammation and its impact on cancer progression. Discovery that PJ and L + E + P are inhibitory of metastatic processes in breast cancer cells in addition to prostate cancer cells indicate that they are potentially a very effective treatment to prevent cancer progression in general. PMID:23065001

  17. 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.

  18. 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?"

  19. Molecular dynamical simulation of the behavior of early precipitated stage in aging process in dilute Cu-Cr alloy

    SciTech Connect

    Feng, J.; Liu, L.; Chen, J.; Du, Y.; Zhou, R.; Xiao, B.

    2010-06-15

    The aging behaviors of Cu-Cr alloys in the early stage at different temperatures are investigated by molecular dynamics simulations. First principles potentials are used for the interactions between Cu and Cr atoms. The initial behavior of precipitation is characterized by transmission electron microscope and electron energy disperse spectroscopy. The results showed that Cu-Cr supersaturated solid solution is thermodynamically unstable. The mean-square displacements of the atoms are used to describe the diffusivity. At room temperature, the atoms only show harmonic vibrations near the equilibrium positions. The mutual diffusion at 873 K is different from the unidirectional diffusion in low temperatures. The calculation shows that aging process is accelerated with increasing temperature, which is not only due to the lower diffusion activation energy of Cr at higher temperature, but also because Cu atoms are also participated in the aging process. When ''aging'' at 1073 K, the precipitation of Cr element is dissolved again into Cu matrix, which is an ''over-aging'' state of Cu-Cr alloy at high temperature.

  20. Direct transfer-adsorption: The new molecular dynamics transition mechanism of nano-diamond preparation by laser shock processing

    NASA Astrophysics Data System (ADS)

    Ren, X. D.; Tang, S. X.; Zheng, L. M.; Yuan, S. Q.; Ren, N. F.; Yang, H. M.; Wang, Y.; Zhou, W. F.; Xu, S. D.

    2015-07-01

    Laser shock processing induced structural transformation in graphite cluster of about 3 nm diameter is simulated through molecular dynamics simulations. The Brenner potential is utilized to characterize short-range order while Lennard-Jones potential for long-range order. The effect of high-energy laser shock on graphite was simulated with corresponding temperature and pressure load applied to the graphite cluster. The graphite cluster was found to transform into nano-diamond, crystal structures and amorphous carbon after heating-pressing and annealing-decompression by analyzing pair distribution function g(r) and atomic snapshots process. An interesting mechanism 'direct transfer-adsorption' for promoting peripheral carbon atoms of the graphite cluster into the inner layer and transforming bonds from sp2-type to sp3-type within the inner carbon atoms is investigated. The 'direct transfer-adsorption' mechanism, which prevails under the conditions of a temperature higher than 4300 K and a pressure higher than 15 GPa, is at fast cooling rates and high densities. And the 'direct transfer-adsorption' mechanism plays a key role in the conversion from graphite to diamond.

  1. 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,?E) 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

  2. Inelastic rate processes in molecular junctions: Current-induced nuclear excitation and bath-induced vibrational decoherence

    NASA Astrophysics Data System (ADS)

    Jorn, Ryan Paul

    The technological potential for constructing electronic devices comprised of active elements on the nano- and subnanoscale has inspired a surge of interest in the conductance of individual molecules. Several demonstrations now exist which show that the tunneling current through a molecular device can interact with the vibrational degrees of freedom to initiate chemical dynamics and mechanical manipulation. Targeting single molecules provides ample motivations for both new fundamental studies in surface chemistry as well as the construction of individually driven molecular machines. The thrust of the research presented here is to understand these large amplitude motions and develop theoretical tools capable of describing nuclear dynamics initiated in a molecular junction. The focus in the subsequent chapters is on inelastic resonance transport which has been well studied in the contexts of gas phase scattering and surface electron spectroscopies. The rate for current-induced excitation is introduced as the observable for the nuclear dynamics and is formulated within a time independent scattering theory. Application is made to both bound-bound and bound-free transitions in the nuclear subspace and the effect of the coordinate dependence of the electronic coupling on the dynamics is discussed extensively. Having established the rigorous formulation for the excitation process, the qualitative Menzel-Gomer-Redhead theory is used along with established electronic structure methods to investigate the nature of the resonance state and its impact on the inelasticity of the charge transport. Application is made to a candidate molecular machine, a lithium rattle, and a hybrid silicon-organic system previously probed with scanning tunneling microscopy. The former study elucidates the role of charge localization in determining the extent of nuclear dynamics initiated by the current. Focusing on the dynamics induced for cyclopentene on the silicon surface demonstrates the importance of charge localization on the silicon dimer to produce inelastic events leading to desorption and possible failure of an electronic device. The role of the environment to dissipate energy away from the reaction coordinate is examined within density matrix theory incorporating the role of electrode phonons and generation of electron-hole pairs. Vibrational relaxation is implemented using the well-known Redfield theory and adapted to the Bloch model to describe the relaxation rates to these external degrees of freedom. The model system of CO adsorbed to various transition metals is examined to validate the methods used and qualitative agreement with experiment is shown. Finally, a scattering theory of density matrices is constructed to unite the description of the current-induced excitation with energy relaxation to the dissipative environment. The competition between these rate processes is explored for a variety of bias voltages and temperatures. It is shown that the use of master equations within the secular approximation neglects important components of the quantum dynamics.

  3. Molecular organic tracers of biogeochemical processes in a saline meromictic lake (Ace Lake)

    NASA Astrophysics Data System (ADS)

    Schouten, S.; Rijpstra, W. I. C.; Kok, M.; Hopmans, E. C.; Summons, R. E.; Volkman, J. K.; Sinninghe Damsté, J. S.

    2001-05-01

    The chemical structures, distribution and stable carbon isotopic compositions of lipids in a sediment core taken in meromictic Ace Lake (Antarctica) were analyzed to trace past biogeochemical cycling. Biomarkers from methanogenic archaea, methanotrophic bacteria and photosynthetic green sulfur bacteria were unambiguously assigned using organic geochemical understanding and by reference to what is known about the lake's present-day ecosystem. For instance, saturated and unsaturated 2,6,10,15,19-pentamethylicosane, archaeol and sn2-hydroxyarchaeol were derived from methanogenic archaea. Carotenoid analysis revealed chlorobactene and isorenieratene derived from the green-colored and brown-colored strains of the green sulfur bacteria (Chlorobiaceae); isotopic analyses showed that they were 13C-enriched. Phytenes appear to be derived from photoautotrophs that use the Calvin-Benson cycle, while phytane has a different source, possibly within the archaea. The most 13C-depleted compounds (ca. -55‰) identified were 4-methyl-5?-cholest-8(14)-en-3?-ol, identified using an authentic standard, and co-occurring 4-methylsteradienes: these originate from the aerobic methanotrophic bacterium Methylosphaera hansonii. Lipids of photoautotrophic origin, steranes and alkenones, are relatively depleted (ca. -28 to -36‰) whilst archaeal biomarkers are relatively enriched in 13C (ca. -17 to -25‰). The structural and carbon isotope details of sedimentary lipids thus revealed aspects of in situ biogeochemical processes such as methane generation and oxidation and phototrophic sulfide oxidation.

  4. Dried Blood Spots - Preparing and Processing for Use in Immunoassays and in Molecular Techniques

    PubMed Central

    Grüner, Nico; Stambouli, Oumaima; Ross, R. Stefan

    2015-01-01

    The idea of collecting blood on a paper card and subsequently using the dried blood spots (DBS) for diagnostic purposes originated a century ago. Since then, DBS testing for decades has remained predominantly focused on the diagnosis of infectious diseases especially in resource-limited settings or the systematic screening of newborns for inherited metabolic disorders and only recently have a variety of new and innovative DBS applications begun to emerge. For many years, pre-analytical variables were only inappropriately considered in the field of DBS testing and even today, with the exception of newborn screening, the entire pre-analytical phase, which comprises the preparation and processing of DBS for their final analysis has not been standardized. Given this background, a comprehensive step-by-step protocol, which covers al the essential phases, is proposed, i.e., collection of blood; preparation of blood spots; drying of blood spots; storage and transportation of DBS; elution of DBS, and finally analyses of DBS eluates. The effectiveness of this protocol was first evaluated with 1,762 coupled serum/DBS pairs for detecting markers of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus infections on an automated analytical platform. In a second step, the protocol was utilized during a pilot study, which was conducted on active drug users in the German cities of Berlin and Essen. PMID:25867233

  5. Synthesis and photovoltaic response of a solution-processable dithienyldiketopyrrolopyrrole-based molecular semiconductor with thienylvinylthienyl endgroups

    NASA Astrophysics Data System (ADS)

    Zhang, Chun-Hui; Tan, Wan-Yi; Wang, Li-Ping; Li, Qing-Duan; Zhou, Rui; Huang, Ju; Wei, Xin-Feng; Xia, Yan; He, Yi-Feng; Zhu, Xu-Hui; Peng, Junbiao; Cao, Yong

    2015-01-01

    We describe the synthesis and preliminary photovoltaic performance of a solution-processable organic small-molecule electron donor DT that consists of dithienyldiketopyrrolopyrrole (DT-DPP) as the core and thienylvinylthiophene (TVT) as the endgroups. The new compound is a crystalline solid with a Tm of approximately 216°C. Cyclic voltammetry indicates that DT exhibits two quasi-reversible one-electron oxidation waves at ca. 0.68 and 0.90 V versus an Ag/AgCl reference electrode, respectively, leading to an estimated highest occupied molecular orbital (HOMO) level of about -5.08 eV. Introducing the branched 2-hexyldecyl side chain provides DT with a high solubility in chloroform up to ca. 36 mg mL-1 at room temperature. Thermal annealing increases the crystallinity of the as-cast film from chloroform solution, thereby rendering slightly red-shifted charge-transfer absorption maxima. Fitting the space-charge-limited current characteristics of the thermally annealed thin film yields an improved hole mobility of ˜2.14×10-4 cm2 V-1 s-1 at low voltages versus ˜1.46×10-4 cm2 V-1 s-1 of the as-cast film. A first characterization of the solar cell [ITO/PEDOT: PSS/DT: PC61BM/Al] produces a power conversion efficiency of ˜3% with VOC?0.78 V, JSC?7.91 mA cm-2, and FF?48.7%, under simulated AM1.5G with an illumination intensity of 100 mW cm-2. It should be noted that the thermal effect on the thin film absorption of DT does not seem to be completely similar to the molecular donor DPP reported earlier, which bears 6-fluoronaphthyl endgroups.

  6. Chemical Potential of Triethylene Glycol Adsorbed on Surfaces Relevant to Gas Transport and Processing - Studies Using Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kvamme, B.; Olsen, R.; Sjöblom, S.; Leirvik, K. N.; Kuznetsova, T.

    2014-12-01

    Natural gas will inevitably contain trace amounts of water and other impurities during different stages of processing and transport. Glycols, such as triethylene glycol (TEG), will in many cases follow the water. The glycol contents of the gas can originate from preceding glycol-drying units or it can be a residue from the direct injection of glycols used to prevent hydrate formation. Thus, it is important to know how glycol contents will affect the different paths leading to hydrate formation. Glycols may in some cases dominate the condensed water phase. If this occurs, it will lead to the well-documented shift in the hydrate stability curve, due to the altered activity of the water. A great deal of information on the molecular path of a glycol through the system can be obtained from calculating the chemical potential. Due to difficulties in measuring interfacial chemical potentials, these often need to be estimated using theoretical tools. We used molecular dynamics (MD) to study how TEG behaves in the vicinity of mineral surfaces such as calcite and hematite. Many methods exist for estimating chemical potentials based on MD trajectories. These include techniques such as free energy perturbation theory (FEP) and thermodynamic integration (TI). Such methods require sufficient sampling of configurations where free energy is to be estimated. Thus, it can be difficult to estimate chemical potentials on surfaces. There are several methods to circumvent this problem, such as blue moon sampling and umbrella sampling. These have been considered and the most important have been used to estimate chemical potentials of TEG adsorbed on the mineral surfaces. The resulting chemical potentials were compared to the chemical potential of TEG in bulk water, which was estimated using temperature thermodynamic integration.

  7. Gravitropism of cut shoots is mediated by oxidative processes: A physiological and molecular study

    NASA Astrophysics Data System (ADS)

    Philosoph-Hadas, Sonia; Friedman, Haya; Meir, Shimon

    2012-07-01

    The signal transduction events occurring during shoot gravitropism are mediated through amyloplasts sedimentation, reorientation of actin filaments in the endodermis, and differential changes in level and action of auxin, associated with differential growth leading to shoot curvature. Since increase in reactive oxygen species (ROS) was shown to be associated with growth, we examined the possible use of antioxidants in controlling the gravitropic response, via their interaction with events preceding shoot bending. Reoriented snapdragon (Antirrhinum majus L.) spikes and tomato (Solanum lycopersicum cv. MicroTom) shoots showed a visual upward bending after a lag period of 3 or 5 h, respectively, which was inhibited by the antioxidants N-acetyl-cysteine (NAC) and reduced glutathione (GSH). This suggests the involvement of oxidative reactions in the process. The two antioxidants prevented the sedimentation of amyloplasts to the bottom of the endodermis cells following 0.5-5 h of snapdragon shoot reorientation, suggesting that oxidative reactions are involved already at a very early signal perception stage prior to the visual bending. In addition, a differential distribution in favor of the lower shoot side of various oxidative elements, including H2O2 concentrations and activity of the NADPH-oxidase enzyme, was observed during reorientation of snapdragon spikes. Application of the two antioxidants reduced the levels of these elements and abolished their differential distribution across the shoot. On the other hand, the activity of the antioxidative enzyme, superoxide dismutase (SOD), which was not differentially distributed across the shoot, increased significantly following application of the two antioxidants. The auxin redistribution in reoriented shoots was analyzed using transgenic tomato plants expressing the GUS reporter gene under the Aux/IAA4 promoter (a generous gift of M. Bouzayen, France). GUS response, detected in control shoots 4 h after their reorientation in favor of the lower shoot side was completely eliminated in the NAC-treated shoots, in which the bending response was inhibited. These results suggest that the gravitropic-induced asymmetric auxin redistribution precedes shoot bending, and NAC inhibits this response by abolishing the auxin gradient across the shoot. Our microarray analysis of tomato shoots, using the Affymetrix Tomato GeneChip, revealed differential changes in expression of 266 genes, occurring during the initial 0.5-5 h of shoot reorientation prior to bending. The differential changes in expression of auxin-related genes in favor of the lower shoot side occurred already following 0.5 h of reorientation, while those of cell wall-related genes, associated with shoot bending, occurred only 3 h following shoot reorientation. Among the identified genes, 11 genes were related to auxin, and 36 genes were associated with oxidative processes, demonstrating the involvement of ROS in early events of shoot gravitropism. Taken together, our results suggest that ROS mediate the early gravity-induced amyloplast sedimentation required for signal perception, as well as the lateral auxin movement across the shoot, which is necessary for the auxin asymmetric distribution leading to shoot upward bending.

  8. Molecular Dynamics simulations of the electrospray process: formation of NaCl clusters via the charged residue mechanism.

    PubMed

    Konermann, Lars; McAllister, Robert G; Metwally, Haidy

    2014-10-16

    Electrospray ionization (ESI) produces desolvated ions from solution phase analytes for mass spectrometric detection. The final steps of gas phase ion formation from nanometer-sized solvent droplets remain a matter of debate. According to the ion evaporation model (IEM), analytes are ejected from the droplet surface via field emission, whereas the charged residue model (CRM) envisions that ions are released upon droplet evaporation to dryness. Exposure of salt solutions to ESI conditions produces a range of cluster ions. Despite the rich literature on these systems, it is still unclear if these salt clusters form via the CRM or the IEM. The current study explores the formation of Na(n)Cl(m)((n-m)+) clusters from aqueous sodium chloride solution under positive and negative polarity conditions. Molecular dynamics (MD) methods are used for simulating the temporal evolution of charged NaCl-containing water droplets. A trajectory stitching approach is developed for continuously removing evaporated moieties from the simulation, thereby dramatically reducing computational cost. In addition, this procedure ensures adequate temperature control and eliminates evaporative cooling that would otherwise slow down the process. Continuous water evaporation leads to progressive droplet shrinkage, while the emission of solvated single ions ensures that the system remains at ca. 90% of the Rayleigh limit. Early during the process all ions in the droplet behave as freely dissolved species, but after a few nanoseconds at 370 K the systems gradually morph into amorphous wet salt aggregates. Ultimately, free Na(n)Cl(m)((n-m)+) clusters form as the last solvent molecules evaporate. Our data therefore provide direct evidence that sodium chloride cluster formation during ESI proceeds via the CRM. The IEM nonetheless plays an ancillary role, as it allows the system to shed charge (mostly in the form of hydrated Na(+) or Cl(-)) during droplet shrinkage. It appears that this study marks the first successful MD simulation of complete CRM processes. PMID:25242574

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

    SciTech Connect

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

    2008-08-06

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

  10. Molecular recognition and processing of periodic signals in cells: study of activation of membrane ATPases by alternating electric fields.

    PubMed

    Tsong, T Y

    1992-03-26

    A molecule which is immobilized, oriented or tumbling more slowly than the frequency of a periodic field, may interact with the field to produce chemical effects that are uncommon in a homogeneous solution. Among these effects are the alteration of the rate of a chemical reaction and the exchange of energy between the oscillating field and the conformation of the molecule. When certain conditions are satisfied, this exchange allows the molecule to absorb and couple the energy of the field to drive an endergonic reaction. The efficiency of energy coupling depends on field strength and frequency and on the ligand concentration. There are windows of these parameters to achieve efficient coupling. These windows can be expressed in terms of the rate constants and equilibrium constants of the catalytic reactions, and the amplitude and frequency of the periodic field. This mechanism allows cells to receive, process and transmit energy of high and medium level periodic potentials by means of membrane enzymes or receptors. A theory for the transduction of electric energy, electroconformational coupling (ECC) will be discussed. The electric field induced cation pumping activities of Na,K-ATPase and Ca-ATPase of human erythrocytes and the ATP synthetic activity of beef heart mitochondrial ATPase will then be used to test an ECC membrane transport model. For the processing of low level periodic signals, a theory of an oscillatory activation barrier (OAB), which considers resonance transduction between an oscillating field and the activation barrier of the rate limiting step in an enzymic reaction, will be discussed. The OAB mechanism successfully interprets the AC stimulated ATP hydrolysis activity of Ecto-ATPase from chicken oviduct and F0F1-ATPase from beef heart. We propose that mechanisms similar to an OAB model are adopted by cells to sense weak electric, acoustic, mechanical, concentration (i.e., chemical potential) and other types of signals, and to communicate with other cells by these signals. The experimental data and mechanistic information presented in this communication give us a glimpse of the molecular electronic designs in living cells. This information is also relevant with respect to environmental issues. Environmental electromagnetic fields and sonic pollutants may interfere with normal communications of cells and organisms. Their benefit, if any, and detrimental effects can be assessed and dealt with only if we fully understand mechanisms of cellular interactions with these fields and pollutants, at the molecular level. PMID:1532330

  11. Preparation of phthalocyanine and octacyanophthalocyanine films by CVD on metal surfaces, and in SITU observation of the molecular processes by Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Ishii, Kikujiro; Mitsumura, Satoshi; Hibino, Yukinobu; Hagiwara, Ryoji; Nakayama, Hideyuki

    1988-09-01

    Copper phthalocyanine and copper octacyanophthalocyanine films were prepared by direct thermal reactions of phthalonitrile or tetracyanobenzene vapors on copper surfaces. Although the reaction rates were very slow, homogeneous films of phthalocyanines were obtained. Raman spectra were measured during the reactions, and intermediate molecular states were found to exist during the process of film formation.

  12. 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...

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

    SciTech Connect

    Otec, Roman; /Prague, Tech. U.

    2006-09-01

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

  14. Monte Carlo-based fluorescence molecular tomography reconstruction method accelerated by a cluster of graphic processing units

    NASA Astrophysics Data System (ADS)

    Quan, Guotao; Gong, Hui; Deng, Yong; Fu, Jianwei; Luo, Qingming

    2011-02-01

    High-speed fluorescence molecular tomography (FMT) reconstruction for 3-D heterogeneous media is still one of the most challenging problems in diffusive optical fluorescence imaging. In this paper, we propose a fast FMT reconstruction method that is based on Monte Carlo (MC) simulation and accelerated by a cluster of graphics processing units (GPUs). Based on the Message Passing Interface standard, we modified the MC code for fast FMT reconstruction, and different Green's functions representing the flux distribution in media are calculated simultaneously by different GPUs in the cluster. A load-balancing method was also developed to increase the computational efficiency. By applying the Fréchet derivative, a Jacobian matrix is formed to reconstruct the distribution of the fluorochromes using the calculated Green's functions. Phantom experiments have shown that only 10 min are required to get reconstruction results with a cluster of 6 GPUs, rather than 6 h with a cluster of multiple dual opteron CPU nodes. Because of the advantages of high accuracy and suitability for 3-D heterogeneity media with refractive-index-unmatched boundaries from the MC simulation, the GPU cluster-accelerated method provides a reliable approach to high-speed reconstruction for FMT imaging.

  15. Coupled Molecular Switching Processes in Ordered Mono- and Multilayers of Stimulus-Responsive Rotaxanes on Gold Surfaces

    PubMed Central

    2015-01-01

    Interfaces provide the structural basis for function as, for example, encountered in nature in the membrane-embedded photosystem or in technology in solar cells. Synthetic functional multilayers of molecules cooperating in a coupled manner can be fabricated on surfaces through layer-by-layer self-assembly. Ordered arrays of stimulus-responsive rotaxanes undergoing well-controlled axle shuttling are excellent candidates for coupled mechanical motion. Such stimulus-responsive surfaces may help integrate synthetic molecular machines in larger systems exhibiting even macroscopic effects or generating mechanical work from chemical energy through cooperative action. The present work demonstrates the successful deposition of ordered mono- and multilayers of chemically switchable rotaxanes on gold surfaces. Rotaxane mono- and multilayers are shown to reversibly switch in a coupled manner between two ordered states as revealed by linear dichroism effects in angle-resolved NEXAFS spectra. Such a concerted switching process is observed only when the surfaces are well packed, while less densely packed surfaces lacking lateral order do not exhibit such effects. PMID:25782057

  16. Effect of twin boundary on nanoimprint process of bicrystal Al thin film studied by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Xie, Yue-Hong; Xu, Jian-Gang; Song, Hai-Yang; Zhang, Yun-Guang

    2015-02-01

    The effects of a twin boundary (TB) on the mechanical properties of two types of bicrystal Al thin films during the nanoimprint process are investigated by using molecular dynamics simulations. The results indicate that for the TB direction parallel to the imprinting direction, the yield stress reaches the maximum for the initial dislocation nucleation when the mould directly imprints to the TB, and the yield stress first decreases with the increase of the marker interval and then increases. However, for the TB direction perpendicular to the imprinting direction, the effect of the TB location to the imprinting forces is very small, and the yield stress is greater than that with the TB direction parallel to the imprinting direction. The results also demonstrate that the direction of the slip dislocations and the deformation of the thin film caused by spring-back are different due to various positions and directions of the TB. Project supported by the National Natural Science Foundation of China (Grant No. 10902083), the Program for New Century Excellent Talent in University of Ministry of Education of China (Grant No. NCET-12-1046), the Program for New Scientific and Technological Star of Shaanxi Province, China (Grant No. 2012KJXX-39), and the Program for Natural Science Basic Research Plan in Shaanxi Province, China (Grant No. 2014JQ1036).

  17. Mechanical and electrical properties of carbon nanotube/Cu nanocomposites by molecular-level mixing and controlled oxidation process.

    PubMed

    Lim, Byung K; Mo, Chan B; Nam, Dong H; Hong, Soon H

    2010-01-01

    A molecular-level mixing and controlled oxidation process is proposed as a novel fabrication technique for the production of CNT/Cu nanocomposite powders. The fabricated CNT/Cu2O nanocomposite powders showed microstructures with homogeneous dispersion of implanted CNTs in a Cu2O matrix. The CNT/Cu2O nanocomposite powders were reduced to CNT/Cu nanocomposite powders with H2 gas and then the as-prepared CNT/Cu nanocomposite powders were spark plasma sintered to fabricate CNT/Cu nanocomposites. The mechanical properties of the Cu and the CNT/Cu nanocomposites were characterized by tensile testing before and after hot compression. Before hot compression, the CNT/Cu nanocomposites were brittle, but after hot compression both yield strength and elongation were increased, while the yield strength of the Cu was decreased after hot compression. Hot compression enhanced the ductility and strength of the CNT/Cu nanocomposites due to alignment of Cu grains and CNTs. Electrical conductivity was also enhanced due to a reduced scattering of electrons because of the alignment of the CNTs and Cu grains as well as the annealing effects of the Cu matrix. PMID:20352814

  18. Fluorescence molecular tomography using a two-step three-dimensional shape-based reconstruction with graphics processing unit acceleration.

    PubMed

    Wang, Daifa; Qiao, Huiting; Song, Xiaolei; Fan, Yubo; Li, Deyu

    2012-12-20

    In fluorescence molecular tomography, the accurate and stable reconstruction of fluorescence-labeled targets remains a challenge for wide application of this imaging modality. Here we propose a two-step three-dimensional shape-based reconstruction method using graphics processing unit (GPU) acceleration. In this method, the fluorophore distribution is assumed as the sum of ellipsoids with piecewise-constant fluorescence intensities. The inverse problem is formulated as a constrained nonlinear least-squares problem with respect to shape parameters, leading to much less ill-posedness as the number of unknowns is greatly reduced. Considering that various shape parameters contribute differently to the boundary measurements, we use a two-step optimization algorithm to handle them in a distinctive way and also stabilize the reconstruction. Additionally, the GPU acceleration is employed for finite-element-method-based calculation of the objective function value and the Jacobian matrix, which reduces the total optimization time from around 10 min to less than 1 min. The numerical simulations show that our method can accurately reconstruct multiple targets of various shapes while the conventional voxel-based reconstruction cannot separate the nearby targets. Moreover, the two-step optimization can tolerate different initial values in the existence of noises, even when the number of targets is not known a priori. A physical phantom experiment further demonstrates the method's potential in practical applications. PMID:23262613

  19. Demographic processes in the montane Atlantic rainforest: molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei.

    PubMed

    Amaro, Renata Cecília; Rodrigues, Miguel Trefaut; Yonenaga-Yassuda, Yatiyo; Carnaval, Ana Carolina

    2012-03-01

    Historical climatic refugia predict genetic diversity in lowland endemics of the Brazilian Atlantic rainforest. Yet, available data reveal distinct biological responses to the Last Glacial Maximum (LGM) conditions across species of different altitudinal ranges. We show that species occupying Brazil's montane forests were significantly less affected by LGM conditions relative to lowland specialists, but that pre-Pleistocene tectonics greatly influenced their geographic variation. Our conclusions are based on palaeoclimatic distribution models, molecular sequences of the cytochrome b, 16S, and RAG-1 genes, and karyotype data for the endemic frog Proceratophrys boiei. DNA and chromosomal data identify in P. boiei at least two broadly divergent phylogroups, which have not been distinguished morphologically. Cytogenetic results also indicate an area of hybridization in southern São Paulo. The location of the phylogeographic break broadly matches the location of a NW-SE fault, which underwent reactivation in the Neogene and led to remarkable landscape changes in southeastern Brazil. Our results point to different mechanisms underpinning diversity patterns in lowland versus montane tropical taxa, and help us to understand the processes responsible for the large number of narrow endemics currently observed in montane areas of the southern Atlantic forest hotspot. PMID:22108674

  20. 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.

  1. Behavioral and molecular processing of visceral pain in the brain of mice: impact of colitis and psychological stress

    PubMed Central

    Jain, Piyush; Hassan, Ahmed M.; Koyani, Chintan N.; Mayerhofer, Raphaela; Reichmann, Florian; Farzi, Aitak; Schuligoi, Rufina; Malle, Ernst; Holzer, Peter

    2015-01-01

    Gastrointestinal disorders with abdominal pain are associated with central sensitization and psychopathologies that are often exacerbated by stress. Here we investigated the impact of colitis induced by dextran sulfate sodium (DSS) and repeated water avoidance stress (WAS) on spontaneous and nociception-related behavior and molecular signaling in the mouse brain. DSS increased the mechanical pain sensitivity of the abdominal skin while both WAS and DSS enhanced the mechanical and thermal pain sensitivity of the plantar skin. These manifestations of central sensitization were associated with augmented c-Fos expression in spinal cord, thalamus, hypothalamus, amygdala and prefrontal cortex. While WAS stimulated phosphorylation of mitogen-activated protein kinase (MAPK) p42/44, DSS activated another signaling pathway, both of which converged on c-Fos. The DSS- and WAS-induced hyperalgesia in the abdominal and plantar skin and c-Fos expression in the brain disappeared when the mice were subjected to WAS+DSS treatment. Intrarectal allyl isothiocyanate (AITC) evoked aversive behavior (freezing, reduction of locomotion and exploration) in association with p42/44 MAPK and c-Fos activation in spinal cord and brain. These effects were inhibited by morphine, which attests to their relationship with nociception. DSS and WAS exerted opposite effects on AITC-evoked p42/44 MAPK and c-Fos activation, which indicates that these transduction pathways subserve different aspects of visceral pain processing in the brain. In summary, behavioral perturbations caused by colitis and psychological stress are associated with distinct alterations in cerebral signaling. These findings provide novel perspectives on central sensitization and the sensory and emotional processing of visceral pain stimuli in the brain. PMID:26217204

  2. Detect the sensitivity and response of protein molecular structure of whole canola seed (yellow and brown) to different heat processing methods and relation to protein utilization and availability using ATR-FT/IR molecular spectroscopy with chemometrics

    NASA Astrophysics Data System (ADS)

    Samadi; Theodoridou, Katerina; Yu, Peiqiang

    2013-03-01

    The objectives of this experiment were to detect the sensitivity and response of protein molecular structure of whole canola seed to different heat processing [moisture (autoclaving) vs. dry (roasting) heating] and quantify heat-induced protein molecular structure changes in relation to protein utilization and availability. In this study, whole canola seeds were autoclaved (moisture heating) and dry (roasting) heated at 120 °C for 1 h, respectively. The parameters assessed included changes in (1) chemical composition profile, (2) CNCPS protein subfractions (PA, PB1, PB2, PB3, PC), (3) intestinal absorbed true protein supply, (4) energy values, and (5) protein molecular structures (amide I, amide II, ratio of amide I to II, ?-helix, ?-sheet, ratio of ?-helix to ?-sheet). The results showed that autoclave heating significantly decreased (P < 0.05) but dry heating increased (P < 0.05) the ratio of protein ?-helix to ?-sheet (with the ratios of 1.07, 0.95, 1.10 for the control (raw), autoclave heating and dry heating, respectively). The multivariate molecular spectral analyses (PCA, CLA) showed that there were significantly molecular structural differences in the protein amide I and II fingerprint region (ca. 1714-1480 cm-1) among the control, autoclave and dry heating. These differences were indicated by the form of separate class (PCA) and group of separate ellipse (CLA) between the treatments. The correlation analysis with spearman method showed that there were significantly and highly positive correlation (P < 0.05) between heat-induced protein molecular structure changes in terms of ?-helix to ?-sheet ratios and in situ protein degradation and significantly negative correlation between the protein ?-helix to ?-sheet ratios and intestinal digestibility of undegraded protein. The results indicated that heat-induced changes of protein molecular structure revealed by vibration molecular spectroscopy could be used as a potential predictor to protein degradation and intestinal protein digestion of whole canola seed. Future study is needed to study response and impact of heat processing to each inherent layer of canola seed from outside to inside tissues and between yellow canola and brown canola.

  3. Rotational state-changing cold collisions of hydroxyl ions with helium

    NASA Astrophysics Data System (ADS)

    Hauser, Daniel; Lee, Seunghyun; Carelli, Fabio; Spieler, Steffen; Lakhmanskaya, Olga; Endres, Eric S.; Kumar, Sunil S.; Gianturco, Franco; Wester, Roland

    2015-06-01

    Cold molecules are important for many applications, from fundamental precision measurements, quantum information processing, quantum-controlled chemistry, to understanding the cold interstellar medium. Molecular ions are known to be cooled efficiently in sympathetic collisions with cold atoms or ions. However, little knowledge is available on the elementary cooling steps, because the determination of quantum state-to-state collision rates at low temperature is very challenging for both experiment and theory. Here we present a method to manipulate molecular quantum states by non-resonant photodetachment. Based on this we provide absolute quantum scattering rate coefficients under full quantum state control for the rotationally inelastic collision of hydroxyl anions with helium. Experiment and quantum scattering theory show excellent agreement without adjustable parameters. Very similar rate coefficients are obtained for two different isotopes, which is linked to several quantum scattering resonances appearing at different energies. The presented method is also applicable to polyatomic systems and will help elucidate non-radiative processes in polyaromatic hydrocarbons and protein chromophores.

  4. Photochemical Heating of Dense Molecular Gas

    E-print Network

    Glassgold, A E

    2015-01-01

    Photochemical heating is analyzed with emphasis on the heating generated by chemical reactions initiated by the products of photodissociation and photoionization. The immediate products are slowed down by collisions with the ambient gas and heat the gas. In addition to this direct process, heating is also produced by the subsequent chemical reactions initiated by these products. Some of this chemical heating comes from the kinetic energy of the reaction products and the rest from collisional de-excitation of the product atoms and molecules. In considering dense gas dominated by molecular hydrogen, we find that the chemical heating is sometimes as large if not much larger than the direct heating. In very dense gas the total photochemical heating approaches 10 eV per photodissociation (or photoionization), competitive with other ways of heating molecular gas.

  5. Biosensors combine the high selectivity and sensitivity of molecular recognition processes of biologi-cal macromolecules with a transducer. The increase in mass by the recognition process can in princi-

    E-print Network

    Turova, Varvara

    Biosensors combine the high selectivity and sensitivity of molecular recognition processes. Keywords: biosensor, linear electro-elasticity, multi-layer structure, fluid-structure interaction, finite for Sensors and Actuators Modeling and Simulation Wave Propagation in Biosensors K.-H. Hoffmann N. Botkin, M

  6. Intramembranous Bone Healing Process Subsequent to Tooth Extraction in Mice: Micro-Computed Tomography, Histomorphometric and Molecular Characterization

    PubMed Central

    Vieira, Andreia Espindola; Repeke, Carlos Eduardo; Ferreira Junior, Samuel de Barros; Colavite, Priscila Maria; Biguetti, Claudia Cristina; Oliveira, Rodrigo Cardoso; Assis, Gerson Francisco; Taga, Rumio; Trombone, Ana Paula Favaro; Garlet, Gustavo Pompermaier

    2015-01-01

    Bone tissue has a significant potential for healing, which involves a significant the interplay between bone and immune cells. While fracture healing represents a useful model to investigate endochondral bone healing, intramembranous bone healing models are yet to be developed and characterized. In this study, a micro-computed tomography, histomorphometric and molecular (RealTimePCRarray) characterization of post tooth-extraction alveolar bone healing was performed on C57Bl/6 WT mice. After the initial clot dominance (0h), the development of a provisional immature granulation tissue is evident (7d), characterized by marked cell proliferation, angiogenesis and inflammatory cells infiltration; associated with peaks of growth factors (BMP-2-4-7,TGF?1,VEGFa), cytokines (TNF?, IL-10), chemokines & receptors (CXCL12, CCL25, CCR5, CXCR4), matrix (Col1a1-2, ITGA4, VTN, MMP1a) and MSCs (CD105, CD106, OCT4, NANOG, CD34, CD146) markers expression. Granulation tissue is sequentially replaced by more mature connective tissue (14d), characterized by inflammatory infiltrate reduction along the increased bone formation, marked expression of matrix remodeling enzymes (MMP-2-9), bone formation/maturation (RUNX2, ALP, DMP1, PHEX, SOST) markers, and chemokines & receptors associated with healing (CCL2, CCL17, CCR2). No evidences of cartilage cells or tissue were observed, strengthening the intramembranous nature of bone healing. Bone microarchitecture analysis supports the evolving healing, with total tissue and bone volumes as trabecular number and thickness showing a progressive increase over time. The extraction socket healing process is considered complete (21d) when the dental socket is filled by trabeculae bone with well-defined medullary canals; it being the expression of mature bone markers prevalent at this period. Our data confirms the intramembranous bone healing nature of the model used, revealing parallels between the gene expression profile and the histomorphometric events and the potential participation of MCSs and immune cells in the healing process, supporting the forthcoming application of the model for the better understanding of the bone healing process. PMID:26023920

  7. Molecular Astrophysics

    NASA Astrophysics Data System (ADS)

    Hartquist, T. W.

    2005-07-01

    Part I. Molecular Clouds and the Distribution of Molecules in the Milky Way and Other Galaxies: 1. Molecular clouds in the Milky Way P. Friberg and A. Hjalmarson; 2. Molecules in galaxies L. Blitz; Part II. Diffuse Molecular Clouds: 3. Diffuse cloud chemistry E. F. Van Dishoeck; 4. Observations of velocity and density structure in diffuse clouds W. D. Langer; 5. Shock chemistry in diffuse clouds T. W. Hartquist, D. R. Flower and G. Pineau des Forets; Part III. Quiescent Dense Clouds: 6. Chemical modelling of quiescent dense interstellar clouds T. J. Millar; 7. Interstellar grain chemistry V. Buch; 8. Large molecules and small grains in astrophysics S. H. Lepp; Part IV. Studies of Molecular Processes: 9. Molecular photoabsorption processes K. P. Kirby; 10. Interstellar ion chemistry: laboratory studies D. Smith, N. G. Adams and E. E. Ferguson; 11. Theoretical considerations on some collisional processes D. R. Bates; 12. Collisional excitation processes E. Roueff; 13. Neutral reactions at Low and High Temperatures M. M. Graff; Part V. Atomic Species in Dense Clouds: 14. Observations of atomic species in dense clouds G. J. Melnick; 15. Ultraviolet radiation in molecular clouds W. G. Roberge; 16. Cosmic ray induced photodissociation and photoionization of interstellar molecules R. Gredel; 17. Chemistry in the molecular cloud Barnard 5 S. B. Charnley and D. A. Williams; 18. Molecular cloud structure, motions, and evolution P. C. Myers; Part VI. H in Regions of Massive Star Formation: 19. Infrared observations of line emission from molecular hydrogen T. R. Geballe; 20. Shocks in dense molecular clouds D. F. Chernoff and C. F. McKee; 21. Dissociative shocks D. A. Neufeld; 22. Infrared molecular hydrogen emission from interstellar photodissociation regions A. Sternberg; Part VII. Molecules Near Stars and in Stellar Ejecta: 23. Masers J. M. Moran; 24. Chemistry in the circumstellar envelopes around mass-losing red giants M. Jura; 25. Atoms and molecules in supernova 1987a R. McCray; Part VIII. Moderately Ionized Gas and Chemistry at Large Redshifts: 26. Charge transfer in astrophysical nebulae G. A. Shields; 27. Molecules at early epochs J. H. Black.

  8. Cold collisions between chromium atoms*

    NASA Astrophysics Data System (ADS)

    Pavlovic, Zoran; Côté, R.; Sadeghpour, H. R.

    2002-05-01

    We report calculations of the elastic and spin exchange cross sections for collisions between two maximally spin-polarized chromium atoms near the ultracold regime, relevant to buffer-gas cooling of chromium atoms. Through a search of available data (calculation and experiment) on transition frequencies, discrete dipole matrix elements, and photoionization oscillator strengths in Cr, we obtain a value for the static polarizability of Cr and the dispersion coefficient C6 for the long range interaction between two Cr atoms. Our calculated polarizability is in good agreement with experiment. By combining the long range interaction potential with ab initio Cr2 molecular potential curves that correlate to two ground state Cr atoms, we explore the effect of shape resonances on elastic and spin-exchange rate coefficients in collision of chromium atoms.

  9. 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.

  10. Atom-molecule collisions in an optically trapped gas

    E-print Network

    Nassim Zahzam; Thibault Vogt; Marcel Mudrich; Daniel Comparat; Pierre Pillet

    2005-09-23

    Cold inelastic collisions between confined cesium (Cs) atoms and Cs$\\_2$ molecules are investigated inside a CO$\\_2$ laser dipole trap. Inelastic atom-molecule collisions can be observed and measured with a rate coefficient of $\\sim 2.5 \\times 10^{-11} $cm$^3$ s$^{-1}$, mainly independent of the molecular ro-vibrational state populated. Lifetimes of purely atomic and molecular samples are essentially limited by rest gas collisions. The pure molecular trap lifetime ranges 0,3-1 s, four times smaller than the atomic one, as is also observed in a pure magnetic trap. We give an estimation of the inelastic molecule-molecule collision rate to be $\\sim 10^{-11}$ cm$^{3}$ s$^{-1}$.

  11. Spectroscopic investigation of the NO C 2? de-excitation process by collision with O2 X 3?g? in a low-pressure N2–O2 mixture microwave discharge

    NASA Astrophysics Data System (ADS)

    Tan, Hao; Nezu, Atsushi; Akatsuka, Hiroshi

    2016-01-01

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

  12. Rice phytochemicals concentrated by molecular distillation process and their use as co-surfactant in water dispersion.

    PubMed

    Sawadikiat, Pattong; Setwipattanachai, Prasert; Chaiseri, Siree; Hongsprabhas, Parichat

    2015-12-01

    This study investigated the effects of evaporating temperature during molecular distillation (MD) process employed to deodorizer distillate (DD) on the retention of rice phytochemicals in the unevaporated fraction (UMDs), which were then further used as co-surfactants in the fabrication of water-dispersible vesicles. The pilot-scale MD unit was operated at 120, 140 or 160 °C and 0.1 Pa to concentrate rice phytosterols from 1540.8 mg in 100 g DD to 3990.2-4904.8 mg in 100 g UMDs by evaporating out free fatty acids. Although ?-oryzanol content was increased from 598.9 mg in 100 g DD to 870.0-1018.1 mg in 100 g UMDs when the temperature was raised to 160 °C, such high temperature decreased tocols from 2185.7 mg in 100 g DD to 850.5 mg in 100 g UMDs and antioxidant capacity of UMDs measured as 2,2-diphenyl-1-picrylhydrazyl scavenging capacity. The UMD obtained after distillation at 140 °C was used as co-surfactant with soy lecithin, sucrose palmitate or polyoxyethylene sorbitan monooleate (Tween 80) to fabricate vesicles in pH 7.0 phosphate buffered saline (PBS). This study showed potential use of the UMD as a source of rice phytochemicals and a co-surfactant when used with Tween80 in small vesicle fabrication. The fabricated Tween 80/UMD vesicles in PBS had the size range of 200-300 nm and were stable within a temperature range of 4 to 37 °C for 96 h. PMID:26604373

  13. Molecular spectroscopic investigation on fractionation-induced changes on biomacromolecule of co-products from bioethanol processing to explore protein metabolism in ruminants

    NASA Astrophysics Data System (ADS)

    Zhang, Xuewei; Yan, Xiaogang; Beltranena, Eduardo; Yu, Peiqiang

    2014-03-01

    Fractionation processing is an efficient technology which is capable to redesign/redevelop a new food or feed product with a specified chemical and nutrient profile. This processing technique was able to produce four different fractions (called "A", "B", "C", "D" fractions/treatments) with different nutrient profile form a co-product of bioethanol processing [wheat dried distillers grains with soluble (DDGS)]. To date, there is no study on the effect of fractionation processing on inherent molecular structure of different fractions and how the processing-induced structural change affect the metabolic characteristics of protein and nutrient availability. The objectives of this experiment were to: (1) investigate the effect of fractionation processing on changes of protein functional groups (amide I, amide II, and their ratio) and molecular structure (modeled ?-helix, ?-sheet, and their ratio), and (2) study the relationship between the fractionation processing-induced changes of protein molecular structure and nutrients availability as well as the metabolic characteristics of protein. The hypothesis of this study was that the fractionation processing changes the molecular structure and such changes affect the metabolic characteristics of protein. The protein molecular structure spectral profile of the fractions A, B, C and D were identified by Fourier-transform infrared attenuated total reflection spectroscopy (FT/IR-ATR). The results showed that the fractionation processing significantly affected the protein molecular spectral profiles. The differences in amide I to amide II peak area and height ratios were strongly significant (P < 0.01) among the treatment fractions, ranging from 4.98 to 6.33 and 3.28 to 4.00, respectively. The difference in the modeled protein ?-helix to ?-sheet ratio was also strongly significant (P < 0.01) among the treatment fractions. Multivariate molecular spectral analysis with cluster (CLA) and principal component analyses (PCA) showed that there are no clear distinguished clusters and ellipses among the fractions (A, B, C and D) in the protein amide I and II region ca. 1726-1485 cm-1. The correlation study showed that the modeled ?-helix to ?-sheet ratio tended to have a negative correlation with truly absorbed rumen undegraded protein (ARUPDVE: r = -0.944, P = 0.056 < 0.10) and total truly absorbed protein in the small intestine (DVE: r = -0.946, P = 0.054 < 0.10), but there was no correlation between the ?-helix to ?-sheet ratio and the degraded protein balance (DPBOEB: P = 0.267 < 0.10). In conclusion, the fractionation processing changed the molecular structural spectral profiles in terms of amide I to II ratio and ?-helix to ?-sheet ratio. These changes negatively affected the metabolic characteristics of protein and true protein supply. These results indicated that spectral features of different fractions could be used as a potential tool to predict true protein nutritive value.

  14. Effects of conditioning temperature and time during the pelleting process on feed molecular structure, pellet durability index, and metabolic features of co-products from bio-oil processing in dairy cows.

    PubMed

    Huang, Xuewei; Christensen, Colleen; Yu, Peiqiang

    2015-07-01

    The objectives of this study were to systematically determine effects of conditioning temperature (70, 80, and 90°C), time (50 and 75 s), and interaction (temperature × time) during the pelleting process on co-products from bio-oil processing (canola meal) in terms of processing-induced changes on (1) protein molecular structure, (2) pellet durability index, (3) detailed chemical profile, (4) metabolic features and fractions of protein and carbohydrate, (5) total digestible nutrients and energy values, and (6) rumen degradable and undegradable content. Pellet durability was increased with increasing conditioning time. Chemical and carbohydrate profiles of co-products were not altered by pelleting process under different conditioning temperatures and times. With regard to protein fraction profiles, pellets conditioned for 50 s had higher soluble crude protein (SCP) and lower neutral detergent insoluble crude protein (NDICP) contents than those conditioned for 75 s (21.7 vs. 20.1% SCP, 16.0 vs. 16.5% NDICP, respectively). Total digestible nutrients and energy values were not altered by processing. Samples conditioned for 50 s had a higher content of rapidly degradable protein fraction (PA2) than those conditioned for 75 s (21.7 vs. 21.1% crude protein). In addition, the slowly degradable true protein fraction (PB2) was affected by the interaction of conditioning temperature and time. However, carbohydrate fractions did not differ with different conditioning temperatures and time. Different temperatures and time of conditioning during pelleting process greatly affect protein profiles without altering carbohydrate profiles. Molecular structure analyses also showed that pelleting altered inherent protein molecular structures of the co-products from bio-oil processing. Future study is needed to detect how molecular structure changes affect nutrient availability in dairy cattle. PMID:25958276

  15. Atomic and molecular physics of controlled thermonuclear fusion

    SciTech Connect

    Joachain, C.J.; Post, D.E.

    1983-01-01

    This book attempts to provide a comprehensive introduction to the atomic and molecular physics of controlled thermonuclear fusion, and also a self-contained source from which to start a systematic study of the field. Presents an overview of fusion energy research, general principles of magnetic confinement, and general principles of inertial confinement. Discusses the calculation and measurement of atomic and molecular processes relevant to fusion, and the atomic and molecular physics of controlled thermonuclear research devices. Topics include recent progress in theoretical methods for atomic collisions; current theoretical techniques for electron-atom and electronion scattering; experimental aspects of electron impact ionization and excitation of positive ions; the theory of charge exchange and ionization by heavy particles; experiments on electron capture and ionization by multiply charged ions; Rydberg states; atomic and molecular processes in high temperature, low-density magnetically confined plasmas; atomic processes in high-density plasmas; the plasma boundary region and the role of atomic and molecular processes; neutral particle beam production and injection; spectroscopic plasma diagnostics; and particle diagnostics for magnetic fusion experiments.

  16. Molecular localization induced by collisions Vincenzo Grecchi

    E-print Network

    of the metastable states. We show also that the red shift effect of the inversion line can be given by this model, vanishes (red shift) in the limit of large pressure of the gas and we have the pyramidal shape with full of the splitting (red shift of the inversion line) at a critical pressure; at this value of the pressure (frequency

  17. The effect of cross-linking on the molecular dynamics of the segmental and ? Johari-Goldstein processes in polyvinylpyrrolidone-based copolymers.

    PubMed

    Redondo-Foj, Belén; Sanchis, María Jesús; Ortiz-Serna, Pilar; Carsí, Marta; García, José Miguel; García, Félix Clemente

    2015-09-28

    The effect of the cross-link density on the molecular dynamics of copolymers composed of vinylpyrrolidone (VP) and butyl acrylate (BA) was studied using differential scanning calorimetry (DSC) and dielectric relaxation spectroscopy (DRS). A single glass transition was detected by DSC measurements. The dielectric spectra exhibit conductive processes and three dipolar relaxations labeled as ?, ? and ? in the decreasing order of temperatures. The cross-linker content affects both ? and ? processes, but the fastest ? process is relatively unaffected. An increase of cross-linking produces a typical effect on the ? process dynamics: (i) the glass transition temperature is increased, (ii) the dispersion is broadened, (iii) its strength is decreased and (iv) the relaxation times are increased. However, the ? process, which possesses typical features of a pure Johari-Goldstein relaxation, unexpectedly loses the intermolecular character for the highest cross-linker content. PMID:26255757

  18. Antiproton production in heavy ion collisions

    SciTech Connect

    Jacak, B.V.; NA44 Collaboration

    1993-12-31

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

  19. Collision of H+ + CH4 at 30 eV: A simulation study

    NASA Astrophysics Data System (ADS)

    Gao, Cong-Zhang; Wang, Jing; Zhang, Feng-Shou

    2013-07-01

    The process of proton impinging upon CH4 molecule has been theoretically studied at 30 eV. The study is based on time-dependent local density approximation coupled with molecular dynamics model. The electronic density evolution, ionic motion, and the scattering angle are presented. We found that the mechanism of target ionization in present simulation is electron capture. The predicted rainbow angle is in good agreement with experiments and previous calculations. By comparing the scattering angle from present calculation with that from classical collision, we found that the nuclear stopping is dominant in small impact parameters, and the discrepancy in large impact parameters may be due to the neglect of electronic stopping in classical collision.

  20. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  1. Processing, Characterization and Fretting Wear of Zinc Oxide and Silver Nanoparticles Reinforced Ultra High Molecular Weight Polyethylene Biopolymer Nanocomposite

    NASA Astrophysics Data System (ADS)

    Alam, Fahad; Kumar, Anil; Patel, Anup Kumar; Sharma, Rajeev K.; Balani, Kantesh

    2015-04-01

    Ultra-high molecular weight polyethylene (UHMWPE) is the most widely used biopolymer for articulating surfaces, such as an acetabular cup liner interfacing with a metal/ceramic femoral head. However, the formation of wear debris leads to the aseptic loosening of implants. Thus, in order to improve the life span via enhancing the fretting wear resistance, UHMWPE is reinforced with ZnO/Ag nanoparticles. It is envisaged that the ZnO/Ag addition will also exhibit antibacterial properties. In the current study, the synergetic effect of the reinforcement of ZnO/Ag nanoparticles (0-3 wt.% combinations) on the fretting wear behavior of a UHMWPE matrix is assessed. The phase characterization of compression- molded UHMWPE-Ag-ZnO biopolymer nanocomposites has elicited the retention of starting phases. All samples were processed at >98% density using compression molding. Silver and ZnO reinforcement showed enhanced hardness ~20.4% for U3A and 42.0% for U3Z. Fretting wear performance was evaluated at varying loads (5-15 N), keeping in mind the weight at different joints, with constant frequency (5 Hz) as well as amplitude of oscillation (100 µm). Laser surface profilometry showed change of wear volume from 8.6 × 10-5 mm3 for neat polymer to 5.8 × 10-5 mm3 with 1 wt.% Ag + 1 wt.% ZnO reinforcement (at 15 N load). Consequently, the mechanics of resistance offered by Ag and ZnO is delineated in the UHMWPE matrix. Further, S. aureus viability reduction is ~28.7% in cases with 1 wt.% Ag addition, ~42.5% with 1 wt.% ZnO addition, but synergistically increase to ~58.6% and 47.1% when each of Ag and ZnO is added with 1 wt.% and 3 wt.%, respectively (when compared to that of the UHMWPE control sample). Increased wear resistance and superior bioactivity and enhanced anti-bacterial properties of 1 wt.% Ag + 1 wt.% ZnO and 3 wt.% Ag + 3 wt.% ZnO shows the potential use of ZnO-Ag-UHMWPE biopolymer composites as an articulating surface.

  2. Direct Photons in Heavy-Ion Collisions

    E-print Network

    Klaus Reygers

    2006-11-06

    A brief overview of direct-photon measurements in ultra-relativistic nucleus-nucleus collisions is given. The results for Pb+Pb collisions at sqrt{s_NN} = 17.3 GeV and for Au+Au collisions at sqrt{s_NN} = 200 GeV are compared to estimates of the direct-photon yield from hard scattering. Both results leave room for a significant thermal photon component. A description purely based on hard scattering processes, however, is not ruled out so far.

  3. 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.

  4. Generation of metastable rare-gas beams and studies of electron-metastable collision processes. Final technical report, January 1, 1990--September 30, 1991

    SciTech Connect

    McKoy, V.; Trajmar, S.

    1993-12-31

    The basic goals of this research effort of designing, developing, and testing a high-flux, high-purity metastable rare-gas beam source suitable for measurements of electron-collisions have been achieved. Here the authors briefly describe the status of this effort. This effort will be pursued with support from other sources of funding and results of this subsequent effort will be made available to Los Alamos National Laboratory. On the theoretical side they have extended their procedure for calculating the cross sections for electron impact excitation of molecules to determine these cross sections for collisions with metastable states of molecules. As a relevant application they have studied the differential and integral cross sections for the a {sup 1}{Delta}{sub g} {yields} b {sup 1}{Sigma}{sub g}{sup +} transition in O{sub 2} for which measurements (R.I. Hall and S. Trajmar, J. Phys. B 8, L293 (1975)) were available at a single energy (4.5 eV). The agreement between the calculated and measured values of these cross sections is encouraging and support the large value reported experimentally.

  5. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    E-print Network

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V

    2015-01-01

    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

  6. Nucleon and Baryons densities in heavy ion collisions at 1 to 3 GeV/A

    NASA Astrophysics Data System (ADS)

    Alharbi, Hamoud; Almalki, Masaud

    2014-03-01

    Excited Baryons resonance production is investigated within the Ultra-Relativistic Quantum Molecular Dynamics model (UrQMD). The evolution of density at the collision center for different collision times was investigated. The maximum densities yields at maximum compression time was calculated at deferent projectile energies. Radial and angular distribution for nucleon density was calculated for each collision energy. Baryon resonances produced in relativistic heavy ion collisions are present for time much longer than the free Baryon lifetime would suggest, which means that there is a continues baryon reproduction. Our results was in qualitative agreement with previous calculations using Isospin dependent Quantum Molecular Dynamics (IQMD).

  7. A 3-YEAR DOCTORAL SCHOLARSHIP IN MOLECULAR ENZYMOLOGY APPLIED TO THE DEVELOPMENT OF ENZYMES FOR BIOREFINING PROCESSES

    E-print Network

    Papanicolaou, Vassilis

    A 3-YEAR DOCTORAL SCHOLARSHIP IN MOLECULAR ENZYMOLOGY APPLIED TO THE DEVELOPMENT OF ENZYMES of biofuels, enzymes will play increasingly important roles in the fractionation and the optimal transformation of the different biomass components. To develop new enzyme tools the Laboratory of Systems Biology

  8. 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.

  9. Newton's cradle versus nonbinary collisions.

    PubMed

    Sekimoto, Ken

    2010-03-26

    Newton's cradle is a classical example of a one-dimensional impact problem. In the early 1980s the naive perception of its behavior was corrected: For example, the impact of a particle does not exactly cause the release of the farthest particle of the target particle train, if the target particles have been just in contact with their own neighbors. It is also known that the naive picture would be correct if the whole process consisted of purely binary collisions. Our systematic study of particle systems with truncated power-law repulsive force shows that the quasibinary collision is recovered in the limit of hard core repulsion, or a very large exponent. In contrast, a discontinuous steplike repulsive force mimicking a hard contact, or a very small exponent, leads to a completely different process: the impacting cluster and the targeted cluster act, respectively, as if they were nondeformable blocks. PMID:20366538

  10. 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.

  11. Phase shifts in the collision of massive particles

    SciTech Connect

    Sidharth, B.G.

    1989-03-01

    In this paper phase shifts for inverse power potentials and their superpositions are considered. These potentials govern a large number of collision processes involving massive particles. But they are problematic as they do not conform to the norms obeyed by standard potentials: The usual rules for estimating the error of the phase shifts break down and an abnormally large number of phase shifts have to be computed, even if they are small. A sufficiency condition is deduced for the applicability of the Born approximation which shows that, for a given potential strength and l, surprisingly, the Born approximation is good at low energies and bad at high energies. The magnitude and direction of the error committed are also estimated. These conclusions are then verified in a number of special cases, for instance, the inverse fourth power potential used in the scattering of electrons by atoms and the Lennard--Jones potential used in the scattering of beams of molecular hydrogen with mercury atoms.

  12. Collision induced ultraviolet structure in nitrogen radar REMPI spectra

    SciTech Connect

    McGuire, S. Miles, R.

    2014-12-28

    We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}?{sub g} ? X{sup 1}?{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ?1}?{sub g}{sup +} electronic state.

  13. Two-photon total annihilation of molecular positronium

    NASA Astrophysics Data System (ADS)

    Pérez-Ríos, Jesús; Love, Sherwin T.; Greene, Chris H.

    2015-03-01

    The rate for complete two-photon annihilation of molecular positronium Ps2 is reported. This decay channel involves a four-body collision among the fermions forming Ps2, and two photons of 1.022 MeV, each, as the final state. The quantum electrodynamics result for the rate of this process is found to be ?Ps2 ? ??= 9.0× 10-12 \\text{s}-1 . This decay channel completes the most comprehensive decay chart for Ps2 up to date.

  14. Collision-spike Sputtering of Au Nanoparticles.

    PubMed

    Sandoval, Luis; Urbassek, Herbert M

    2015-12-01

    Ion irradiation of nanoparticles leads to enhanced sputter yields if the nanoparticle size is of the order of the ion penetration depth. While this feature is reasonably well understood for collision-cascade sputtering, we explore it in the regime of collision-spike sputtering using molecular-dynamics simulation. For the particular case of 200-keV Xe bombardment of Au particles, we show that collision spikes lead to abundant sputtering with an average yield of 397 ± 121 atoms compared to only 116 ± 48 atoms for a bulk Au target. Only around 31 % of the impact energy remains in the nanoparticles after impact; the remainder is transported away by the transmitted projectile and the ejecta. The sputter yield of supported nanoparticles is estimated to be around 80 % of that of free nanoparticles due to the suppression of forward sputtering. PMID:26245857

  15. Collision-spike Sputtering of Au Nanoparticles

    NASA Astrophysics Data System (ADS)

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-01

    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.

  16. 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.

  17. Collision-spike sputtering of Au nanoparticles

    DOE PAGESBeta

    Sandoval, Luis; Urbassek, Herbert M.

    2015-08-06

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

  18. State-to-state dynamics of molecular energy transfer

    SciTech Connect

    Gentry, W.R.; Giese, C.F.

    1993-12-01

    The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

  19. Basins in ARC-continental collisions

    USGS Publications Warehouse

    Draut, Amy E.; Clift, Peter D.

    2012-01-01

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

  20. Collision statistics in sheared inelastic hard spheres

    E-print Network

    Marcus N. Bannerman; Thomas E. Green; Paul Grassia; Leo Lue

    2009-03-24

    The dynamics of sheared inelastic-hard-sphere systems are studied using non-equilibrium molecular dynamics simulations and direct simulation Monte Carlo. In the molecular dynamics simulations Lees-Edwards boundary conditions are used to impose the shear. The dimensions of the simulation box are chosen to ensure that the systems are homogeneous and that the shear is applied uniformly. Various system properties are monitored, including the one-particle velocity distribution, granular temperature, stress tensor, collision rates, and time between collisions. The one-particle velocity distribution is found to agree reasonably well with an anisotropic Gaussian distribution, with only a slight overpopulation of the high velocity tails. The velocity distribution is strongly anisotropic, especially at lower densities and lower values of the coefficient of restitution, with the largest variance in the direction of shear. The density dependence of the compressibility factor of the sheared inelastic hard sphere system is quite similar to that of elastic hard sphere fluids. As the systems become more inelastic, the glancing collisions begin to dominate more direct, head-on collisions. Examination of the distribution of the time between collisions indicates that the collisions experienced by the particles are strongly correlated in the highly inelastic systems. A comparison of the simulation data is made with DSMC simulation of the Enskog equation. Results of the kinetic model of Montanero et al. {[}Montanero et al., J. Fluid Mech. 389, 391 (1999){]} based on the Enskog equation are also included. In general, good agreement is found for high density, weakly inelastic systems.

  1. Control of Ultracold Collisions with Frequency-Chirped Light

    SciTech Connect

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

    2005-08-05

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

  2. Translational Molecular Nuclear Cardiology.

    PubMed

    Thackeray, James T; Bengel, Frank M

    2016-02-01

    Increased rollout and availability of preclinical imaging provides a foundation for development of novel molecular nuclear imaging agents. The current armamentarium of radiotracers available for nuclear cardiology allows for the interrogation of critical molecular processes involved in a myriad of cardiovascular disorders, including altered metabolism, ventricular remodeling, sympathetic neuronal activation, and systemic inflammation. Effective translational molecular imaging requires coordination of clinical need with tracer development and molecular biology, leading to the identification of ideal translational imaging compounds. PMID:26590789

  3. A novel “correlated ion and neutral time of flight” method: Event-by-event detection of neutral and charged fragments in collision induced dissociation of mass selected ions

    SciTech Connect

    Teyssier, C.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.; Université de Lyon, F-69003, Lyon; CNRS Märk, T. D.

    2014-01-15

    A new tandem mass spectrometry (MS/MS) method based on time of flight measurements performed on an event-by-event detection technique is presented. This “correlated ion and neutral time of flight” method allows to explore Collision Induced Dissociation (CID) fragmentation processes by directly identifying not only all ions and neutral fragments produced but also their arrival time correlations within each single fragmentation event from a dissociating molecular ion. This constitutes a new step in the characterization of molecular ions. The method will be illustrated here for a prototypical case involving CID of protonated water clusters H{sup +}(H{sub 2}O){sub n=1–5} upon collisions with argon atoms.

  4. Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media

    SciTech Connect

    Bourg, I.C.; Sposito, G.

    2009-12-01

    In this paper, we address the manner in which the continuum-scale diffusive properties of smectite-rich porous media arise from their molecular- and pore-scale features. Our starting point is a successful model of the continuum-scale apparent diffusion coefficient for water tracers and cations which decomposes it as a sum of pore-scale terms describing diffusion in macropore and interlayer 'compartments.' We then apply molecular dynamics (MD) simulations to determine molecular-scale diffusion coefficients D{sub interlayer} of water tracers and representative cations (Na{sup +}, Cs{sup +}, Sr{sup 2+}) in Na-smectite interlayers. We find that a remarkably simple expression relates D{sub interlayer} to the pore-scale parameter {delta}{sub nanopore} {<=} 1, a constrictivity factor that accounts for the lower mobility in interlayers as compared to macropores: {delta}{sub nanopore} = D{sub interlayer}/D{sub 0}, where D{sub 0} is the diffusion coefficient in bulk liquid water. Using this scaling expression, we can accurately predict the apparent diffusion coefficients of tracer H{sub 2}O, Na{sup +}, Sr{sup 2+} and Cs{sup +}+ in compacted Na-smectite-rich materials.

  5. Self-interaction-free time-dependent density-functional theory for molecular processes in strong fields:? High-order harmonic generation of H2 in intense laser fields

    E-print Network

    Chu, Shih-I; Chu, Xi

    2001-01-17

    We present a self-interaction-free time-dependent density-functional theory (TDDFT) for nonperturbative treatment of multiphoton processes of many-electron molecular systems in intense laser fields. The time-dependent exchange-correlation (xc...

  6. Quantum Chaos in Ultracold Collisions of Erbium

    E-print Network

    Frisch, Albert; Aikawa, Kiyotaka; Ferlaino, Francesca; Bohn, John L; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana

    2013-01-01

    Atomic and molecular samples reduced to temperatures below 1 microkelvin, yet still in the gas phase, afford unprecedented energy resolution in probing and manipulating how their constituent particles interact with one another. For simple atoms, such as alkalis, scattering resonances are extremely well-characterized. However, ultracold physics is now poised to enter a new regime, where far more complex species can be cooled and studied, including magnetic lanthanide atoms and even molecules. For molecules, it has been speculated that a dense forest of resonances in ultracold collision cross sections will likely express essentially random fluctuations, much as the observed energy spectra of nuclear scattering do. According to the Bohigas-Giannoni-Schmit conjecture, these fluctuations would imply chaotic dynamics of the underlying classical motion driving the collision. This would provide a paradigm shift in ultracold atomic and molecular physics, necessitating new ways of looking at the fundamental interaction...

  7. 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 ?m 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.

  8. Evolution and stability of shock waves in dissipative gases characterized by activated inelastic collisions

    NASA Astrophysics Data System (ADS)

    Sirmas, N.; Radulescu, M. I.

    2015-02-01

    Previous experiments have revealed that shock waves driven through dissipative gases may become unstable, for example, in granular gases and in molecular gases undergoing strong relaxation effects. The mechanisms controlling these instabilities are not well understood. We successfully isolated and investigated this instability in the canonical problem of piston-driven shock waves propagating into a medium characterized by inelastic collision processes. We treat the standard model of granular gases, where particle collisions are taken as inelastic, with a constant coefficient of restitution. The inelasticity is activated for sufficiently strong collisions. Molecular dynamic simulations were performed for 30 000 particles. We find that all shock waves investigated become unstable, with density nonuniformities forming in the relaxation region. The wavelength of these fingers is found to be comparable to the characteristic relaxation thickness. Shock Hugoniot curves for both elastic and inelastic collisions were obtained analytically and numerically. Analysis of these curves indicates that the instability is not of the Bethe-Zeldovich-Thompson or D'yakov-Kontorovich type. Analysis of the shock relaxation rates and rates for clustering in a convected fluid element with the same thermodynamic history ruled out the clustering instability of a homogeneous granular gas. Instead, wave reconstruction of the early transient evolution indicates that the onset of instability occurs during repressurization of the gas following the initial relaxation of the medium behind the lead shock. This repressurization gives rise to internal pressure waves in the presence of strong density gradients. This indicates that the mechanism of instability is more likely of the vorticity-generating Richtmyer-Meshkov type, relying on the action of the inner pressure wave development during the transient relaxation.

  9. Evolution and stability of shock waves in dissipative gases characterized by activated inelastic collisions

    E-print Network

    Nick Sirmas; Matei I. Radulescu

    2015-01-14

    Previous experiments have revealed that shock waves driven through dissipative gases may become unstable, for example, in granular gases, and in molecular gases undergoing strong relaxation effects. The mechanisms controlling these instabilities are not well understood. We successfully isolated and investigated this instability in the canonical problem of piston driven shock waves propagating into a medium characterized by inelastic collision processes. We treat the standard model of granular gases, where particle collisions are taken as inelastic with constant coefficient of restitution. The inelasticity is activated for sufficiently strong collisions. Molecular dynamic simulations were performed for 30,000 particles. We find that all shock waves investigated become unstable, with density non-uniformities forming in the relaxation region. The wavelength of these fingers is found comparable to the characteristic relaxation thickness. Shock Hugoniot curves for both elastic and inelastic collisions were obtained analytically and numerically. Analysis of these curves indicate that the instability is not of the Bethe-Zeldovich-Thompson or Dyakov-Kontorovich types. Analysis of the shock relaxation rates and rates for clustering in a convected fluid element with the same thermodynamic history outruled the clustering instability of a homogeneous granular gas. Instead, wave reconstruction of the early transient evolution indicates that the onset of instability occurs during the re-pressurization of the gas following the initial relaxation of the medium behind the lead shock. This re-pressurization gives rise to internal pressure waves in the presence of strong density gradients. This indicates that the mechanism of instability is more likely of the vorticity-generating Richtmyer-Meshkov type, relying on the action of the inner pressure waves development during the transient relaxation.

  10. Evolution and stability of shock waves in dissipative gases characterized by activated inelastic collisions.

    PubMed

    Sirmas, N; Radulescu, M I

    2015-02-01

    Previous experiments have revealed that shock waves driven through dissipative gases may become unstable, for example, in granular gases and in molecular gases undergoing strong relaxation effects. The mechanisms controlling these instabilities are not well understood. We successfully isolated and investigated this instability in the canonical problem of piston-driven shock waves propagating into a medium characterized by inelastic collision processes. We treat the standard model of granular gases, where particle collisions are taken as inelastic, with a constant coefficient of restitution. The inelasticity is activated for sufficiently strong collisions. Molecular dynamic simulations were performed for 30,000 particles. We find that all shock waves investigated become unstable, with density nonuniformities forming in the relaxation region. The wavelength of these fingers is found to be comparable to the characteristic relaxation thickness. Shock Hugoniot curves for both elastic and inelastic collisions were obtained analytically and numerically. Analysis of these curves indicates that the instability is not of the Bethe-Zeldovich-Thompson or D'yakov-Kontorovich type. Analysis of the shock relaxation rates and rates for clustering in a convected fluid element with the same thermodynamic history ruled out the clustering instability of a homogeneous granular gas. Instead, wave reconstruction of the early transient evolution indicates that the onset of instability occurs during repressurization of the gas following the initial relaxation of the medium behind the lead shock. This repressurization gives rise to internal pressure waves in the presence of strong density gradients. This indicates that the mechanism of instability is more likely of the vorticity-generating Richtmyer-Meshkov type, relying on the action of the inner pressure wave development during the transient relaxation. PMID:25768593

  11. Recombination in nuclear collisions

    E-print Network

    Rudolph C. Hwa

    2010-09-02

    Recombination is a hadronization process that converts partons to hadrons at late time, but the description has no quantitative significance without some meaningful input on the parton distributions at earlier time. Thus observations of particle spectra and correlations have definitive implications on the partonic processes at all transverse momenta. After presenting a general review of the subject at the Workshop, I selected two topics in nuclear collisions for more detailed discussion, which are summarized here. One is on the azimuthal anisotropy at low $p_T$ due to hard or semihard scattering of partons that create ridges with or without triggers. The ridge particles are the products of recombination of thermal partons enhanced by the energy loss of hard or semihard partons. Their $\\phi$ dependence at midrapidity can be determined essentially from geometry. The other topic is on the scaling behavior in $\\phi$ and centrality at high $p_T$, where the hadronization process is dominated by TS and SS recombination. The relevant RHIC data are found to have the same scaling behavior. But at LHC such scaling is badly broken at $p_T \\sim 10$ GeV/c if two-jet recombination is important. At the end of this article some comments are made to relate our study of the effects of semihard partons to the observation of minijets in the analyses of STAR data.

  12. Quasimolecular single-nucleon effects in heavy-ion collisions

    SciTech Connect

    Erb, K.A.

    1984-01-01

    Several experimental examples are discussed to illustrate that single-particle molecular orbital behavior has become an established reality in nuclear physics over the last several years. Measurements and analyses of inelastic scattering in the /sup 13/C + /sup 12/C and /sup 17/O + /sup 12/C systems, and of neutron transfer in the /sup 13/C(/sup 13/C, /sup 12/C)/sup 14/C reaction, show that the motion of valence nucleons can be strongly and simultaneously influenced by both collision partners in heavy-ion collisions. This bvehavior is characteristic of a molecular (single-particle) rather than a direct (DWBA) mechanism: it demonstrates that the single-particle analog of atomic molecular motion plays an important role in nuclear reactions at bombarding energies near the Coulomb barrier. Such behavior may be even more pronounced in the collisions of massive nuclei that will be studied with the new generation of heavy-ion accelerators. 19 references.

  13. Data for modeling of positron collisions and transport in gases

    NASA Astrophysics Data System (ADS)

    Petrovi?, Z. Lj.; Bankovi?, A.; Dujko, S.; Marjanovi?, S.; Malovi?, G.; Sullivan, J. P.; Buckman, S. J.

    2013-07-01

    We review the current status of positron cross sections for collisions with atoms and molecules from the viewpoint of their use in studies of positron transport processes in gases, liquids and human tissue. The data include cross sections for positron scattering in rare gases, molecular gases (eg., for N2, H2, CO2, CF4) and in particular for organic molecules and those relevant for applications in medicine (e.g. formic acid and water vapor). The cross sections were taken from an assessment of previously published positron-target cross sections. All of the cross sections are based on binary collision measurements and theoretical calculations, and they were not explicitly modified according to the standard swarm analysis. The main reason for this is systematic lack of experimental data for positron transport properties in gases. However, we believe that our compiled sets of cross sections are at level of sophistication, and of sufficient accuracy, to provide correct interpretation of future positron-based experiments. Using these cross sections as an input in our Monte Carlo simulations and Boltzmann equation treatment, we review some interesting points observed in the profiles of various transport coefficients for positrons in gases. Particular emphasis is placed upon the analysis of kinetic phenomena generated by the explicit influence of Ps formation.

  14. 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.

  15. Collisions of trapped molecules with slow beams

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    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,MJ=3/2,f) molecules with He4 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 He4 + OH collisions are consistent with recent experimental observations at low beam energies [B. C. Sawyer , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.101.203203 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.

  16. Effect of molecular weight and protection ratio on line edge roughness and stochastic defect generation in chemically amplified resist processes of extreme ultraviolet lithography

    NASA Astrophysics Data System (ADS)

    Kozawa, Takahiro; Santillan, Julius Joseph; Itani, Toshiro

    2014-08-01

    The suppression of stochastic effects such as line edge roughness (LER) and stochastic defect generation is required for the high-volume production of semiconductor devices with 11 nm critical dimension using extreme ultraviolet (EUV) lithography. In this study, the effects of the molecular weight and protection ratio of a resist polymer on LER and stochastic defect generation were investigated, assuming line-and-space patterns with 11 nm half-pitch. By increasing the molecular weight, LER and the probability of stochastic defect generation were decreased. The negative effect caused by the increase of molecular weight is the increase of the minimum dissolution block size in the development process. By increasing the protection ratio, a similar effect was expected. However, LER and the probability of stochastic defect generation were not significantly decreased because of the decrease of the quantum efficiency of acid generation caused by the protection of proton sources. It is important to increase the protection ratio without decreasing the quantum efficiency of acid generation for the suppression of LER and stochastic defect generation.

  17. Dynamical constraints and nuclear spin caused restrictions in HmD+ collision systems.

    PubMed

    Gerlich, D; Windisch, F; Hlavenka, P; Plasil, R; Glosik, J

    2006-11-15

    This contribution summarizes a variety of results and ongoing activities, which contribute to our understanding of inelastic and reactive collisions involving hydrogen ions. In an overview of our present theoretical knowledge of various HmD+ collision systems (m + n < or = 5), it is emphasized that although the required potential energy surfaces are well characterized, no detailed treatments of the collision dynamics are available to date, especially at the low energies required for astrochemistry. Instead of treating state-to-state dynamics with state of the art methods, predictions are still based on: (i) simple thermodynamical arguments, (ii) crude reaction models such as H atom exchange or proton jump, or (iii) statistical considerations used for describing processes proceeding via long-lived or strongly interacting collision complexes. A central problem is to properly account for the consequences of the fact that H and D are fermions and bosons, respectively. In the experimental and results sections, it is emphasized that although a variety of innovative techniques are available and have been used for measuring rate coefficients, cross-sections or state-to-state transition probabilities, the definitive experiments are still pending. In the centre of this contribution are our activities on various m + n = 5 systems. We report a few selected additional results for collisions of hydrogen ions with p-H2, o-H2, HD, D2 or well-defined mixtures of these neutrals. Most of the recent experiments are based on temperature variable multipole ion traps and their combination with pulsed gas inlets, molecular beams, laser probing or electron beams. Based on the state-specific model calculations, it is concluded that for completely understanding the gas phase formation and destruction of HmDn+ in a trap, an in situ characterization of all the experimental parameters is required with unprecedented accuracy. Finally, the need to understand the hydrogen chemistry relevant for dense pre-stellar cores is discussed. PMID:17015392

  18. The frequency and nature of `cloud-cloud collisions' in galaxies

    NASA Astrophysics Data System (ADS)

    Dobbs, C. L.; Pringle, J. E.; Duarte-Cabral, A.

    2015-02-01

    We investigate cloud-cloud collisions and giant molecular cloud evolution in hydrodynamic simulations of isolated galaxies. The simulations include heating and cooling of the interstellar medium (ISM), self-gravity and stellar feedback. Over time-scales <5 Myr most clouds undergo no change, and mergers and splits are found to be typically two-body processes, but evolution over longer time-scales is more complex and involves a greater fraction of intercloud material. We find that mergers or collisions occur every 8-10 Myr (1/15th of an orbit) in a simulation with spiral arms, and once every 28 Myr (1/5th of an orbit) with no imposed spiral arms. Both figures are higher than expected from analytic estimates, as clouds are not uniformly distributed in the galaxy. Thus, clouds can be expected to undergo between zero and a few collisions over their lifetime. We present specific examples of cloud-cloud interactions in our results, including synthetic CO maps. We would expect cloud-cloud interactions to be observable, but find they appear to have little or no impact on the ISM. Due to a combination of the clouds' typical geometries, and moderate velocity dispersions, cloud-cloud interactions often better resemble a smaller cloud nudging a larger cloud. Our findings are consistent with the view that spiral arms make little difference to overall star formation rates in galaxies, and we see no evidence that collisions likely produce massive clusters. However, to confirm the outcome of such massive cloud collisions we ideally need higher resolution simulations.

  19. Energy transport through rare collisions

    E-print Network

    François Huveneers

    2011-07-14

    We study a one-dimensional hamiltonian chain of masses perturbed by an energy conserving noise. The dynamics is such that, according to its hamiltonian part, particles move freely in cells and interact with their neighbors through collisions, made possible by a small overlap of size $\\epsilon > 0$ between near cells. The noise only randomly flips the velocity of the particles. If $\\epsilon \\rightarrow 0$, and if time is rescaled by a factor $1/{\\epsilon}$, we show that energy evolves autonomously according to a stochastic equation, which hydrodynamic limit is known in some cases. In particular, if only two different energies are present, the limiting process coincides with the simple symmetric exclusion process.

  20. Collisional and radiative processes in high-pressure discharge plasmas

    NASA Astrophysics Data System (ADS)

    Becker, Kurt H.; Kurunczi, Peter F.; Schoenbach, Karl H.

    2002-05-01

    Discharge plasmas at high pressures (up to and exceeding atmospheric pressure), where single collision conditions no longer prevail, provide a fertile environment for the experimental study of collisions and radiative processes dominated by (i) step-wise processes, i.e., the excitation of an already excited atomic/molecular state and by (ii) three-body collisions leading, for instance, to the formation of excimers. The dominance of collisional and radiative processes beyond binary collisions involving ground-state atoms and molecules in such environments allows for many interesting applications of high-pressure plasmas such as high power lasers, opening switches, novel plasma processing applications and sputtering, absorbers and reflectors for electromagnetic waves, remediation of pollutants and waste streams, and excimer lamps and other noncoherent vacuum-ultraviolet light sources. Here recent progress is summarized in the use of hollow cathode discharge devices with hole dimensions in the range 0.1-0.5 mm for the generation of vacuum-ultraviolet light.

  1. Toward Production of Ultracold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Chen, Kuang

    Ultracold cold molecular ions promise new directions in various studies of fundamental physics, such as precision measurements, ultracold chemistry and quantum information sciences. All these exciting applications require the molecular ion to be prepared at ground state of motional and internal degrees of freedom. It has been proposed that this stringent goal could be achieved through sympa-thetic cooling via collisions with laser-cooled neutral atoms. Three fundamental issues of this method are addressed in this thesis. First, an analytical model is established to accurately describe collision-induced heating of a single ion in contact with cold neutral atoms. This model reveals that micromotion interruption is the cause of heating, and gives results about steady-state temperature and sympathetic cooling rate verified by Monte-Carlo simulations. It also provides insight into the power-law tails observed in the energy distribution of the trapped ion. Next, we consider the case of multiple ions, whose inter-particle Coulomb repulsion causes ions in the Coulomb crystal state to spontaneously melt into a gas phase ion cloud, due to the same micromotion interruption mechanism. The analysis of this problem with a plasma model leads to the experimental determination of a quantity central to plasma physics, Coulomb Logarithm, in an ion trap. Finally, we demonstrate a molecular ion spectroscopy technique through the example of trap-depletion photodissociation of BaCl+ . Although not sensitive to rotational structure, this method already reveals much about the fundamental quantum physics in the photodissociation process. The measured cross-section results paves the road toward state-selective spectroscopy currently going on in our lab.

  2. Elementary processes of H2 plasma-graphene interaction: A combined molecular dynamics and density functional theory study

    NASA Astrophysics Data System (ADS)

    Despiau-Pujo, E.; Davydova, A.; Cunge, G.; Delfour, L.; Magaud, L.; Graves, D. B.

    2013-03-01

    Elementary interactions between H atoms and monolayer graphene are investigated using classical molecular dynamics (CMD) and density functional theory (DFT). C-H interatomic potential curves and associated energy barriers are reported depending on the H impact position (top, bridge, hollow, vacancy, or edge sites of graphene nanoribbons). Chemisorption of atomic hydrogen and formation of molecular hydrogen from chemisorbed H states on graphene are examined. The influence of graphene temperature and incident species energy on adsorption, reflection, and penetration mechanisms is also presented. Except for impacts at graphene nanoribbon (GNR) edges or at defect locations, H atoms are shown to experience a repulsive force due to delocalized ?-electrons which prevents any species with less than 0.4-0.6 eV to chemisorb on the graphene surface. C-H bond formation requires a local sp2-sp3 rehybridization resulting in structural changes of the graphene sample. Chemisorption sites with deep potential wells and no activation barrier are found on GNR edges, which indicate that H thermal radicals can functionalize GNRs on edges while they cannot do it in the basal plane. The presence of one or more H adsorbates on the graphene surface strongly influences subsequent H adsorption and promotes the formation of energetically favourable H pairs at the para- and ortho-locations. Formation of H2 molecule via Eley-Rideal recombination of hot radicals [1-1.3 eV] with chemisorbed H atoms is observed.

  3. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process

    PubMed Central

    Wickstrom, Lauren; He, Peng; Gallicchio, Emilio; Levy, Ronald M.

    2013-01-01

    Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 ?-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies. PMID:25147485

  4. Maxwell's Demon Observing Creation of a Molecular Vibration

    NASA Astrophysics Data System (ADS)

    Chatzidimitriou-Dreismann, C. Aris

    2014-07-01

    Quantum correlations and associated quantum information concepts (e. g. quantum discord, entanglement, quantum Maxwell's demon) provide novel insights in various quantum-information processing tasks, quantum-thermodynamics processes, open-system dynamics, quantum molecular dynamics, and general many-body physics. We investigate a new effect of correlations accompanying collision of two quantum systems A and B, the latter being part of a larger (interacting) system B+D. In contrast to the usual case of a classical `environment' or `demon' (which can have only classical correlations with A+B during and after the collision), the quantum case exhibits striking new features. Here, in the frame of incoherent inelastic neutron scattering (INS) and vibrational dynamics of molecules, we report experimental evidence of a new phenomenon: quantum deficit of momentum transfer in an elementary neutron-molecule collision, in particular, in INS from single H2O molecules confined in channels with sub-nanometer diameter. The INS findings are in clear contrast to conventional theoretical expectations, but are naturally (albeit qualitative) interpreted in the frame of modern theory of quantumness of correlations, thus also proposing a new operational meaning of quantum discord and related measures.

  5. 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.

  6. Constructing and enhanced degradation rate of N-AZO/TiO2 core/shell nanocomposite by idiopathic molecular cladding process

    NASA Astrophysics Data System (ADS)

    Deng, Ya-Juan; Wang, Jian-Dong; Liu, Jin-Ku; Tong, Qin; Wang, Jiang-Jie; Yang, Xiao-Hong

    2015-07-01

    The N-AZO/TiO2 heterogeneous nanocomposite with core/shell structure revealed a better photocatalytic activity than the single N-AZO nanocrystals (NCs) even though it has a good photocatalytic effect. The recombination degree of photo-induced electrons and holes reduced significantly after molecular TiO2 layer composited on the surface of N-AZO NCs. From the experiment of degrading rhodamine B solution (2 × 10-5 g/L) under solar light, the optimum photocatalytic efficiency was the N-AZO/TiO2 composite prepared by idiopathic molecule-cladding (IMC) process and the best proportion of Zn/Ti was 2:1 in our research, which improved by 67% than pure N-AZO. Moreover, the N-AZO/TiO2 composite prepared by IMC process achieved a molecular combination level between the two components, which not only can improve the immobility of composite structure, but also can make the photogenerated electrons and holes transport easier.

  7. Synthesis of Late Cretaceous-Quaternary tectonic, sedimentary and magmatic processes and basin formation related to episodic subduction-collision in the easternmost Mediterranean region

    NASA Astrophysics Data System (ADS)

    Robertson, Alastair; Kinnaird, Timothy; McCay, Gillian; Palamakumbura, Romesh; Tasl?, Kemal

    2015-04-01

    Mesozoic oceanic crust of the easternmost Mediterranean has experienced northwards subduction during Late Cretaceous-Cenozoic, either continuously or discontinuously based on kinematic evidence. Much of the existing information on sedimentation within the easternmost Mediterranean oceanic basin comes from the non-emplaced continental margins of the Levant and North Africa. In addition, sedimentary basins related to plate convergence are recorded along the northern margin of the Southern Neotethyan ocean, mainly in the Kyrenia Range of northern Cyprus and its extension into the Misis Mountains of southern Turkey, coupled with the adjacent submerged areas. In a setting of only incipient continental collision such as the easternmost Mediterranean the sedimentary basins would be expected to remain entirely submarine. In contrast, the Kyrenia Range has been strongly uplifted and subaerially exposed during Late Pliocene-Quaternary time. This allows the recognition of a number of discrete phases of sedimentary basin formation: 1. Late Cretaceous (Campanian-Maastrichtian): silicic volcanism to create a subaqueous volcaniclastic apron; 2. Maastrichtian-Paleocene: pelagic carbonate deposition interspersed with proximal gravity flows and within-plate type alkaline volcanics; 3. Early Eocene: large-scale sedimentary melange (olistostrome) emplacement; 4. Late Eocene-Late Miocene: terrigenous gravity-flow deposition in a deep-water fault dissected 'fore arc' setting. Initial, Late Eocene non-marine coarse clastic alluvial fan deposition was succeeded by Oligocene-Miocene deep-marine siliciclastic gravity flow deposits, fining and shallowing upwards during the Late Miocene; 5. Messinian: localised precipitation of evaporites in small fault-controlled basins; 6. Pliocene: shallow-marine siliciclastic-carbonate deposition in a shelf-depth, overall regressive setting; 7. Latest Pliocene to mid-Pleistocene: gravitational accumulation of coarse talus along a strongly uplifting subaerial lineament; 8. Mid-Late Quaternary: gradual tectonic uplift giving rise to a flight of shallow marine to non-marine terrace deposits, that were also influenced by eustatic sea-level fluctuations and climatic change. The stages of basin development were punctuated by four main episodes of compression/uplift. A. Late Miocene underthrusting/metamorphism/exhumation; B. Mid-Eocene southwards thrusting; C. Late Miocene southward thrusting/left-lateral transpression; D. Late Pliocene-Mid Quaternary tectonic uplift. In a setting of continuing plate convergence why did the nature of sedimentation change so dramatically through time? The deformation front between the Kyrenia Range and the Troodos Massif is delineated by the Ovgos Fault which shows an episodic development including Late Miocene compression (transpression) and Quaternary left-lateral strike slip. The Late Cretaceous volcanogenic rocks relate to a phase of regional arc magmatism also documented in SE Turkey. Subduction appears to have slowed or ceased during the Maastrichtian-Palaeocene while the active margin experienced extension or transtension. Following final closure of a Tethyan oceanic basin further north ('northern Neotethys') subduction appears to have relocated southwards and re-activated/accelerated during the Early Eocene triggering large-scale collapse of the over-riding plate and olistostrome formation. Diachronous continental collision was in progress during Early Miocene causing strong uplift of the over-riding plate, intense erosion and voluminous siliciclastic sediment supply to a fore-arc type basin in the N Cyprus-Misis area (becoming foreland basin further east, in SE Turkey). The Pliocene was characterised by eastward 'tectonic escape' of the Anatolian plate towards the Aegean and this allowed relatively fine-grained deposition to accumulate along the former convergent continental margin in northern Cyprus and adjacent areas (e.g. Mesaoria basin). The dramatic late Pliocene to mid-Quaternary uplift of the Kyrenia-Misis lineament, plus the Troodos massif to the south, can be explaine

  8. Bose condensation of nuclei in heavy ion collisions

    NASA Technical Reports Server (NTRS)

    Tripathi, Ram K.; Townsend, Lawrence W.

    1994-01-01

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

  9. Improved control over spontaneously formed GaN nanowires in molecular beam epitaxy using a two-step growth process.

    PubMed

    Zettler, J K; Corfdir, P; Geelhaar, L; Riechert, H; Brandt, O; Fernández-Garrido, S

    2015-11-01

    We investigate the influence of modified growth conditions during the spontaneous formation of GaN nanowires (NWs) on Si(111) in plasma-assisted molecular beam epitaxy. We find that a two-step growth approach, where the substrate temperature is increased during the nucleation stage, is an efficient method to gain control over the area coverage, average diameter, and coalescence degree of GaN NW ensembles. Furthermore, we also demonstrate that the growth conditions employed during the incubation time that precedes nanowire nucleation do not influence the properties of the final nanowire ensemble. Therefore, when growing GaN NWs at elevated temperatures or with low Ga/N ratios, the total growth time can be reduced significantly by using more favorable growth conditions for nanowire nucleation during the incubation time. PMID:26457772

  10. MSG-7: Molecular absorption processes related to the penetration of ultraviolet solar radiation into the middle atmosphere

    NASA Technical Reports Server (NTRS)

    Frederick, J. E.; Blake, A. J.; Freeman, D. E.; Nicholls, R. W.; Ogawa, T.; Simon, P. C.

    1983-01-01

    The information presently available on the absorption cross sections of O2 and O3 with attention to the application of these data in middle atmospheric science is reviewed. The cross sections values reported by different groups are intercompared in tabular form where feasible, and specific values are recommended when there is a basis for preferring a particular set of results over other available data. When no such basis exists, the differences among published cross sections then serve to indicate a range of uncertainty. In these cases the need for additional work is indicated. Specific topics addressed are the absorption of molecular oxygen at Lyman alpha, in the Schumann-Runge continuum, in the Schumann-Runge bands, and in the Herzberg continuum. For ozone, the Hartley and Huggins bands are considered.

  11. Improved control over spontaneously formed GaN nanowires in molecular beam epitaxy using a two-step growth process

    NASA Astrophysics Data System (ADS)

    Zettler, J. K.; Corfdir, P.; Geelhaar, L.; Riechert, H.; Brandt, O.; Fernádez-Garrido, S.

    2015-11-01

    We investigate the influence of modified growth conditions during the spontaneous formation of GaN nanowires (NWs) on Si(111) in plasma-assisted molecular beam epitaxy. We find that a two-step growth approach, where the substrate temperature is increased during the nucleation stage, is an efficient method to gain control over the area coverage, average diameter, and coalescence degree of GaN NW ensembles. Furthermore, we also demonstrate that the growth conditions employed during the incubation time that precedes nanowire nucleation do not influence the properties of the final nanowire ensemble. Therefore, when growing GaN NWs at elevated temperatures or with low Ga/N ratios, the total growth time can be reduced significantly by using more favorable growth conditions for nanowire nucleation during the incubation time.

  12. Ab initio molecular dynamics of Al irradiation-induced processes during Al{sub 2}O{sub 3} growth

    SciTech Connect

    Music, Denis; Nahif, Farwah; Friederichsen, Niklas; Schneider, Jochen M.; Sarakinos, Kostas

    2011-03-14

    Al bombardment induced structural changes in {alpha}-Al{sub 2}O{sub 3} (R-3c) and {gamma}-Al{sub 2}O{sub 3} (Fd-3m) were studied using ab initio molecular dynamics. Diffusion and irradiation damage occur for both polymorphs in the kinetic energy range from 3.5 to 40 eV. However, for {gamma}-Al{sub 2}O{sub 3}(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to {alpha}-Al{sub 2}O{sub 3}. Consequently, fast diffusion along {gamma}-Al{sub 2}O{sub 3}(001) gives rise to preferential {alpha}-Al{sub 2}O{sub 3}(0001) growth, which is consistent with published structure evolution experiments.

  13. 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.

  14. Aggregation of a Crown Ether Decorated Zinc-Phthalocyanine by Collision-Induced Desolvation of Electrospray Droplets.

    PubMed

    Kellner, Ina D; Hahn, Uwe; Dürr, Maximilian; Torres, Tomás; Ivanovi?-Burmazovi?, Ivana; Drewello, Thomas

    2015-11-19

    The aggregation of phthalocyanines is well-known in solution but has never before been studied in the gas phase. We investigated the tetra-[18]crown-6 ether functionalized zinc-phthalocyanine (ZnPcTetCr, M) with electrospray ionization mass spectrometry (ESI-MS) in the absence of coordinating metal cations. Apart from the molecular ion M(+•), singly and multiply charged aggregates Mn(z(+•)) were observed, bound together by electrostatic interactions, without alkali metal cations inside the crown ethers. Collision-induced dissociation (CID) experiments indicate that these clusters consist of stacked neutral M and radical cations M(+•). After the oxidation of individual molecules at the electrospray needle, the aggregation occurs during desolvation of the charged droplets created in the source. Complete evaporation of the solvent and detection of the aggregates was found to require an additional acceleration of the droplets in the transfer region of the instrument, the resulting collisions with neutral gas assisting the desolvation process. PMID:26501883

  15. Morphological stability of Cu-Nb nanocomposites under high-energy collision cascades

    E-print Network

    Zhang, Liang

    We use molecular dynamics and phase field simulations to demonstrate that Cu-Nb multilayered nanocomposites with individual layer thicknesses above 2–4?nm remain morphologically stable when subjected to 100?keV collision ...

  16. 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…

  17. 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.

  18. Non-adiabatic ab initio molecular dynamics of supersonic beam epitaxy of silicon carbide at room temperature

    SciTech Connect

    Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; Beccara, Silvio a; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; and others

    2013-01-28

    In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C{sub 60} collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C{sub 60} impact on the Si surface is in good agreement with our experimental findings.

  19. Vertical distribution of vibrational energy of molecular nitrogen in a stable auroral red arc and its effect on ionospheric electron densities. Ph.D. Thesis - Catholic Univ. of Am.

    NASA Technical Reports Server (NTRS)

    Newton, G. P.

    1973-01-01

    Previous solutions of the problem of the distribution of vibrationally excited molecular nitrogen in the thermosphere have either assumed a Boltzmann distribution and considered diffusion as one of the loss processes or solved for the energy level populations and neglected diffusion. Both of the previous approaches are combined by solving the time dependent continuity equations, including the diffusion process, for the first six energy levels of molecular nitrogen for conditions in the thermosphere corresponding to a stable auroral red arc. The primary source of molecular nitrogen excitation was subexcitation, and inelastic collisions between thermal electrons and molecular nitrogen. The reaction rates for this process were calculated from published cross section calculations. The loss processes for vibrational energy were electron and atomic oxygen quenching and vibrational energy exchange. The coupled sets of nonlinear, partial differential equations were solved numerically by employing finite difference equations.

  20. Second blows in the head-on collisions of spherical nano polymer droplets

    NASA Astrophysics Data System (ADS)

    Kim, Sangrak

    2014-03-01

    We report observations of a weird but interesting phenomenon from molecular dynamics simulations: the occurrence of second blows in head-on collisions of two equal-sized spherical nano polymer droplets. In head-on collisions, we usually expect single-peak impact forces between the two colliding droplets. However, a second peak of the impact force is actually observed in the simulations. Its underlying mechanisms on a molecular scale are proposed.