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1

Semiclassical theory of electronically nonadiabatic transitions in molecular collision processes  

NASA Technical Reports Server (NTRS)

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.

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

1979-01-01

2

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

SciTech Connect

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.

Rakshit, Arpita [Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India); Deb, Bimalendu [Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India); Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 (India)

2011-02-15

3

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

NASA Astrophysics Data System (ADS)

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

Gans, Timo

2008-10-01

4

Molecular collisions coming into focus.  

PubMed

The Stark deceleration method exploits the concepts of charged particle accelerator physics to produce beams of neutral polar molecules with an almost perfect quantum state purity, a tunable velocity and a narrow velocity distribution. These monochromatic molecular beams offer interesting perspectives for precise studies of molecular scattering processes, in particular when used in conjunction with state-of-the-art laser-based detection techniques such as velocity map imaging. Here, we describe crossed beam scattering experiments in which the Stark deceleration method is combined with the velocity map imaging technique. The narrow velocity spread of Stark-decelerated molecular beams results in scattering images with unprecedented velocity and angular resolution. We demonstrate this by resolving quantum diffraction oscillations in state-to-state inelastic differential scattering cross sections for collisions between NO radicals and rare gas atoms. We describe the future prospects of this "best-of-two-worlds" combination, ranging from scattering studies at low collision energies to bimolecular scattering using two decelerators, and discuss the challenges that lie ahead to achieve these goals. PMID:24967721

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

2014-08-14

5

Accelerating spectral atomic and molecular collisions methods with graphics processing units  

NASA Astrophysics Data System (ADS)

We present a computation method to accelerate the calculation of the Hamiltonian of a three-body time independent Schrödinger equation for collisions. The Hamiltonian is constructed with one dimensional (basis overlaps) and two dimensional (interparticle interaction) integrals that are mapped into a computational grid in a Graphics Processing Unit (GPU). We illustrate the method for the case of an electron impact single ionization of a two electron atom. This proposal makes use of a Generalized Sturmian Basis set for each electron, which are obtained numerically on a quadrature grid that is used to compute the integrals in the GPU. The optimal computation is more than twenty times faster in the GPU than the calculation in CPU. The method can be easily scaled to computers with several Graphics Processing Units or clusters.

Colavecchia, F. D.

2014-07-01

6

Molecular Dissociation Induced by Electron Collisions  

NASA Astrophysics Data System (ADS)

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

Wolf, Andreas

2009-05-01

7

Wave packet methods for the direct calculation of energy-transfer moments in molecular collisions  

Microsoft Academic Search

The authors present a new wave packet based theory for the direct calculation of energy-transfer moments in molecular collision processes. This theory does not contain any explicit reference to final state information associated with the collision dynamics, thereby avoiding the need for determining vibration-rotation bound states (other than the initial state) for the molecules undergoing collision and also avoiding the

Kimberly S. Bradley; George C. Schatz; Gabriel G. Balint-Kurti

1999-01-01

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

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.

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

2015-01-01

9

Atomic and Molecular Depolarizing Collision Rates  

NASA Astrophysics Data System (ADS)

This paper is divided in three parts: after having recalled the different types of collisions with the different types of perturbers and having provided rough orders of magnitude of the collision rates, three cases are discussed. Although the most frequent type of depolarizing collision is the one of the collisions with the surrounding Hydrogen atoms, we discuss in the first part a particular case where the depolarizing collision effect is due to collisions with electrons and protons. This is the case of the Hydrogen lines observed in solar prominences. We recall how the interpretation of polarization observations in two lines has led to the joint determination of the magnetic field vector and the electron and proton density, and we show that this density determination gives results in agreement with the densities determined by interpretation of the Stark effect, provided that this last effect be evaluated in the impact approximation scheme which is indeed more valid than the quasistatic approach at these densities. In the second part, we describe a method that has been recently developed for the computation of the depolarizing rates in the case of collisions with the neutral Hydrogen atom. The case of molecular lines is less favourable, because, even if depolarizing collision rates computation may be soon expected and begin to be done inside the ground level of the molecule, calculations inside the excited states are far from the present ability. In the third part, we present an example where the excited state depolarizing rates were evaluated together with the magnetic field through the differential Hanle effect interpretation, based on the fact that the molecule provides a series of lines of different sensitivities that can be compared. This led to an experimental/observational determination of these rates, waiting for future theoretical computations for comparison.

Bommier, V.

2009-06-01

10

Division XII / Commission 14 / Working Group Collision Processes  

E-print Network

Research in atomic and molecular collision processes and spectral line broadening has been very active since our last report, Peach, Dimitrijevic & 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.

Peach, Gillian

2012-01-01

11

Division XII / Commission 14 / Working Group Collision Processes  

NASA Astrophysics Data System (ADS)

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.

Peach, Gillian; Dimitrijevic, Milan S.

2012-04-01

12

Molecular flow and wall collision age distributions  

NASA Astrophysics Data System (ADS)

The use of storage cells has become a standard technique for internal gas targets in conjunction with high energy storage rings. In case of spin-polarized hydrogen and deuterium gas targets the interaction of the injected atoms with the walls of the storage cell can lead to depolarization and recombination. Thus the number of wall collisions of the atoms in the target gas is important for modeling the processes of spin relaxation and recombination. It is shown in this article that the diffusion process of rarefied gases in long tubes or storage cells can be described with the help of the one-dimensional diffusion equation. Mathematical methods are presented that allow one to calculate collision age distributions (CAD) and their moments analytically. These methods provide a better understanding of the different aspects of diffusion than Monte Carlo calculations. Additionally it is shown that measurements of the atomic density or polarization of a gas sample taken from the center of the tube allow one to determine the possible range of the corresponding density weighted average values along the tube. The calculations are applied to the storage cell geometry of the HERMES internal polarized hydrogen and deuterium gas target.

Baumgarten, C.; Braun, B.; Court, G.; Ciullo, G.; Ferretti, P.; Graw, G.; Haeberli, W.; Henoch, M.; Hertenberger, R.; Koch, N.; Kolster, H.; Lenisa, P.; Nass, A.; Pod'Yachev, S. P.; Reggiani, D.; Rith, K.; Simani, M. C.; Steffens, E.; Stewart, J.; Wise, T.

2002-01-01

13

Modeling asteroid collisions and impact processes  

E-print Network

As a complement to experimental and theoretical approaches, numerical modeling has become an important component to study asteroid collisions and impact processes. In the last decade, there have been significant advances in both computational resources and numerical methods. We discuss the present state-of-the-art numerical methods and material models used in "shock physics codes" to simulate impacts and collisions and give some examples of those codes. Finally, recent modeling studies are presented, focussing on the effects of various material properties and target structures on the outcome of a collision.

Jutzi, Martin; Wünneman, Kai; Michel, Patrick

2015-01-01

14

Reactive collisions involving the BeH molecular system  

NASA Astrophysics Data System (ADS)

In the divertor and fusion edge plasma regions reactive collisions involving the BeH molecular system are taking place. Theoretical ab initio quantum studies of electron collisions with BeH+ resulting in either dissociative recombination, vibrational excitation or dissociative excitation are performed for ions in different vibrational states as well for different isotopologues. Furthermore, the mutual neutralization reaction in collisions of H? with Be+ is studied semiclassically.

Larson, Åsa; Roos, Johanna B.; Hedberg, Hanae; Orel, Ann E.

2015-01-01

15

Molecular Processes in Comets  

NASA Technical Reports Server (NTRS)

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.

Dalgarno, A.

1998-01-01

16

Gaussian Process Model for Collision Dynamics of Complex Molecules  

E-print Network

We show that a Gaussian Process model can be combined with a small number of scattering calculations to provide an accurate multi-dimensional dependence of scattering observables on the experimentally controllable parameters (such as the collision energy, temperature or external fields) as well as the potential energy surface parameters. This can be used for solving the inverse scattering problem, the prediction of collision properties of a specific molecular system based on the information for another molecule, the efficient calculation of thermally averaged observables and for reducing the error of the molecular dynamics calculations by averaging over the potential energy surface variations. We show that, trained by a combination of classical and quantum dynamics calculations, the model provides an accurate description of the scattering cross sections, even near scattering resonances. In this case, the classical calculations stabilize the model against uncertainties arising from wildly varying correlations ...

Cui, Jie

2015-01-01

17

Molecular vibration in cold-collision theory  

Microsoft Academic Search

Cold collisions of ground-state oxygen molecules with helium have been investigated in a wide range of cold-collision energies (from 1 muK up to 10 K) treating the oxygen molecule first as a rigid rotor and then introducing the vibrational degree of freedom. The comparison between the two models shows that at low energies the rigid-rotor approximation is very accurate and

Alessandro Volpi; John L. Bohn

2002-01-01

18

Molecular vibration in cold collision theory  

E-print Network

Cold collisions of ground state oxygen molecules with Helium have been investigated in a wide range of cold collision energies (from 1 $\\mu$K up to 10 K) treating the oxygen molecule first as a rigid rotor and then introducing the vibrational degree of freedom. The comparison between the two models shows that at low energies the rigid rotor approximation is very accurate and able to describe all the dynamical features of the system. The comparison between the two models has also been extended to cases where the interaction potential He - O$_2$ is made artificially stronger. In this case vibration can perturb rate constants, but fine-tuning the rigid rotor potential can alleviate the discrepancies between the two models.

Alessandro Volpi; John L. Bohn

2002-02-13

19

Electron capture processes in Li2+ + H collisions  

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

20

Microwave Collision Diameters II. Theory and Correlation with Molecular Quadrupole Moments  

Microsoft Academic Search

Observed microwave collision diameters are interpreted as arising exclusively from transitions induced during the collision. Collision diameters greater than kinetic theory values arise from dipole-dipole or dipole-quadrupole interactions. The former case affords a quantitative test of the theory. In the latter case measurements of collision diameters yield quadrupole moment measurements which are correlated with molecular structure.

William V. Smith; Raydeen Howard

1950-01-01

21

Atomic Collision Processes in Dense Plasmas  

NASA Astrophysics Data System (ADS)

In the present work a detailed investigation of various atomic collision processes important to the determination of the structure and evolution of dense plasmas is presented. In volume 1 a study of general collisional processes in dense plasmas is given, while in volume 2 specific mechanisms by which energy is transferred among the constituents of a dense plasma is studied. Specifically, in chapter I, attention will be focused upon ion-ion recombination processes in dense plasmas, which involves the full set of multicomponent BBGKY equations appropriate for a three component gas composed of positive and negative ions, and neutral particles. This yields a set of coupled Boltzmann-type equations to be solved for the full phase-space evolution of the plasma, valid for arbitrary neutral gas density. In the limit of low (neutral) gas densities the theory in chapter I naturally tends to the exact quasi-equilibrium treatment of ion-ion recombination of Bates and Moffett, and Bates and Flannery. It also provides a firm basis for developing a fully general theory of recombination in dense plasmas subject to external electromagnetic fields as well as for dense plasmas with arbitrary ion densities. In chapter II symmetric resonance charge transfer processes Rg('+) + Rg (--->) Rg + Rg('+) for Rg = Ne, Ar, Kr, and Xe are studied via a quantal phase shift analysis. Accurate ab-initio and density functional potentials for the Rg(,2)('+), dimer are to be used, with the effects of spin-orbit coupling included, in order to compute elastic, charge-transfer, diffusion, and viscosity cross sections in the thermal energy region. In chapters III, IV of volume 2 the electron-impact excitation of excited hydrogen and helium atoms, respectively, are studied via the multichannel eikonal theory (MET) of Flannery and McCann. The MET is modified to account, asymptotically, for the strong dipole couplings present between the excited states of hydrogen and helium, thereby allowing accurate computation of differential and integral cross sections and the relevant orientation and alignment parameters.

Mansky, Edmund Jacob, II

22

Quantitative uniform in time chaos propagation for Boltzmann collision processes  

E-print Network

This paper is devoted to the study of mean-field limit for systems of indistinguables particles undergoing collision processes. As formulated by Kac \\cite{Kac1956} this limit is based on the {\\em chaos propagation}, and we (1) prove and quantify this property for Boltzmann collision processes with unbounded collision rates (hard spheres or long-range interactions), (2) prove and quantify this property \\emph{uniformly in time}. This yields the first chaos propagation result for the spatially homogeneous Boltzmann equation for true (without cut-off) Maxwell molecules whose "Master equation" shares similarities with the one of a L\\'evy process and the first {\\em quantitative} chaos propagation result for the spatially homogeneous Boltzmann equation for hard spheres (improvement of the %non-contructive convergence result of Sznitman \\cite{S1}). Moreover our chaos propagation results are the first uniform in time ones for Boltzmann collision processes (to our knowledge), which partly answers the important question...

Mischler, Stéphane

2010-01-01

23

Calculation of total cross sections for charge exchange in molecular collisions  

NASA Technical Reports Server (NTRS)

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

Ioup, J.

1979-01-01

24

Low-temperature collisions between neutral molecules in merged molecular beams.  

PubMed

We have developed an experiment for the investigation of neutral molecular collisions in the gas phase at temperatures as low as 100 mK. These low temperatures are obtained by merging two supersonic expansions, using an electric and a magnetic guide, and by matching the velocities of the beams. Since the energy available for the collisions, or the temperature, is determined only by the relative velocity of the reaction partners this enables the study of chemical processes at very low temperatures without the need to prepare slow molecules in the laboratory frame of reference. This paper describes the method and presents results on the Ne((3)P2)+NH3 Penning ionization. PMID:24983610

Bertsche, Benjamin; Jankunas, Justin; Osterwalder, Andreas

2014-01-01

25

Quantum Simulation of Molecular Collisions with Superconducting Qubits  

E-print Network

We introduce a protocol for the fast simulation of $n$-dimensional quantum systems on $n$-qubit quantum computers with tunable couplings. A mapping is given between the control parameters of the quantum computer and the matrix elements of $H_{\\rm s}(t)$, an arbitrary, real, time-dependent $n\\times n$ dimensional Hamiltonian that is simulated in the $n$-dimensional `single excitation' subspace of the quantum computer. A time-dependent energy/time rescaling minimizes the simulation time on hardware having a fixed coherence time. We demonstrate how three tunably coupled phase qubits simulate a three-channel molecular collision using this protocol, then study the simulation's fidelity as a function of total simulation time.

Pritchett, Emily J; Galiautdinov, Andrei; Geller, Michael R; Sornborger, Andrew T; Stancil, Phillip C; Martinis, John M

2010-01-01

26

Quantum Simulation of Molecular Collisions with Superconducting Qubits  

E-print Network

We introduce a protocol for the fast simulation of $n$-dimensional quantum systems on $n$-qubit quantum computers with tunable couplings. A mapping is given between the control parameters of the quantum computer and the matrix elements of $H_{\\rm s}(t)$, an arbitrary, real, time-dependent $n\\times n$ dimensional Hamiltonian that is simulated in the $n$-dimensional `single excitation' subspace of the quantum computer. A time-dependent energy/time rescaling minimizes the simulation time on hardware having a fixed coherence time. We demonstrate how three tunably coupled phase qubits simulate a three-channel molecular collision using this protocol, then study the simulation's fidelity as a function of total simulation time.

Emily J. Pritchett; Colin Benjamin; Andrei Galiautdinov; Michael R. Geller; Andrew T. Sornborger; Phillip C. Stancil; John M. Martinis

2010-08-04

27

Laboratory studies of atomic collision processes of importance in planetary atmospheres  

NASA Technical Reports Server (NTRS)

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

Stebbings, R. F.; Smith, K.

1984-01-01

28

Rotational cooling of HD+ molecular ions by superelastic collisions with electrons.  

PubMed

Merging an HD+ beam with velocity matched electrons in a heavy ion storage ring we observed rapid cooling of the rotational excitations of the HD+ ions by superelastic collisions (SEC) with the electrons. The cooling process is well described using theoretical SEC rate coefficients obtained by combining the molecular R-matrix approach with the adiabatic nuclei rotation approximation. We verify the DeltaJ=-2 SEC rate coefficients, which are predicted to be dominant as opposed to the DeltaJ=-1 rates and to amount to (1-2)x10;{-6} cm;{3} s;{-1} for initial angular momentum states with J< or =7, to within 30%. PMID:19658863

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

2009-06-01

29

ALPGEN, a generator for hard multiparton processes in hadronic collisions  

Microsoft Academic Search

This paper presents a new event generator, ALPGEN, dedicated to the study of multiparton hard processes in hadronic collisions. The code performs, at the leading order in QCD and EW interactions, the calculation of the exact matrix elements for a large set of parton-level processes of interest in the study of the Tevatron and LHC data. The current version of

Michelangelo L. Mangano; Fulvio Piccinini; Antonio D. Polosa; Mauro Moretti; Roberto Pittau

2003-01-01

30

Applications of cross sections for electron-molecule collision processes  

SciTech Connect

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

Cartwright, D.C.

1985-01-01

31

Theoretical studies of molecular processes  

NASA Astrophysics Data System (ADS)

The current thesis concerns with theoretical studies of molecular processes and consists of two parts. The first part includes theoretical studies of dynamics of unimolecular and bimolecular reactions, in particular those involving non-adiabatic processes. In chapter 2 and 3, we have presented our studies of detailed mechanisms for the photodissociation of C2H2 and C2H, and the ion-molecule reactions of C2H2+ + CH4 or NH3, respectively. In chapter 4, we have presented our study that extends TST to non-adiabatic reactions, and an application of the theory of the spin-forbidden reaction of CH(2/Pi)+N2. In chapter 5, we have included our analyses on the photodissociation of triplet ketene, where an extensive seam has been found all along the reaction coordinate. Finally, in Chapter 6, we have presented our study on the photodissociation of O3/sp-, which includes qualitative electronic structure calculations and construction of global potential energy functions for coupled electronic states. The second part of the thesis deals with theoretical studies of organometallic reactions, metal clusters, and gas-surface interactions. With theoretical calculations, one can study the reactivities of transition metal compounds systematically, which allows one to understand the key parameters that control the reactivities of those compounds. In chapter 2, we have presented our implementation of analytical hessian for effective core potential, which makes normal mode analysis possible for large organometallic systems and has proven to be very useful in the study of systems containing transition metals. In chapter 3-5, we have included our studies on the detailed mechanisms of several interesting reactions including platinum/palladium(0) catalyzed diboration and thioboration reactions of acetylene and olefin, and H- H/C-H bond activation on small metal clusters Pt/Pdn(n = 1[-]3). For truly large systems such as surfaces or proteins, full quantum mechanical treatments are computationally too demanding, and methods that combine molecular orbital (MO) theories and molecular mechanics (MM), or higher level and lower level of MO theories (IMOMO) become favorable. In chapter 6, we have presented our DFT and IMOMO study on the iodine etching of the Si(100) reconstructed surface, where we have demonstrated that IMOMO method was indeed able to provide accurate description of large systems.

Cui, Qiang

1997-09-01

32

Grid methods for solving the Schrödinger equation and time dependent quantum dynamics of molecular photofragmentation and reactive scattering processes  

Microsoft Academic Search

This review will concentrate on new theoretical methods for solving the quantum dynamics of molecular systems. The approach will be that of solving the time dependent Schrödinger equation, and extracting from it the measurable quantities of experimental interest. Applications to the modelling of molecular photodissociation processes and to the theory of reactive molecular collisions will be discussed.

Gabriel G. Balint-Kurti; Richard N. Dixon; C. Clay Marston

1992-01-01

33

Wall-collision line broadening of molecular oxygen within nanoporous materials  

SciTech Connect

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

Xu, Can T.; Lewander, Maerta; Andersson-Engels, Stefan; Svensson, Tomas; Svanberg, Sune [Department of Physics, Lund University, P. O. Box 118, SE-221 00 Lund (Sweden); Adolfsson, Erik [Ceramic Materials, SWEREA IVF, Box 104, SE-431 22 Moelndal (Sweden)

2011-10-15

34

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

SciTech Connect

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

Yoon, J.-S.; Song, M.-Y.; Kato, H.; Hoshino, M.; Tanaka, H.; Brunger, M. J.; Buckman, S. J.; Cho, H. [National Fusion Research Institute, Gwahangno 113, Yuseong-gu, Daejeon 305-333 (Korea, Republic of); Department of Material and Life Sciences, Sophia University, Tokyo 102-8554 (Japan); ARC Centre for Antimatter-Matter Studies, School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001 (Australia); ARC Centre for Antimatter-Matter Studies, Research School of Physics and Engineering, Australian National University, Canberra, Australian Capital Territory 0200 (Australia); Physics Department, Chungnam National University, Daejeon 305-764 (Korea, Republic of)

2010-09-15

35

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

SciTech Connect

The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas molecule collisions (gas molecules with altered trajectories by the potential interaction) without tracking grazing trajectories are further discussed. The presented calculation techniques should enable more accurate collision cross section predictions under experimentally relevant conditions than pre-existing approaches, and should enhance the ability of collision cross section measurement schemes to discern the structures of gas phase entities.

Larriba, Carlos, E-mail: clarriba@umn.edu; Hogan, Christopher J.

2013-10-15

36

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

SciTech Connect

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

Sun Jizhong; Li Shouyang; Wang Dezhen [Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Ministry of Education), School of Physics and Optoelectronic Technology and College of Advanced Science and Technology, Dalian University of Technology, Dalian 116024 (China); Stirner, Thomas [University of Applied Sciences Deggendorf, Edlmairstr. 6-8, D-94469 Deggendorf (Germany); Chen Junlin [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China)

2010-06-15

37

FORMATION OF MASSIVE MOLECULAR CLOUD CORES BY CLOUD-CLOUD COLLISION  

SciTech Connect

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.

Inoue, Tsuyoshi [Department of Physics and Mathematics, Aoyama Gakuin University, Sagamihara, Kanagawa 252-5258 (Japan); Fukui, Yasuo, E-mail: inouety@phys.aoyama.ac.jp [Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

2013-09-10

38

On the evaluation of the classical phase for reactive molecular collisions in semiclassical collision theory  

Microsoft Academic Search

A new formula for the generator of a cartesian to action-angle change of variables for a Morse oscillator is presented. It can be used to calculate the classical phase of semiclassical collision theory for both inelastic and reactive collisions. In the reactive case, the calculation of the phase is equivalent to using action-angle variables for the initial (final) oscillator during

J. N. L. Connor; Antonio Laganà

1981-01-01

39

Atomic site-sensitive processes in low energy ion-dimer collisions.  

PubMed

Electron capture processes for low energy Ar(9+) ions colliding with Ar(2) dimer targets are investigated, focusing attention on charge sharing between the two Ar atoms as a function of the molecular orientation and the impact parameter. A preference for charge-asymmetric dissociation channels is observed, with a strong correlation between the projectile scattering angle and the molecular ion orientation. The measurements here provide clear evidence that projectiles distinguish each atom in the target and that electron capture from near-site atoms is favored. Monte Carlo calculations based on the classical over-the-barrier model, with dimer targets represented as two independent atoms, are compared to the data. They give new insight into the dynamics of the collision by providing, for the different electron capture channels, the two-dimensional probability maps p(b), where b is the impact parameter vector in the molecular frame. PMID:25325640

Iskandar, W; Matsumoto, J; Leredde, A; Fléchard, X; Gervais, B; Guillous, S; Hennecart, D; Méry, A; Rangama, J; Zhou, C L; Shiromaru, H; Cassimi, A

2014-10-01

40

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

NASA Technical Reports Server (NTRS)

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.

Green, S.

1984-01-01

41

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

SciTech Connect

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.

Chu, P.M.Y.

1991-10-01

42

Isolating Quantum Mechanical Processes in Billiard Ball Collisions  

NASA Astrophysics Data System (ADS)

The few-body problem remains an important unsolved Physics problem. In atomic collisions, while the interactions are well understood, the problem is still not solvable. However, at intermediate or high energies, the contributions to ionization from binary collisions may be isolated and studied directly. Final-state interactions between the charged projectile and the ejected electron following ionization have been calculated to give cusp-like structures in the differential ionization cross section when the projectile and ejected electron emerge in the same direction with the same speed.(See for example, M.W. Lucas, K.F. Man and W. Steckelmacher, in Lecture Notes in Physics vol. 213, ed K.O. Groeneveld, W. Meckbach and I. Sellin (Berlin: Springer), p1 (1984).) These processes are known as ``capture to the continuum" for a positive projectile and "anticapture to the continuum" for a negative projectile.(L.H. Thomas, Proc. Roy. Soc. A114 561 (1927).)^,(See J.S. Briggs, Comments At. Mol. Phys. 23, 175 (1989), for more recent work.) The projectile can transfer significant momentum in these collisions and two or more outgoing particles can significant velocity after the collision which cannot be accounted for theoretically. Therefor experimental measurements can provide guidance for further theoretical development. We have reported the first experimental evidence of electron anticapture to the continuum at about 45^circ in e^- - Ar scattering at 1000 eV. This double-binary collision mechanism (the electron scattering analogue of the Thomas forward peak in ion-atom scattering) has been isolated by studying correlated projectile and ejected electrons traveling in the same direction following e^--Ar collisions. The cross section for this process rises as 45^circ is approached, but drops precipitously at about 45^circ. This dip is the signature of anticapture to the continuum for negative projectiles and corresponds to a zero Coulomb density of states factor at 45^circ. In addition, a significant departure from the Rutherford formula have been found for the one-electron differential cross section at large scattering angles.

Golden, D. E.

1997-10-01

43

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

NASA Astrophysics Data System (ADS)

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.

Hall, Felix H. J.; Willitsch, Stefan

2012-12-01

44

Doppler spectroscopy, a powerful tool for studying molecular collision dynamics  

SciTech Connect

The present review describes the application of Doppler spectroscopy to studies in collision dynamics. The method was originally introduced by Kinsey (J. Chem. Phys. 66, 2560 (1976)). The authors used it to obtain angular and velocity distributions of Ba(6s6p{sup 1}P{sub 1}) atoms scattered in the 6s6p{sup 3}P{sub 2} level by collisions with argon and simple molecules. After a short review of their recent work, the authors outline those areas where Doppler spectroscopy is a valuable tool (sometimes the only tool) for exploring gas phase collision dynamics. In particular they make clear that Doppler spectroscopy should not be considered as alternative but rather as complementary to the standard way of measuring differential cross sections where a rotating mass spectrometer rather than laser induced fluorescence is used to detect the scattered particles.

Mestdagh, J.M.; Visticot, J.P. [CEA/CEN Saclay, Gif-sur-Yvette (France). Service des Photons, Atomes et Molecules; Suits, A.G. [Lawrence Berkeley Lab., CA (United States). Chemical Sciences Division

1994-12-31

45

Doppler spectroscopy: a powerful tool for studying molecular collision dynamics  

NASA Astrophysics Data System (ADS)

The present review describes the application of Doppler spectroscopy to studies in collision dynamics. The method was originally introduced by Kinsey. We used it to obtain angular and velocity distributions of Ba(6s6p1P1) atoms scattered in the 6s6p3P2 level by collisions with Argon and simple molecules. After a short review of our recent work, we outline those areas where Doppler spectroscopy is a valuable tool (sometimes the only tool) for exploring gas phase collision dynamics. In particular we make clear the Doppler spectroscopy should not be considered as alternative but rather as complementary to the standard way of measuring differential cross sections where a rotating mass spectrometer rather than laser induced fluorescence is used to detect the scattered particles.

Mestdagh, Jean-Michel; Visticot, J. P.; Suits, Arthur G.

1994-06-01

46

Measurements of scattering processes in negative ion-atom collisions  

SciTech Connect

This Technical Progress Report describes the progress made on the research objectives during the past twelve months. This research project is designed to provide measurements of various scattering processes which occur in H{sup {minus}} collisions with atomic (specifically, noble gas and atomic hydrogen) targets at intermediate energies. These processes include: elastic scattering,single- and double-electron detachment, and target excitation/ionization. For the elastic and target inelastic processes where H{sup {minus}} is scattered intact, the experimental technique of Ion Energy-Loss Spectroscopy (IELS) will be employed to identify the final target state(s). In most of the above processes, cross sections are unknown both experimentally and theoretically. The measurements in progress will provide either experimentally-determined cross sections or set upper limits to those cross sections. In either case, these measurements will be stringent tests of our understanding in energetic negative ion-atom collisions. This series of experiments required the construction of a new facility and the initial ion beam was accelerated through the apparatus in April 1991.

Kvale, T.J.

1992-01-01

47

Reaction of formaldehyde cation with molecular hydrogen: Effects of collision energy and H2CO  

E-print Network

Reaction of formaldehyde cation with molecular hydrogen: Effects of collision energy and H2CO¿ vibrations Jianbo Liu and Scott L. Andersona) Department of Chemistry, University of Utah, Salt Lake City, Utah 84112 Received 29 December 2003; accepted 12 February 2004 The effects on the title reaction

Anderson, Scott L.

48

Bibliography of atomic and molecular processes, 1983  

SciTech Connect

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.

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. (comps.)

1984-10-01

49

1984 Bibliography of atomic and molecular processes  

SciTech Connect

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.

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. (comps.)

1985-04-01

50

1982 bibliography of atomic and molecular processes  

SciTech Connect

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.

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. (comps.)

1984-05-01

51

1985 bibliography of atomic and molecular processes  

SciTech Connect

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.

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. (comps.)

1986-06-01

52

Molecular sieving silica membrane fabrication process  

DOEpatents

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.

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

53

Molecular sieving silica membrane fabrication process  

DOEpatents

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.

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

1999-01-01

54

Collision-induced vibrational absorption in molecular hydrogens  

SciTech Connect

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.

Reddy, S.P.

1993-05-01

55

Theoretical treatments of fusion processes in collisions of weakly bound nuclei  

E-print Network

We review the theoretical methods to evaluate fusion cross sections in collisions of weakly bound nuclei. We piont out that in such collisions the coupling to the breakup channel leads to the appearance of different fusion processes. The extentsion of the coupled-channel method to coupling with the continuum is the most successful treatment for these collisions. However, evaluating separate cross section for each fusion process remains a very hard task.

L. F. Canto; R. Donangelo; M. S. Hussein

2007-04-17

56

Application of molecular modeling to biological processing  

NASA Astrophysics Data System (ADS)

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

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

1993-07-01

57

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

SciTech Connect

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

Andrianarijaona, V. M. [Pacific Union College; Draganic, Ilija N [ORNL; Seely, D. G. [Albion College; Havener, Charles C [ORNL

2011-01-01

58

Target isotope effects for vibrationally-resolved electron capture in low-energy collisions of O3+ with molecular hydrogen  

E-print Network

Target isotope effects for vibrationally-resolved electron capture in low-energy collisions of O3+ with molecular hydrogen P. C. Stancil Department of Physics and Astronomy and the Center for Simulational Physics hydrogen isotopomers (H2, HD, T2) for collision energies of 1 and 100 eV/u. Potential energy surfaces

Stancil, Phillip C.

59

Comparisons between statistics of low energy collision cascades generated by full molecular dynamics and by its binary collision approximation  

NASA Astrophysics Data System (ADS)

Collision cascades in Cu, Au and Cu3Au are generated by full molecular dynamics (MD) and by its binary collision approximation (BCA) with the Marlowe program. Cu and Au primaries have 1 keV initial energy. The same Molière repulsive potential is used in both models for close encounters. In the MD model, this potential is carefully splined to the pair component of the N-body potential developed by Ackland and Vitek. In the BCA, this N-body interaction is roughly modeled by a constant isotropic 4 eV binding energy of the target atoms to their rest positions. Time distributions of the number of atoms moving with a total energy higher than a threshold value Ed are compared and discussed. Recoil range distributions during the cascade development are discussed as well. The agreement between MD and BCA is fairly good in all cases for Ed larger than about 3 eV. In the case of smaller Ed-values, the BCA may result in an overestimate of the number of moving atoms in the late development of the cascades. This discrepancy is suggested to originate in the lack of attractive forces between the moving particles and the surrounding atoms in the BCA.

Hou, M.; Pan, Z. Y.

60

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

SciTech Connect

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.

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

2009-04-03

61

Relativistic hadron-hadron collisions in the ultra-relativistic quantum molecular dynamics model  

Microsoft Academic Search

Hadron-hadron (h-h) collisions at high energies are investigated in the ultra-relativistic quantum molecular dynamics (UrQMD) approach. This microscopic transport model describes the phenomenology of hadronic interactions at low and intermediate energies (sqrt(s))5 GeV, the excitation of colour strings and their subsequent fragmentation into hadrons dominates the multiple production of particles in the UrQMD model. The model shows a fair overall

M. Bleicher; E. Zabrodin; C. Spieles; S. A. Bass; C. Ernst; S. Soff; L. Bravina; M. Belkacem; H. Weber; H. Stöcker; W. Greiner

1999-01-01

62

Interaction potentials of molecular clusters with applications to collision rate calculations  

E-print Network

: William H. Marlow (Chair of Commitee) on R. Hart (M her) Marko aric (M r) J. W, Poston (Head of Department) December 1989 ABSTRACT Interaction Potentials of Molecular Clusters with Applications to Collision Rates. (December 1989) Alexis Sylvain... Parents. . . ACKNOWLEDGEMENTS I would like to thank the persons without whom this work would not have been possible. Among those, I would like to express my gratitude to my Conunittee Chairman Dr, W. H. Marlow for his guidance, kindness and dedication...

Amadon, Alexis Sylvain

1989-01-01

63

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

PubMed

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

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

64

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

65

ON THE EXTERNAL BRANCHES OF COALESCENT PROCESSES WITH MULTIPLE COLLISIONS WITH AN  

E-print Network

ON THE EXTERNAL BRANCHES OF COALESCENT PROCESSES WITH MULTIPLE COLLISIONS WITH AN EMPHASIS for the joint moments of the external branch lengths for coalescents with multi- ple collisions (-coalescents for the moments of the total external branch length of the Bolthausen­Sznitman coalescent. The proof is based

66

Ionization and Fragmentation of Molecular Gases in Collisions with Mev/amu Heavy Ions.  

NASA Astrophysics Data System (ADS)

A detailed study of ionization and fragmentation in molecular gas targets by 2.75 MeV H^ {+} and 40 MeV Ar^{13+ } ions has been performed using the time-of -flight (TOF) method. Ionization of molecular gases by 2.75 MeV H^{+} ions results primarily in single and double ionization, and consequently, the fragmentation patterns are simple to interpret. Energetic highly-charged, heavy ions, such as 40 MeV Ar^ {13+}, were found to be very effective in producing multiple ionization in molecular gas targets either through direct ionization or electron capture. Multiply -charged molecular ions, which are typically very unstable, rapidly dissociate to yield a rich fragmentation pattern containing numerous atomic and molecular fragments. A two stage TOF mass spectrometer was designed, constructed and tested for application to the study of fragmentation in molecular gas targets. The TOF spectrometer was calibrated and optimized for resolution and space focussing using neon and argon gas targets. To verify the proper working conditions for the spectrometer, several experiments were performed using noble gas targets including coincidence measurements of the recoil ion charge state distributions with the post-collision charge states of a 40 MeV Ar ^{13+} beam. Partial cross sections for direct ionization, one-, two- and three-electron capture in neon and argon by 40 MeV Ar^{13+ } ions have been determined and compared to ion-atom collisions theories. The fragmentation patterns for several molecular gases from simple diatomics (N_2, O_2, CO, NO) and triatomics (CO _2, N_2O, NO_2, SO_2) to large polyatomics (C_2F _6, C_2H_4 F_2, SF_6 ) have been measured. The fragmentation patterns for molecular gases measured by the TOF method were found to be useful in providing information about the various pathways for unimolecular dissociation of multiply-charged molecular ions. Moreover, several useful quantities such as fragments yields and average kinetic energies were obtained from the TOF spectrum. Energetic fragments produced in the dissociation of a multiply-charged molecular ion were found to exhibit a characteristic split peak structure in the TOF spectrum, whereas less energetic fragments, such as central atoms in totally symmetric molecules, had very narrow peak widths in the TOF spectrum similar to those observed for noble gas recoil ions. A simple model is proposed to predict the lowest energy pre-dissociative state in multiply-charged molecular ions.

Maurer, Richard Jay

67

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

SciTech Connect

Edge plasma studies are of vital importance for understanding plasma-wall interactions in magnetically confined fusion devices. These interactions determine the transport of neutrals into the plasma, and the properties of the plasma discharge. This presentation deals with optical spectroscopic studies of the plasma boundary, and their role in elucidating the prevailing physical conditions. Recorded spectra are of four types: emission spectra of ions and atoms, produced by electron impact excitation and by charge-exchange recombination, atomic spectra arising from electron impact-induced molecular dissociation and ionisation, visible spectra of molecular hydrogen and its isotopic combinations, and laser-induced fluorescence (LIF) spectra. The atomic spectra are strongly influenced by the confining magnetic field (Zeeman and Paschen-Back effects), which produces characteristic features useful for species identification, temperature determination by Doppler broadening, and studies of chemical and physical sputtering. Detailed analysis of the Zeeman components in both optical and LIF spectra shows that atomic hydrogen is produced in various velocity classes, some related to the relevant molecular Franck-Condon energies. The latter reflect the dominant electron collision processes responsible for production of atoms from molecules. This assignment has been verified by gas-puffing experiments through special test limiters. The higher-energy flanks of hydrogen line profiles probably also show the influence of charge-exchange reactions with molecular ions accelerated in the plasma sheath ('scrape-off layer') separating limiter surfaces from the edge plasma, in analogy to acceleration in the cathode-fall region of gas discharges. While electron collisions play a vital role in generating the spectra, ion collisions with excited atomic radiators act through re-distribution of population among the atomic fine-structure sublevels, and momentum transfer to the atomic nuclei via ion-induced dipole collisions with the bound electrons. The ions are thus important in randomising and equilibrating the velocity distribution of atomic products of molecular dissociation.

Hey, J. D. [School of Physics, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000 (South Africa); Brezinsek, S.; Mertens, Ph.; Unterberg, B. [Institut fuer Plasmaphysik, Forschungszentrum Juelich, Association EURATOM-FZJ, Trilateral Euregio Cluster (Germany)

2006-12-01

68

Processing of cloud condensation nuclei by collision-coalescence in a mesoscale model  

E-print Network

-cloud-drizzle system. Cloud processing, defined to be the reduction of cloud condensation nuclei (CCN) via collision-coalescence, is not uniquely related to total particle concentration, a behavior which stems from the roughly inverse dependence on cloud droplet...

Mechem, David B.; Robinson, Paul C.; Kogan, Yefim L.

2006-09-26

69

Green-solvent-processed molecular solar cells.  

PubMed

High-efficiency bulk heterojunction (BHJ) organic solar cells with power conversion efficiencies of more than 5?% can be fabricated using the green solvent 2-MeTHF. The active layers comprise a blend of a molecular semiconductor donor with intermediate dimensions (X2) and the soluble fullerene derivative [6,6]-phenyl-C61 -butyricacidoctylester (PC61 BC8 ). A switch of the processing solvent from chloroform to 2-MeTHF leads to no negative impacts on the morphology and charge-transport properties of optimally performing BHJ films. Examinations by absorption spectroscopy, atomic force microscopy, and grazing incidence wide-angle X-ray scattering reveal no significant modification of morphology. These results show that green solvents can be excellent alternatives for large-area printing of high-performance organic photovoltaics (OPVs) and thus open new opportunities for sustainable mass production of organic solar cells and other optoelectronic devices. PMID:25389005

Chen, Xiaofen; Liu, Xiaofeng; Burgers, Mark A; Huang, Ye; Bazan, Guillermo C

2014-12-22

70

Analyzing collision processes with the smartphone acceleration sensor  

NASA Astrophysics Data System (ADS)

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.

Vogt, Patrik; Kuhn, Jochen

2014-02-01

71

Processing and thermal properties of molecularly oriented polymers  

E-print Network

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 ...

Skow, Erik (Erik Dean)

2007-01-01

72

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

SciTech Connect

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.

Tasker, Elizabeth J.; Tan, Jonathan C. [Department of Astronomy, University of Florida, Gainesville, FL 32611 (United States)

2009-07-20

73

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

SciTech Connect

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.

Hall, G.E.

2011-05-31

74

Molecular Processing of Polymers with Cyclodextrins  

NASA Astrophysics Data System (ADS)

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

Tonelli, Alan E.

75

Scattering processes in antiprotonic hydrogen - hydrogen atom collisions  

E-print Network

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.

V. P. Popov; V. N. Pomerantsev

2006-01-11

76

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

SciTech Connect

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

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

1980-09-01

77

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

NASA Astrophysics Data System (ADS)

We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH_2(tilde{X}^3B_1)] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH_2(tilde{X}^3B_1) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 ?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(tilde{X}^3B_1) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.

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

2012-09-01

78

An Intestinal Surgery Simulator: Real-Time Collision Processing and Visualization  

E-print Network

An Intestinal Surgery Simulator: Real-Time Collision Processing and Visualization Laks Raghupathi, we present a method for animating the small intestine and the mesentery (the tissue that connects of the intestine. An efficient curvature detection method, along with an adaptive sampling algorithm, is presented

Paris-Sud XI, Université de

79

Relativistic Hadron-Hadron Collisions in the Ultra-Relativistic Quantum Molecular Dynamics Model (UrQMD)  

E-print Network

Hadron-hadron collisions at high energies are investigated in the Ultra-relativistic-Quantum-Molecular-Dynamics approach (UrQMD). This microscopic transport model is designed to study pp, pA and A+A collisions. It describes the phenomenology of hadronic interactions at low and intermediate energies ($\\sqrt s 5$ GeV, the excitation of color strings and their subsequent fragmentation into hadrons dominates the multiple production of particles in the UrQMD model. The model shows a fair overall agreement with a large body of experimental h-h data over a wide range of h-h center-of-mass energies. Hadronic reaction data with higher precision would be useful to support the use of the UrQMD model for relativistic heavy ion collisions.

M. Bleicher; E. Zabrodin; C. Spieles; S. A. Bass; C. Ernst; S. Soff; L. Bravina; M. Belkacem; H. Weber; H. Stöcker; W. Greiner

1999-09-16

80

Hard processes in p-A collisions with MC generator HARDPING 3.0  

NASA Astrophysics Data System (ADS)

Hard processes in p-A collisions at high energies with MC (Monte Carlo) generator HARDPING (HARD Probe IN-teraction Generator) are discussed. Such effects as energy loss and multiple rescattering initial and produced hadrons and their constituents are implemented into the HARDPING. It provides a reasonably good description of hadron production in p-A collisions at 400 GeV (Cronin effect). Predictions by the HARPING 3.0 for lepton pairs production in p-A at proton beam energy 120 GeV ( s=15.08 GeV) at Fermilab Tevatron Booster and s=5.02 TeV at CERN LHC are presented.

Berdnikov, Ya. A.; Ivanov, A. E.; Kim, V. T.; Murzin, V. A.; Suetin, D. P.

2013-12-01

81

Textual collisions: the writing process and the Modernist experiment  

E-print Network

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...

Hollis, Erin Michelle

2005-08-29

82

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

SciTech Connect

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.

Wu, Tai, T.

2011-09-15

83

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

NASA Astrophysics Data System (ADS)

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.

Kim, Sangrak

2012-10-01

84

Chemistry of Molecular Growth Processes in Flames  

Microsoft Academic Search

Chemical mechanisms of pyrolysis, growth, and oxidation processes in flames have traditionally been inferred from spatial profile measurements of species concentrations. Experimental investigations now include the detection of numerous minor species such as reactive radicals and intermediate hydrocarbons. In assessing a proposed mechanism important new constraints can be established when the detailed species profile data are combined with velocity and

Kermit C. Smyth; J. Houston Miller

1987-01-01

85

Chemistry of molecular growth processes in flames  

Microsoft Academic Search

Chemical mechanisms of pyrolysis, growth, and oxidation processes in flames have traditionally been inferred from spatial profile measurements of species concentrations. Experimental investigations now include the detection of numerous minor species such as reactive radicals and intermediate hydrocarbons. In assessing a proposed mechanism important new constraints can be established when the detailed species profile data are combined with velocity and

K. C. Smyth; J. H. Miller

1987-01-01

86

Photochemotherapy: Molecular And Cellular Processes Involved  

NASA Astrophysics Data System (ADS)

In photochemotherapy, as exemplified by the photodynamic therapy of tumors, a photosensitizing drug is administered to the patient; then, after a period of time to permit the most effective anatomical distribution of the drug, the diseased area is illuminated using an appropriate source of light of wavelengths absorbed by the sensitizer. In the tumor case, this results in the photochemical alteration of critical kinds of biornolecules in the diseased tissue, which interferes with the normal activities of certain cell organelles. This, in turn, leads to the injury or death of diseased cells in the treated area. This paper briefly reviews the reactive chemical species that can be formed in biological systems by illuminated sensitizers (triplet states of sensitizer molecules, free radicals of sensitizers and cellular components, singlet oxygen, superoxide, hydrogen peroxide, hydroxyl radical) and the kinds of biochemical changes they produce in essential cellular molecules (nucleic acids, proteins, unsaturated lipids, etc.). Also reviewed are the effects of these molecular changes on the structure and function of mammalian cell organelles (membranes, mitochondria, nuclear components, etc.) and the mechanisms of the resulting injury or killing of the cells.

Spikes, John D.

1989-03-01

87

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

PubMed

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

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

2010-03-01

88

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

NASA Technical Reports Server (NTRS)

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

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

1999-01-01

89

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

NASA Astrophysics Data System (ADS)

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

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

2003-03-01

90

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

SciTech Connect

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

Kadhane, Umesh; Tribedi, Lokesh C. [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India); Montanari, C.C. [Instituto de Astronomia y Fisca del Espacio, CONICET-UBA, Buenos Aires (Argentina)

2003-03-01

91

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

E-print Network

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.

R. A. Kycia; J. Chwastowski; R. Staszewski; J. Turnau

2014-11-21

92

Using relaxation spectra to understand molecular processes in ring polymers  

NASA Astrophysics Data System (ADS)

Rheological characterization of polymeric systems can be used to investigate molecular processes. Some processes, such as entanglement and reptation, cannot be easily seen in the complex modulus or other conventional representations of rheological data. Instead, presenting data as relaxation spectra enhances the understanding of such processes. This will be shown on the example of ring and linear polystyrene polymers and ring/linear-blends, recently published by Kapnistos et al. (Nature Materials, 2008).

Stadler, Florian J.

2012-09-01

93

Photochemical processes in a two-component molecular contaminant film  

NASA Astrophysics Data System (ADS)

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

Luey, Kenneth T.; Coleman, Dianne J.

2008-08-01

94

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

E-print Network

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.

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

95

Electron capture in collisions of H{sup +} ions with S atoms and its reverse process below kilo-electron-volt energies  

SciTech Connect

Electron capture in H{sup +}+S({sup 3}P,{sup 1}D) collisions is studied theoretically by using a semiclassical molecular representation with five molecular channels from the initial ground and excited states at collision energies above 10 eV. Electron capture in S{sup +} ({sup 4}S)+H(1s) collisions is also investigated by using three molecular channels in order to assess the earlier estimation which gave the rate constant of 10{sup {minus}15}cm{sup 3}/s at 10{sup 4}K for the process. The {ital ab initio} potential curves and nonadiabatic coupling matrix elements for the HS{sup +} system are obtained from multireference single- and double-excitation configuration-interaction calculations employing relatively large basis sets. Dominant capture channels corresponding to the [H+S{sup +}({sup 2}P)] and [H+S{sup +}({sup 2}D)] states lie lower by 0.2 and 1.4 eV, and 1.34 and 2.5 eV from the initial ground [H{sup +}+S({sup 3}P)] and excited [H{sup +}+S({sup 1}D)] states, respectively. The present results show that electron capture from the excited species is found to be rather weak at lower energies. But it rapidly becomes comparable to that from the ground state. Electron capture in S{sup +} ({sup 4}S)+H collisions proceeds through the two-step mechanism at lower energies, and therefore, the cross section is found to be small with the value less than 10{sup {minus}17}cm{sup 2} below 1 keV, thus supporting the earlier estimation. {copyright} {ital 1997} {ital The American Physical Society}

Kimura, M. [School of Allied Health Sciences, Yamaguchi University, Ube, Yamaguchi 755 (Japan)] [School of Allied Health Sciences, Yamaguchi University, Ube, Yamaguchi 755 (Japan); [Institute of Space and Astronautical Science, Yoshinodai, Sagamihara 229 (Japan); Gu, J.; Hirsch, G.; Buenker, R.J. [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany)] [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany); Domondon, A.; Watanabe, T. [Department of Physics, International Christian University, Tokyo (Japan)] [Department of Physics, International Christian University, Tokyo (Japan); Sato, H. [Department of Information Science, Ochanomizu University, Tokyo (Japan)] [Department of Information Science, Ochanomizu University, Tokyo (Japan)

1997-09-01

96

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

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

97

1978 bibliography of atomic and molecular processes. [Bibliography  

SciTech Connect

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.

Not Available

1980-03-01

98

1979 bibliography of atomic and molecular processes. [Bibliography  

SciTech Connect

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.

None

1980-08-01

99

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

SciTech Connect

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

Toth, G.; Tanis, J. A. [Department of Physics, Western Michigan University, Kalamazoo, MI 49008 (United States); Zavodszky, P. A. [J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, KS 66506 (United States)

2009-03-10

100

Formation of anions and cations via a binary-encounter process in OH+ + Ar collisions: The role of dissociative excitation and statistical aspects  

NASA Astrophysics Data System (ADS)

Molecular fragmentation leading to the formation of negatively and positively charged hydrogen ions in 7-keV OH+ + Ar collisions is investigated experimentally. The most striking finding is that negative and positive hydrogen ions are emitted with very similar angular dependences. Also, the kinetic energy distribution of the H+ fragment shows strong similarities with that of the ejected H- ion. The kinematics of the emitted H core is found to be essentially driven by its scattering on the atomic target. However, in addition to this binary-encounter process, dissociative electronic excitation of the molecular projectile has to be invoked to explain the observed fragmentation patterns. Though the electron capture process is complex, it is shown that the relative population of the different final charge states of the outgoing fragments can be described by simple statistical laws.

Lattouf, E.; Juhász, Z.; Chesnel, J.-Y.; Kovács, S. T. S.; Bene, E.; Herczku, P.; Huber, B. A.; Méry, A.; Poully, J.-C.; Rangama, J.; Sulik, B.

2014-06-01

101

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

NASA Technical Reports Server (NTRS)

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.

Norbury, John W.

1992-01-01

102

Disintegration of argon clusters in collisions with highly vibrationally excited SF6 molecules in crossed molecular and cluster beams  

NASA Astrophysics Data System (ADS)

It has been found that collisions of highly vibrationally excited SF6 molecules (with the vibrational energy E vib ? 0.5-2.0 eV) with Ar N clusters (where N ? 30-40 is the number of atoms in a cluster) in crossed molecular and cluster beams result in capture of molecules followed by complete disintegration of the clusters. Possible applications of the effect for selective doping of clusters with molecules, laser separation of isotopes, and selective transport of molecules to the surface are discussed.

Makarov, G. N.; Petin, A. N.

2013-03-01

103

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

NASA Astrophysics Data System (ADS)

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.

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

2011-09-01

104

Theoretical analysis of dynamic processes for interacting molecular motors  

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

105

A model for energy transfer in inelastic molecular collisions applicable at steady state or non-steady state and for an arbitrary distribution of collision energies  

Microsoft Academic Search

A new model for energy exchange between translational and internal degrees of freedom in atom-molecule collisions has been\\u000a developed. It is suitable for both steady state conditions (e.g., a large number of collisions with thermal kinetic energies)\\u000a and non-steady state conditions with an arbitrary distribution of collision energies (e.g., single high-energy collisions).\\u000a In particular, it does not require that the

Wolfgang R. Plass; R. Graham Cooks

2003-01-01

106

Statistical model of energy transfer in molecular collisions: De-energization of highly excited toluene  

NASA Astrophysics Data System (ADS)

Recent experimental data on the collisional de-energization of toluene from initial energies of between 10 000 and 49 000 cm-1 have been analyzed by the partially ergodic collision theory. The data for 11 different gases were obtained by kinetically controlled selective ionization by Luther and co-workers [J. Chem. Phys. 112, 4076 (2000)] and are of exceptional detail and reliability. The semiempirical PECT model starts from the average energy transferred per collision and predicts the full transition probability P(E',E) to good accuracy. The energy transfer efficiency is about a tenth of the ergodic collision limit with only minor dependence on gas molecule or initial toluene energy.

Nilsson, Daniel; Nordholm, Sture

2002-04-01

107

Large scale molecular dynamics modeling of materials fabrication processes  

SciTech Connect

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.

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

1994-02-01

108

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

ERIC Educational Resources Information Center

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…

Donnelly, Denis P.; And Others

1971-01-01

109

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)

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.

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

2014-12-01

110

Interstellar Processes Leading to Molecular Deuterium Enrichment and Their Detection  

NASA Technical Reports Server (NTRS)

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.

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

2001-01-01

111

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

SciTech Connect

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.

Juhasz, Z.; Sulik, B. [Institute of Nuclear Research (ATOMKI), Bem ter, 18/c, H-4026 Debrecen (Hungary); Chesnel, J.-Y.; Fremont, F.; Hajaji, A. [CIRIL Unite Mixte CEA-CNRS-EnsiCaen-Universite de Caen Basse-Normandie, F-14050 Caen Cedex 04 (France)

2008-12-08

112

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

113

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

114

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

NASA Astrophysics Data System (ADS)

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

Pysklywec, Russell; Gray, Robert

2014-05-01

115

High-Resolution Imaging of Velocity-Controlled Molecular Collisions Using Counterpropagating Beams  

NASA Astrophysics Data System (ADS)

We present ultrahigh-resolution measurements of state-to-state inelastic differential cross sections for NO-Ne and NO-Ar collisions, obtained by combining the Stark deceleration and velocity map imaging techniques. We show that for counterpropagating crossed beam geometries, the effect of the velocity spreads of the reagent beams on the angular resolution of the images is minimized. Furthermore, the counterpropagating geometry results in images that are symmetric with respect to the relative velocity vector. This allows for the use of inverse Abel transformation methods that enhance the resolution further. State-resolved diffraction oscillations in the differential cross sections are measured with an angular resolution approaching 0.3°. Distinct structures observed in the cross sections gauge the quality of recent ab initio potential energy surfaces for NO-rare-gas atom collisions with unprecedented precision.

Vogels, Sjoerd N.; Onvlee, Jolijn; von Zastrow, Alexander; Groenenboom, Gerrit C.; van der Avoird, Ad; van de Meerakker, Sebastiaan Y. T.

2014-12-01

116

High-resolution imaging of velocity-controlled molecular collisions using counterpropagating beams.  

PubMed

We present ultrahigh-resolution measurements of state-to-state inelastic differential cross sections for NO-Ne and NO-Ar collisions, obtained by combining the Stark deceleration and velocity map imaging techniques. We show that for counterpropagating crossed beam geometries, the effect of the velocity spreads of the reagent beams on the angular resolution of the images is minimized. Furthermore, the counterpropagating geometry results in images that are symmetric with respect to the relative velocity vector. This allows for the use of inverse Abel transformation methods that enhance the resolution further. State-resolved diffraction oscillations in the differential cross sections are measured with an angular resolution approaching 0.3°. Distinct structures observed in the cross sections gauge the quality of recent ab initio potential energy surfaces for NO-rare-gas atom collisions with unprecedented precision. PMID:25615327

Vogels, Sjoerd N; Onvlee, Jolijn; von Zastrow, Alexander; Groenenboom, Gerrit C; van der Avoird, Ad; van de Meerakker, Sebastiaan Y T

2014-12-31

117

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

NASA Astrophysics Data System (ADS)

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.

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

1990-01-01

118

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

E-print Network

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.

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

119

Collision tectonics  

SciTech Connect

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.

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

1985-01-01

120

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

NASA Astrophysics Data System (ADS)

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

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

2012-04-01

121

Inhibition Of Molecular And Biological Processes Using Modified Oligonucleotides  

DOEpatents

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.

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

2003-04-15

122

Deep process of the collision and deformation on the northern margin of the Tibetan Plateau: Revelation from investigation of the deep seismic profiles  

Microsoft Academic Search

The seismic investigation achievements from three kinds of methods have revealed the lithospheric structure and the deep process\\u000a of deformation caused by collision. It is found that convergent collision and deep subduction of the continental lithosphere\\u000a are in progress along the northern margin of the Tibetan Plateau. The deep process of due collision and deformation is different\\u000a from that of

Rui Gao; Pengwu Li; Qiusheng Li; Ye Guan; Danian Shi; Xiangru Kong; Hongbing Liu

2001-01-01

123

Finding Novel Molecular Connections between Developmental Processes and Disease  

PubMed Central

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

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

2014-01-01

124

Finding novel molecular connections between developmental processes and disease.  

PubMed

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

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

2014-05-01

125

Ionization and Fragmentation of Molecular Gases in Collisions with Mev\\/amu Heavy Ions  

Microsoft Academic Search

A detailed study of ionization and fragmentation in molecular gas targets by 2.75 MeV H^ {+} and 40 MeV Ar^{13+ } ions has been performed using the time-of -flight (TOF) method. Ionization of molecular gases by 2.75 MeV H^{+} ions results primarily in single and double ionization, and consequently, the fragmentation patterns are simple to interpret. Energetic highly-charged, heavy ions,

Richard Jay Maurer

1988-01-01

126

On cosmic ray processing of ices in molecular clouds  

NASA Astrophysics Data System (ADS)

We investigated theoretically the transformation of the energy dependence of the cosmic ray proton flux in the keV to GeV region when penetrating inside molecular clouds. Our computations suggest that energy losses of the cosmic ray particles by interaction with the matter of the molecular cloud are principally caused by the inelastic (electronic) interaction potential; the transformed energy distribution of energetic protons is determined mainly by the column density of the absorbing medium. Up to now there are no detailed investigations on an energetic particle processing of various ices by ions, modeling the cosmic ray irradiation over the whole energy range from eV to GeV. Our studies on the ion induced conversion of ices include an examination of the linear energy transfer due to stopping processes, by which the input projectile loses its original energy to particles in the target. In particular, a cosmic ray irradiation dose up to AV = 50 for icy methane is calculated and discussed. The results can be used to predict a radiation induced chemical conversion rate of simple chemical species to complex ones by means of forthcoming experimental data.

Yeghikyan, Ararat

2010-11-01

127

Absolute cross sections for multi-electron processes in low energy Arq+Ar collisions: Comparison with theory  

Microsoft Academic Search

Absolute cross sections have been measured for a variety of multi-electron processes in low-energy collisions of multiply charged argon recoil ions with neutral argon. The cross sections are compared with theoretical estimates based on an extension of the classical barrier model. Comparison is also made with the statistical theory of Müller et al.

A. Bárány; G. Astner; H. Cederquist; H. Danared; S. Huldt; P. Hvelplund; A. Johnson; H. Knudsen; L. Liljeby; K.-G. Rensfelt

1985-01-01

128

INELASTIC PROCESSES IN 0.11000 keV/u COLLISIONS OF Ne q+ (q=710) IONS WITH ATOMIC HYDROGEN  

E-print Network

4 INELASTIC PROCESSES IN 0.1­1000 keV/u COLLISIONS OF Ne q+ (q=7­10) IONS WITH ATOMIC HYDROGEN D and engineering study of burning plasmas. Therefore, with the production of significant quantities of fusion to recycle hydrogen, and how to remove heat from the plasma. Cooling is required both to extract heat to run

129

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

NASA Astrophysics Data System (ADS)

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.

Hong, Woo-Pyo; Jung, Young-Dae

2014-10-01

130

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

SciTech Connect

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.

Hong, Woo-Pyo [Department of Electronics Engineering, Catholic University of Daegu, Hayang 712-702 (Korea, Republic of); Jung, Young-Dae, E-mail: ydjung@hanyang.ac.kr [Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180-3590 (United States); Department of Applied Physics and Department of Bionanotechnology, Hanyang University, Ansan, Kyunggi-Do 426-791 (Korea, Republic of)

2014-10-15

131

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

SciTech Connect

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.

Lu Zhenzhong; Chen Deying; Fan Rongwei; Xia Yuanqin

2012-01-02

132

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

NASA Astrophysics Data System (ADS)

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 s=7TeV collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 1.1fb-1. From the dominant uu¯, dd¯??*/Z??-?+ process, the effective weak mixing angle parameter is measured to be sin?2?eff=0.2287±0.0020(stat.)±0.0025(syst.). This result is consistent with measurements from other processes, as expected within the standard model.

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Fabjan, C.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hammer, J.; Hänsel, S.; Hoch, M.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Krammer, M.; Liko, D.; Mikulec, I.; Pernicka, M.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Teischinger, F.; Trauner, C.; Wagner, P.; Waltenberger, W.; Walzel, G.; Widl, E.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Bansal, S.; Benucci, L.; de Wolf, E. A.; Janssen, X.; Luyckx, S.; Maes, T.; Mucibello, L.; Ochesanu, S.; Roland, B.; Rougny, R.; Selvaggi, M.; van Haevermaet, H.; van Mechelen, P.; van Remortel, N.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Gonzalez Suarez, R.; Kalogeropoulos, A.; Maes, M.; Olbrechts, A.; van Doninck, W.; van Mulders, P.; van Onsem, G. P.; Villella, I.; Charaf, O.; Clerbaux, B.; de Lentdecker, G.; Dero, V.; Gay, A. P. R.; Hammad, G. H.; Hreus, T.; Marage, P. E.; Raval, A.; Thomas, L.; Vander Marcken, G.; Vander Velde, C.; Vanlaer, P.; Adler, V.; Cimmino, A.; Costantini, S.; Grunewald, M.; Klein, B.; Lellouch, J.; Marinov, A.; McCartin, J.; Ryckbosch, D.; Thyssen, F.; Tytgat, M.; Vanelderen, L.; Verwilligen, P.; Walsh, S.; Zaganidis, N.; Basegmez, S.; Bruno, G.; Caudron, J.; Ceard, L.; Cortina Gil, E.; de Favereau de Jeneret, J.; Delaere, C.; Favart, D.; Forthomme, L.; Giammanco, A.; Grégoire, G.; Hollar, J.; Lemaitre, V.; Liao, J.; Militaru, O.; Nuttens, C.; Ovyn, S.; Pagano, D.; Pin, A.; Piotrzkowski, K.; Schul, N.; Beliy, N.; Caebergs, T.; Daubie, E.; Alves, G. A.; Brito, L.; de Jesus Damiao, D.; Pol, M. E.; Souza, M. H. G.; Aldá Júnior, W. L.; Carvalho, W.; da Costa, E. M.; de Oliveira Martins, C.; Fonseca de Souza, S.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Oguri, V.; Prado da Silva, W. L.; Santoro, A.; Silva Do Amaral, S. M.; Sznajder, A.; Anjos, T. S.; Bernardes, C. A.; Dias, F. A.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Lagana, C.; Marinho, F.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Darmenov, N.; Genchev, V.; Iaydjiev, P.; Piperov, S.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Tcholakov, V.; Trayanov, R.; Vutova, M.; Dimitrov, A.; Hadjiiska, R.; Karadzhinova, A.; Kozhuharov, V.; Litov, L.; Mateev, M.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Jiang, C. H.; Liang, D.; Liang, S.; Meng, X.; Tao, J.; Wang, J.; Wang, J.; Wang, X.; Wang, Z.; Xiao, H.; Xu, M.; Zang, J.; Zhang, Z.; Ban, Y.; Guo, S.; Guo, Y.; Li, W.; Mao, Y.; Qian, S. J.; Teng, H.; Zhu, B.; Zou, W.; Cabrera, A.; Gomez Moreno, B.; Ocampo Rios, A. A.; Osorio Oliveros, A. F.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Lelas, K.; Plestina, R.; Polic, D.; Puljak, I.; Antunovic, Z.; Dzelalija, M.; Kovac, M.; Brigljevic, V.; Duric, S.; Kadija, K.; Luetic, J.; Morovic, S.; Attikis, A.; Galanti, M.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Finger, M.; Finger, M., Jr.; Assran, Y.; Ellithi Kamel, A.; Khalil, S.; Mahmoud, M. A.; Radi, A.; Hektor, A.; Kadastik, M.; Müntel, M.; Raidal, M.; Rebane, L.; Tiko, A.; Azzolini, V.; Eerola, P.; Fedi, G.; Voutilainen, M.; Czellar, S.; Härkönen, J.; Heikkinen, A.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Ungaro, D.; Wendland, L.; Banzuzi, K.; Karjalainen, A.; Korpela, A.; Tuuva, T.; Sillou, D.; Besancon, M.; Choudhury, S.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Marionneau, M.; Millischer, L.; Rander, J.; Rosowsky, A.; Shreyber, I.; Titov, M.; Baffioni, S.; Beaudette, F.; Benhabib, L.; Bianchini, L.; Bluj, M.; Broutin, C.; Busson, P.; Charlot, C.; Dahms, T.; Dobrzynski, L.; Elgammal, S.; Granier de Cassagnac, R.; Haguenauer, M.; Miné, P.; Mironov, C.; Ochando, C.; Paganini, P.; Sabes, D.; Salerno, R.; Sirois, Y.; Thiebaux, C.; Veelken, C.; Zabi, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Bodin, D.; Brom, J.-M.; Cardaci, M.; Chabert, E. C.; Collard, C.; Conte, E.; Drouhin, F.; Ferro, C.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Greder, S.; Juillot, P.; Karim, M.; Le Bihan, A.-C.; Mikami, Y.; van Hove, P.; Fassi, F.; Mercier, D.; Baty, C.; Beauceron, S.; Beaupere, N.; Bedjidian, M.; Bondu, O.; Boudoul, G.; Boumediene, D.; Brun, H.; Chasserat, J.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Gascon, S.; Ille, B.; Kurca, T.; Le Grand, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Sordini, V.; Tosi, S.; Tschudi, Y.; Verdier, P.; Viret, S.; Lomidze, D.; Anagnostou, G.; Beranek, S.; Edelhoff, M.; Feld, L.; Heracleous, N.; Hindrichs, O.; Jussen, R.

2011-12-01

133

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

SciTech Connect

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.

Tamascelli, Dario; Dambrosio, Francesco Saverio [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy)] [Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Conte, Riccardo [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States)] [Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Ceotto, Michele, E-mail: michele.ceotto@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)] [Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano (Italy)

2014-05-07

134

Energy conversion processes based on molecular excited states  

NASA Astrophysics Data System (ADS)

The major emphasis of our DOE-supported research efforts remains the use of molecular excited states in energy conversion processes. In the past year we have made significant progress in the distinct areas of: (1) electronic structure, photophysical and photochemical properties of MLCT-based excited states, (2) design and characterization of metallopolymeric films as a basis for photoelectrodes containing MLCT-based chromophores, and (3) excited state photoelectrochemical cells based on excited state redox quenching. We have continued to develop synthetic routes to new MLCT excited states, most recently to a series of complexes. Systematic variations (from electron-donating to electron-withdrawing properties) allow control to be gained over changes in emission energies (E sub em), excited state redox potentials, ground state absorption energies, and radiative and nonradiative decay rate constants and perhaps, most importantly, open up two new families of excited states for photoredox applications.

Meyer, T. J.

1987-03-01

135

Solution processed molecular floating gate for flexible flash memories  

PubMed Central

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

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

2013-01-01

136

Genomic Signal Processing: Predicting Basic Molecular Biological Principles  

NASA Astrophysics Data System (ADS)

Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. Mapping genome-scale protein binding data using pseudoinverse projection onto patterns of RNA expression data that had been extracted by SVD and GSVD, a novel correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast, that might be due to a previously unknown mechanism of regulation, is predicted. (1) Alter & Golub, Proc. Natl. Acad. Sci. USA 101, 16577 (2004). (2) Alter, Golub, Brown & Botstein, Miami Nat. Biotechnol. Winter Symp. 2004 (www.med.miami.edu/mnbws/alter-.pdf)

Alter, Orly

2005-03-01

137

Implementation of exterior complex scaling in B-splines to solve atomic and molecular collision problems  

SciTech Connect

B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without their explicit analytic application. In this paper, an implementation of exterior complex scaling in B-splines is described that can bring the well-developed technology of B-splines to bear on new problems, including multiple ionization and breakup problems, in a straightforward way. The approach is demonstrated for examples involving the continuum motion of nuclei in diatomic molecules as well as electronic continua. For problems involving electrons, a method based on Poisson's equation is presented for computing two-electron integrals over B-splines under exterior complex scaling.

McCurdy, C. William; Martin, Fernando

2003-11-18

138

[Spin-catalysis in the processes of photo- and bioactivation of molecular oxygen].  

PubMed

Rational explanation of the mechanisms of bioactivation of molecular oxygen by enzymes is impossible without understanding more simple mechanisms of the O2 photoactivation in collision complexes of gases and solvents. Production of peroxides in oxidases and more complicated oxidation processes by molecular oxygen are spin forbidden reactions and bioactivation of dioxygen is connected with enzymatic spin-catalysis by acceleration of the triplet-singlet (T-S) quantum transitions. Internal magnetic perturbations in the free oxygen molecule and in O2 complexes with solvents or with coenzyme in biopolymers bear characteristic entirely similar features and removal of spin prohibition on T-S transitions is quantified by some common physical mechanisms. An account of specific spin-orbit coupling (SOC) in the open pi(g)-shell of dioxygen permits to explain the T-S transitions intensity of the red atmospheric band in the O2, molecule and the selective enhancement of the radiative alpha1delta(g)-->X3Sigma(g)- transition intensity in various solvents (P). Charge transfer contribution P+ O2- leads to increase of SOC between the T-S oxygen states that enhances the O2 (alpha1delta(g)) quenching. Similar T-S transitions mechanisms and SOC enhancement is realized upon dioxygen activation by enzymes of the glucoseoxidase type. Three electronic mechanisms of reductive bioactivation of O2 by oxidases coenzymes are considered on the basis of physical mechanisms of the O2 photoactivation. They include intermediate stages of the superoxide and peroxide ion formation. Study of the O2 activation mechanisms by T-S transitions in enzymatic complexes of dioxygen binding open new potentialities in biotechnology and medicine. PMID:19877428

Minaev, B F

2009-01-01

139

Instanton-Like Processes in Particle Collisions: a Numerical Study of the SU(2)-Higgs Theory below the Sphaleron Energy  

E-print Network

We use semiclassical methods to calculate the probability of inducing a change of topology via a high-energy collision in the SU(2)-Higgs theory. This probability is determined by a complex solution to a classical boundary value problem on a contour in the complex time plane. In the case of small particle number it is the probability of instanton-like processes in particle collisions. We obtain numerically configurations with the correct topological features and expected properties in the complex time plane. Our work demonstrates the feasibility of the numerical approach to the calculation of instanton-like processes in gauge theories. We present our preliminary results for the suppression factor of topology changing processes, which cover a wide range of incoming particle numbers and energies below the sphaleron energy.

F. Bezrukov; C. Rebbi; V. Rubakov; P. Tinyakov

2001-10-08

140

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

NASA Technical Reports Server (NTRS)

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.

Cheung, Wang K.; Norbury, John W.

1992-01-01

141

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

NASA Astrophysics Data System (ADS)

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.

Beach, Daniel G.; Gabryelski, Wojciech

2012-05-01

142

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)

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.

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

2014-08-01

143

Molecular Specificity of Multiple Hippocampal Processes Governing Fear Extinction  

PubMed Central

SYNOPSIS Over many years, fear extinction has been conceptualized as one dominant process, new inhibitory learning, which serves to dampen previously acquired fear. Here we present an alternative view, that brain region-specific processing of representations, expectations and emotional attributes of the fear-provoking event, recruits unique mechanisms that interdependently contribute to the conditioning and extinction of fear. The co-occurrence of these mechanisms within the fear circuit can thus be tracked and differentiated at a molecular and cellular level. Among others, the transcriptional regulators cFos, cAMP-dependent response element binding protein (CREB), Zif268, and extracellular signal-regulated kinases (Erk) stand out as hippocampal nuclear markers signaling novelty, arousal, retrieval, and prediction error, respectively. Consistent with evidence from human studies, these findings indicate that, beyond inhibitory learning, fear extinction requires modification of the emotional attributes and expectations that define the threatening context. Given the likely dysregulation of one or more of these processes in anxiety disorders, a key research challenge for the future is the identification and enhancement of individual extinction mechanisms to target the specific components of fear. Environmental stimuli lacking affective properties (conditioned stimuli, CS) rapidly become threatening if presented with stressful events (unconditioned stimuli, US). Consequently, based on a CS-US association, the presentation of the CS triggers species-specific fear responses until the US consistently stops occurring. At that point, new learning takes place and the fear response declines, a phenomenon termed extinction. The view that extinction occurs because a new, inhibitory CS-noUS association gains control over behavior 106, has remained dominant in the field (reviewed by 20,33,35,100). The implications of impaired fear regulation in the development of anxiety disorders have stimulate-d intense research in this area. Rodent studies identified the circuits involved in the conditioning and extinction of fear of salient cues 99,98,85,93,150, generating data that were confirmed in humans with brain imaging approaches 114,130. Nevertheless, research with experimental animals has not fully taken advantage of human data in order to better interpret extinction mechanisms in the framework of learning, expectation and emotion governing fear-motivated behavior. The present article aims to summarize recent molecular evidence on fear extinction, focusing on hippocampal mechanisms and experimental models of contextual fear, and compare the results with other relevant fear paradigms and human imaging studies. Instead of conceptualizing extinction learning as one process, such as CS-noUS association or inhibitory learning 19,26,96, we propose that fear extinction reflects the behavioral output of several region-specific learning processes that modify different components of the conditioning memory. The significance of these findings is discussed in the framework of fear regulation and anxiety disorders. PMID:20458884

Radulovic, Jelena; Tronson, Natalie C.

2010-01-01

144

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

NASA Astrophysics Data System (ADS)

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

Mihesan, Claudia; Glodi?, Pavle; Velegrakis, Michalis

2015-03-01

145

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

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

146

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

NASA Astrophysics Data System (ADS)

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.

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

2015-04-01

147

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

NASA Technical Reports Server (NTRS)

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.

Cheung, Wang K.; Norbury, John W.

1994-01-01

148

Complex physiological and molecular processes underlying root gravitropism  

NASA Technical Reports Server (NTRS)

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.

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

2002-01-01

149

Substitution processes in molecular evolution. III. Deleterious alleles.  

PubMed

The substitution processes for various models of deleterious alleles are examined using computer simulations and mathematical analyses. Most of the work focuses on the house-of-cards model, which is a popular model of deleterious allele evolution. The rate of substitution is shown to be a concave function of the strength of selection as measured by alpha = 2N sigma, where N is the population size and sigma is the standard deviation of fitness. For alpha < 1, the house-of-cards model is essentially a neutral model; for alpha > 4, the model ceases to evolve. The stagnation for large alpha may be understood by appealing to the theory of records. The house-of-cards model evolves to a state where the vast majority of all mutations are deleterious, but precisely one-half of those mutations that fix are deleterious (the other half are advantageous). Thus, the model is not a model of exclusively deleterious evolution as is frequently claimed. It is argued that there are no biologically reasonable models of molecular evolution where the vast majority of all substitutions are deleterious. Other models examined include the exponential and gamma shift models, the Hartl-Dykhuizen-Dean (HDD) model, and the optimum model. Of all those examined, only the optimum and HDD models appear to be reasonable candidates for silent evolution. None of the models are viewed as good candidates for protein evolution, as none are both biologically reasonable and exhibit the variability in substitutions commonly observed in protein sequence data. PMID:7851786

Gillespie, J H

1994-11-01

150

Photoinduced Charge and Energy Transfer Processes in Molecular Aggregates  

SciTech Connect

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.

John F. Endicott

2009-10-20

151

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

PubMed

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

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

152

A distonic radical-ion for detection of traces of adventitious molecular oxygen (O2) in collision gases used in tandem mass spectrometers.  

PubMed

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 [(•)SO(2)(CH(3)); 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 (O(2)) 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. PMID:25001381

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

2014-09-01

153

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

NASA Technical Reports Server (NTRS)

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

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

1986-01-01

154

Experimental Observation of Post-Collision Interaction and Interference Effects in Resonant Double Photoionization Processes  

NASA Astrophysics Data System (ADS)

The combined effects of post-collision interaction in the final state and interference due to the indistinguishability of the two electrons have been studied in a selected case of resonant double photoionization of neon. In our coincidence experiments, the photo- and Auger-electron pair was measured when the two electrons have nearly equal energy and are ejected at small mutual angle. The obtained energy distributions exhibit a strong interplay of post-collision interaction and interference effects, in agreement with the theoretical prediction of Sheinerman and Schmidt [J. Phys. B 30, 1677 (1997)] made on beryllium.

Rioual, S.; Rouvellou, B.; Avaldi, L.; Battera, G.; Camilloni, R.; Stefani, G.; Turri, G.

2001-02-01

155

Tight-binding molecular-dynamics simulations of C{sub 61} formation and decomposition in C+C{sub 60} collisions  

SciTech Connect

The formation and decomposition of C{sub 61} clusters by collisions of carbon atoms with C{sub 60} clusters have been studied within tight-binding molecular-dynamics simulations. It is found that a carbon projectile can be strongly bound outside a C{sub 60} cage; C{sub 61} may decay into C{sub 60}+C, in which the projectile carbon atom substitutes for a carbon atom in the C{sub 60} target, into C{sub 59}+C{sub 2} and C{sub 58}+C+C{sub 2}. The results are in good agreement with experiments. The C{at}C{sub 60} clusters are found to be formed at high collision energies. The critical energies for formations and decompositions of C{sub 61} clusters with the projectile carbon atoms incident in radial directions are given. {copyright} {ital 1997} {ital The American Physical Society}

Cui, Y. [Shanghai Institute of Nuclear Research, Chinese Academy of Sciences, Shanghai 201800, Peoples Republic of (China)] [Shanghai Institute of Nuclear Research, Chinese Academy of Sciences, Shanghai 201800, Peoples Republic of (China); Liu, L. [Department of Physics, Fudan University, Shanghai 200433, Peoples Republic of (China)] [Department of Physics, Fudan University, Shanghai 200433, Peoples Republic of (China)

1997-08-01

156

From subduction to collision: Control of deep processes on the evolution of convergent plate boundary  

E-print Network

of oceanic subduction, (3) an episode of continental subduction, during which the trench absorbs all: Plate boundary-- general (3040); KEYWORDS: subduction, collision, continental subduction, oceanic of an oceanic basin. However, several orders of evidence indicate that arrival at the trench of a continental

157

Odyssey and oddity: Photo-and collision processes you would not R. Stephen Berry  

E-print Network

-threshold three-photon ionization, (c) measurements of cross sections for superelastic collisions of slow detachment than for Penning ionization. If Penning detach- ment does have large cross sections, then one. The outcome, reviewed here, has been (a) predicted cross sections for Penning detachment of electrons from

Berry, R. Stephen

158

Exclusive processes in electron-ion collisions in the dipole formalism  

SciTech Connect

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.

Cazaroto, E. R.; Navarra, F. S. [Instituto de Fisica, Universidade de Sao Paulo, C.P. 66318, 05314-970 Sao Paulo, SP (Brazil); Carvalho, F. [Departamento de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo, Campus Diadema, Rua Prof. Artur Riedel, 275, Jd. Eldorado, 09972-270 Diadema, SP (Brazil); Goncalves, V. P. [Instituto de Fisica e Matematica, Universidade Federal de Pelotas, Caixa Postal 354, 96010-900 Pelotas, RS (Brazil)

2013-03-25

159

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

SciTech Connect

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.

Chatrchyan, S. [Yerevan Physics Institute (Armenia); et al.,

2011-12-01

160

Measurements of scattering processes in negative ion-atom collisions. Technical progress report, 1 September 1991--31 August 1992  

SciTech Connect

This Technical Progress Report describes the progress made on the research objectives during the past twelve months. This research project is designed to provide measurements of various scattering processes which occur in H{sup {minus}} collisions with atomic (specifically, noble gas and atomic hydrogen) targets at intermediate energies. These processes include: elastic scattering,single- and double-electron detachment, and target excitation/ionization. For the elastic and target inelastic processes where H{sup {minus}} is scattered intact, the experimental technique of Ion Energy-Loss Spectroscopy (IELS) will be employed to identify the final target state(s). In most of the above processes, cross sections are unknown both experimentally and theoretically. The measurements in progress will provide either experimentally-determined cross sections or set upper limits to those cross sections. In either case, these measurements will be stringent tests of our understanding in energetic negative ion-atom collisions. This series of experiments required the construction of a new facility and the initial ion beam was accelerated through the apparatus in April 1991.

Kvale, T.J.

1992-04-01

161

Elastic and inelastic processes in H{sup +}+C{sub 2}H{sub 2} collisions below the 1.5-keV regime  

SciTech Connect

Electron capture and direct elastic scattering in collisions of H{sup +} ions with C{sub 2}H{sub 2} molecules are studied by using a molecular representation within a fully quantum-mechanical approach below 1.5 keV. Calculations are carried out at two different molecular configurations: (i) {ital C}{sub 00{ital v}} symmetry, in which H{sup +} approaches the H atom along a C{emdash}H bond in the acetylene (C{sub 2}H{sub 2}), and (ii) {ital C}{sub 2{ital v}} symmetry, in which H{sup +} approaches perpendicularly toward the midpoint between two carbon atoms. We find that electron capture in the {ital C}{sub 00{ital v}} symmetry configuration takes place preferentially over that in the {ital C}{sub 2{ital v}} symmetry configuration at scattering angles above 15{degree}. The results for the {ital C}{sub 2{ital v}} and {ital C}{sub 00{ital v}} symmetries are comparable in magnitude below 10{degree}, although the {ital C}{sub 2{ital v}} symmetry dominates slightly at still smaller angles. Hence, interferences arising from these molecular configurations in differential cross sections for electron capture and elastic scattering processes are strongly present at angles smaller than a few degrees. Accordingly, the total cross section for the {ital C}{sub 2{ital v}} symmetry is larger by a factor of 3 at 1 keV, and the difference widens as the energy decreases to the eV regime. This is because in {ital C}{sub 2{ital v}} symmetry, H{sup +} can have a larger overlap with the charge distribution of the C{sub 2}H{sub 2} molecule, thus causing a stronger interaction. {copyright} {ital 1996 The American Physical Society.}

Kimura, M. [School of Allied Health Sciences, Yamaguchi University, Ube 755, Yamaguchi (Japan)] [School of Allied Health Sciences, Yamaguchi University, Ube 755, Yamaguchi (Japan); [Institute of Physical and Chemical Research (RIKEN), Wako, Saitama 351-01 (Japan); Li, Y.; Hirsch, G.; Buenker, R.J. [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany)] [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany)

1996-12-01

162

Inelastic processes in collisions of H{sup +} ions with C, N, O, and Si atoms below 1 keV  

SciTech Connect

Electron capture in collisions of C, N, O, and Si atoms with H{sup +} ions is studied theoretically based on a molecular representation within a fully quantum framework by including six molecular channels both for the ground and excited states for the [H{sup +}+C] system, and four channels for the ground-state [H{sup +}+N] and [H{sup +}+O] systems. For the [H{sup +}+Si] system, we employed the molecular representation both in fully quantum and semiclassical frameworks to investigate electron capture at higher energy as well. The {ital ab initio} potential curves and nonadiabatic coupling matrix elements for all these systems are obtained from multireference single- and double-excitation configuration interaction calculations. For all systems, the effect of excited atoms on electron capture is examined in addition to that from the ground state. Because of a small asymptotic energy defect (near-resonant processes) between the initial and closest electron capture channels for almost all systems, electron capture cross sections from the ground-state atoms are large with values of approximately 10{sup {minus}16}{minus}10{sup {minus}15}cm{sup 2} for all systems at above 100 eV. Corresponding rate coefficients are found to be much smaller than those previously reported for the NH{sup +} and OH{sup +}, but, on the contrary, found to be larger by a few orders of magnitude than the previously estimated value for the SiH{sup +} system. Those from excited states are also found to be extremely efficient for all cases. {copyright} {ital 1997} {ital The American Physical Society}

Kimura, M. [School of Allied Health Sciences, Yamaguchi University, Ube, Yamaguchi 755 (Japan)] [School of Allied Health Sciences, Yamaguchi University, Ube, Yamaguchi 755 (Japan); [Department of Physics, Rice University, Houston, Texas 77251 (United States); Gu, J.P.; Hirsch, G.; Buenker, R.J. [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany)] [Theoretische Chemie, Bergische Universitaet-Gesamthochschule Wuppertal, D-42097 Wuppertal (Germany)

1997-04-01

163

Driving Ordering Processes in Molecular-Dynamics Simulations  

NASA Astrophysics Data System (ADS)

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

Dittmar, Harro; Kusalik, Peter G.

2014-05-01

164

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

165

Local vs. non-local energy loss of low energy ions: Influence of charge exchange processes in close collisions  

NASA Astrophysics Data System (ADS)

We investigate the contribution of charge exchange processes in close collisions between projectile and target atoms to the electronic energy loss of low energy ions. We measure the energy loss of slow hydrogen and He ions in ultrathin Al films through which the ions are transmitted before and after backscattering by the atoms of a Ta substrate. The individual contributions to the energy loss are analyzed. The roles of thresholds for reionization and of scattering kinematics as key parameters for the coupling between elastic and inelastic losses are discussed. The implications of the obtained results for different experimental approaches to deduce stopping cross sections are outlined.

Primetzhofer, D.; Goebl, D.; Bauer, P.

2013-12-01

166

Competition between exchange and dissociation processes in He+H 2+ collisions  

NASA Astrophysics Data System (ADS)

The dynamics of (He, H 2+) collisions on an accurate ab initio potential-energy surface (PES) has been investigated using the three-dimensional (3D) quasiclassical trajectory (QCT) approach for ?=0-5 and j= 0 of H 2+ over a wide range of relative translational energies ( Etrans) of the reactants. In addition to the substantial agreement between theory and experiment for the exchange reaction as was reported earlier, we find that the computed collision-induced dissociation (CID) cross section (? D) values and their dependence on ? and Etrans also are in near-quantitative accord with the available experimental results. The dominance of CID over exchange at high energies and the increase in the branching ratio ?=? D/? E with ? are also nearly quantitatively reproduced by our computations, thus lending credence to the accuracy of the PES and the reliability of the trajectory approach.

Kumar, Sanjay; Sathyamurthy, N.

1989-10-01

167

Galaxy Collisions  

E-print Network

Theories of how galaxies, the fundamental constituents of large-scale structure, form and evolve have undergone a dramatic paradigm shift in the last few decades. Earlier views were of rapid, early collapse and formation of basic structures, followed by slow evolution of the stellar populations and steady buildup of the chemical elements. Current theories emphasize hierarchical buildup via recurrent collisions and mergers, separated by long periods of relaxation and secular restructuring. Thus, collisions between galaxies are now seen as a primary process in their evolution. This article begins with a brief history; we then tour parts of the vast array of collisional forms that have been discovered to date. Many examples are provided to illustrate how detailed numerical models and multiwaveband observations have allowed the general chronological sequence of collisional morphologies to be deciphered, and how these forms are produced by the processes of tidal kinematics, hypersonic gas dynamics, collective dynamical friction and violent relaxation. Galaxy collisions may trigger the formation of a large fraction of all the stars ever formed, and play a key role in fueling active galactic nuclei. Current understanding of the processes involved is reviewed. The last decade has seen exciting new discoveries about how collisions are orchestrated by their environment, how collisional processes depend on environment, and how these environments depend on redshift or cosmological time.

Curtis Struck

1999-08-24

168

Long Timestep Molecular Dynamics on the Graphical Processing Unit  

PubMed Central

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

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

2013-01-01

169

Molecular connections between nuclear and ciliary import processes  

PubMed Central

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

2013-01-01

170

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

SciTech Connect

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.

Williams, J.M.

1995-12-31

171

Applying CLIPS to control of molecular beam epitaxy processing  

NASA Technical Reports Server (NTRS)

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.

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

1990-01-01

172

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

SciTech Connect

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.

Yu,P.

2007-01-01

173

Photonic, Electronic and Atomic Collisions  

NASA Astrophysics Data System (ADS)

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

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

2006-11-01

174

Molecular Modeling of Environmentally Important Processes: Reduction Potentials  

ERIC Educational Resources Information Center

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.

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

2004-01-01

175

Atmospheric processes on ice nanoparticles in molecular beams  

PubMed Central

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

Fárník, Michal; Poterya, Viktoriya

2014-01-01

176

Electron capture processes in slow collisions of Ne6+ ions with CO2 and H2O  

NASA Astrophysics Data System (ADS)

Energy-gain spectra and absolute total cross-sections for single-, double-, and triple-electron capture processes in collisions of Ne6+ ions with CO2 and H2O at laboratory impact energies between 450 and 2400 eV, have been studied experimentally by means of a translational energy-gain spectroscopy technique. The energy-gain spectra for single-electron capture show that the dominant reaction channels are due to capture into the n=4 state of Ne5+, in agreement with classical over-the-barrier model calculations. In both cases, contributions due to transfer excitation into the 2s2p (1,3P) 3 l states are also detected. The energy-gain spectra are interpreted qualitatively in terms of the reaction windows, which are calculated using the single-crossing Landau-Zener (LZ) model and the extended version of the classical over-the-barrier (ECOB) model. The energy dependence of cross-sections for electron capture are also measured and found to be slowly increased with increasing collision energy. The data for single-electron capture are also compared with theoretical results based on the multi-channel Landau-Zener (MCLZ) model.

Abu-Haija, O.; Hasan, A.; Kayani, A.; Kamber, E. Y.

2011-01-01

177

Turbulent thermalization process in heavy-ion collisions at ultrarelativistic energies  

NASA Astrophysics Data System (ADS)

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

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

2014-04-01

178

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

179

Substitution Processes in Molecular Evolution. 111. Deleterious Alleles  

Microsoft Academic Search

The substitution processes for various models of deleterious alleles are examined using computer simulations and mathematical analyses. Most of the work focuses on the house-ofcards model, which is a popular model of deleterious allele evolution. The rate of substitution is shown to be a concave function of the strength of selection as measured by a = 2Nu, where N is

John H. Gillespie

1994-01-01

180

Molecular Dynamics Study of the Role of Transition Metal Atoms in Nucleation Process of SWNTs  

E-print Network

Molecular Dynamics Study of the Role of Transition Metal Atoms in Nucleation Process of SWNTs-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan The role of transition metal atoms in the nucleation process atoms and several transition metal atoms (Fe, Co and Ni) based on DFT calculations of small metal

Maruyama, Shigeo

181

Molecular Dynamics of Generation Process of Double-Walled Carbon Nanotubes from Peapods  

E-print Network

Molecular Dynamics of Generation Process of Double-Walled Carbon Nanotubes from Peapods Yasushi Department of Mechanical Engineering, The University of Tokyo, Japan Abstract The generation process-walled carbon nanotube (SWNT), polymerized fullerenes, a peanut-like structure and an almost nanotube

Maruyama, Shigeo

182

Molecular Dynamics of Generation Process of Double-Walled Carbon Nanotubes from Peapods  

E-print Network

* *1 *1 Molecular Dynamics of Generation Process of Double-Walled Carbon Nanotubes from Peapods process of double-walled carbon nanotubes from peapods. Starting from a peapod with five C60 molecules inside a (10,10) SWNT, polymerized fullerenes, peanuts-like structure and almost nanotube structure were

Maruyama, Shigeo

183

Molecular processes in a high temperature shock layer  

NASA Technical Reports Server (NTRS)

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

Guberman, S. L.

1985-01-01

184

Molecular Cell SMADs Stimulate miRNA Processing  

E-print Network

the impact that miRNAs have on cell function, their expression and function has to be tightly regulated regula- tion, miRNAs can also be regulated at various processing steps during their biogenesis. mi.meister@vkl.uni-regensburg.de DOI 10.1016/j.molcel.2010.07.020 MicroRNAs (miRNAs) are potent regulators of gene expression

Bedwell, David M.

185

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

SciTech Connect

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

Professor Francisco Zaera

2007-08-09

186

Rydberg state population due to multicapture processes in Kr[sup q+] (q=17-18) on Kr collisions  

SciTech Connect

Initial population distributions in principal quantum numbers n of excited states were obtained in multicapture processes for Kr[sup q+] (q=17-18) on Kr collisions at low energy ([approx]5 keV/u). Radiative decay curves of Rydberg transitions of the projectivle ions have been measured by shifting the target gas jet along the projectile beam, i.e. perpendicularly to the observation axis. As a result for Kr[sup 18+] projectiles, we have found that an Kr[sup 16+] constant initial population from n=14 to n=19 allows the observed Kr XVII 14--15 radiative decay curve to reproduce relatively well. In addition to this, coincidence time of flight spectroscopy between recoil ion photons and recoil ions have been performed in order to determine the decay curves of recoil ion transitions. We found an initial population distribution centered around n=20 for the 7i--8k transition of Kr VII recoil ion.

Martin, S.; Denis, A.; Delon, A.; Desesquelles, J. (LASIM Universite Lyon 1, Campus de la Doua, F-69622 Villeurbanne Cedex (France)); Ouerdane, Y. (TSI Universite de Saint-Etienne, 23 rue du Dr Paul Michelon, F-4202, Saint-Etienne (France))

1993-06-05

187

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

PubMed Central

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

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

2009-01-01

188

Vibrational origin of the fast relaxation processes in molecular glass formers  

NASA Astrophysics Data System (ADS)

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

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

2002-10-01

189

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

SciTech Connect

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

Kusakabe, Toshio; Gotanda, Kazushi; Kimura, Mineo; Rai, Sachchida N.; Liebermann, Heinz-Peter; Buenker, Robert J. [Department of Science, Kinki University, Higashi-osaka, Osaka 577-8502 (Japan); Graduate School of Sciences, Kyushu University, Fukuoka 812-8581 (Japan); Computer Centre, Bijni Complex, North-Eastern Hill University, Shillong-793003, Meghalaya (India); Fachbereich C-Mathematik und Naturwissenschaften, Bergische Universitaet Wuppertal, D-42119 Wuppertal (Germany)

2007-10-15

190

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

PubMed Central

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

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

2014-01-01

191

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

PubMed

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

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

2014-03-01

192

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

NASA Astrophysics Data System (ADS)

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

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

193

Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations  

E-print Network

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

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

2015-01-30

194

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

PubMed

Due to observed collision induced dissociation (CID) fragmentation inefficiency, developing sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) assays for CID resistant compounds is especially challenging. As an alternative to traditional LC-MS/MS, we present here a methodology that preserves the intact analyte ion for quantification by selectively filtering ions while reducing chemical noise. Utilizing a quadrupole-Orbitrap MS, the target ion is selectively isolated while interfering matrix components undergo MS/MS fragmentation by CID, allowing noise-free detection of the analyte's surviving molecular ion. In this manner, CID affords additional selectivity during high resolution accurate mass analysis by elimination of isobaric interferences, a fundamentally different concept than the traditional approach of monitoring a target analyte's unique fragment following CID. This survivor-selected ion monitoring (survivor-SIM) approach has allowed sensitive and specific detection of disulfide-rich cyclic peptides extracted from plasma. PMID:25371986

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

2014-12-01

195

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

SciTech Connect

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.

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

1982-10-01

196

Molecular photoionization processes of astrophysical and aeronomical interest  

NASA Technical Reports Server (NTRS)

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

Langhoff, P. W.

1985-01-01

197

On the fundamental processes in molecular electrical doping of organic semiconductors  

NASA Astrophysics Data System (ADS)

Integer electron transfer between organic semiconductors (OSCs) and strong donor/acceptor molecules has been regarded as the fundamental mechanism of molecular electrical doping. However, this process entails a number of consequences that are in conflict with well-established concepts of organic-semiconductor physics such as the charge-induced appearance of polaronic states within the fundamental gap of the OSC. Here, from the results of (time-dependent) density-functional theory calculations on prototypical OSC/dopant pairs, we derive a new and different picture for the mechanism of molecular electrical doping, which resolves these inconsistencies. Common doping-related observations are rationalized through intermolecular hybridization of OSC and dopant frontier molecular orbitals. Controlling the degree of this hybridization thus naturally emerges as a strategy for the design of improved molecular dopants in future high-performance organic electronic devices.

Heimel, Georg; Salzmann, Ingo; Koch, Norbert

2012-06-01

198

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

199

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

USGS Publications Warehouse

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

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

2004-01-01

200

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

SciTech Connect

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).

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

2014-02-21

201

Visualization of molecular processes associated with seed dormancy and germination using MapMan  

Microsoft Academic Search

Seed dormancy and germination involve the concerted operation of molecular and biochemical programmes. It has become feasible to study these processes in great detail, using the current methods for transcriptome, proteome and metabolome analysis. Yet, the large amounts of data generated by these methods are often dazzling and demand efficient tools for data visualization. We have used the freely available

R. V. L. Joosen; W. Ligterink; S. J. W. Dekkers; H. W. M. Hilhorst

2011-01-01

202

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

EPA Science Inventory

Many of the inorganic and organic contaminants present in sediments at DOE sites can 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 stru...

203

Chemodiversity and molecular plasticity: recognition processes as explored by property spaces.  

PubMed

In the last few years, a need to account for molecular flexibility in drug-design methodologies has emerged, even if the dynamic behavior of molecular properties is seldom made explicit. For a flexible molecule, it is indeed possible to compute different values for a given conformation-dependent property and the ensemble of such values defines a property space that can be used to describe its molecular variability; a most representative case is the lipophilicity space. In this review, a number of applications of lipophilicity space and other property spaces are presented, showing that this concept can be fruitfully exploited: to investigate the constraints exerted by media of different levels of structural organization, to examine processes of molecular recognition and binding at an atomic level, to derive informative descriptors to be included in quantitative structure--activity relationships and to analyze protein simulations extracting the relevant information. Much molecular information is neglected in the descriptors used by medicinal chemists, while the concept of property space can fill this gap by accounting for the often-disregarded dynamic behavior of both small ligands and biomacromolecules. Property space also introduces some innovative concepts such as molecular sensitivity and plasticity, which appear best suited to explore the ability of a molecule to adapt itself to the environment variously modulating its property and conformational profiles. Globally, such concepts can enhance our understanding of biological phenomena providing fruitful descriptors in drug-design and pharmaceutical sciences. PMID:21707401

Vistoli, Giulio; Pedretti, Alessandro; Testa, Bernard

2011-06-01

204

Rotating hyperdeformed quasi-molecular states formed in capture of light nuclei and in collision of very heavy ions  

E-print Network

. The appar- ently observed superheavy nuclear systems in the U+Ni and U+Ge reactions at high excitation-molecular resonances and very high deforma- tions in light nuclear systems remains an open domain in nuclear physics [1 a rotational liquid drop model including the nuclear proximity energy the l-dependent potential barriers

Boyer, Edmond

205

Removal of higher molecular weight organic compounds by the granular activated carbon adsorption unit process.  

PubMed

The granular activated carbon adsorption unit process in drinking water treatment typically removes purgeable organic compounds for time periods on the order of a few weeks. Experimental evidence indicates that less volatile compounds of generally higher molecular weight than the purgeable fraction, but still detectable by gas chromatography, are efficiently removed for longer periods. Field data substantiate this. Explanatory mechanisms may include stronger adsorption affinities or biodegradation. Non-gas chromatographable, higher molecular weight materials such as humic acids, as measured by Total Organic Carbon (TOC) or trihalomethane formation potential, revert to lower removal efficiencies. Biodegradation may be responsible for a continued long term removal of a fraction of these materials. PMID:3694484

Stevens, A A; Seeger, D R; DeMarco, J; Moore, L

1987-01-01

206

Molecular field calculations of the magnetization process in CeBi  

NASA Astrophysics Data System (ADS)

The complicated magnetization processes of CeBi have been studied in terms of a molecular field model. A long range oscillatory exchange interaction between Ce ions along the [001]-axis is employed in a wave-like-form molecular field. Hm( i) = ? q?( q, ? q)< J q>cos(? qi+? q), and strong ferromagnetic interactions within the (001)-planes are included. The wavenumber dependent molecular field coefficient, ?( q, ? q), is a sensitive function of temperature for 12 K < T ? 25 K (= TN), and it takes a maximum at q=1 and ? q = 0 and this stabilizes the magnetic structure with a sequence of + -. For T ? 12 K, the ?( q, ? q) is almost independent of temperature. Calculations reproduce the five-step magnetization process for T ? 12 K and the four-step process for 15 K < T<22 K. Numerical results on the wave-like molecular fields and sums of simple harmonic functions for the thermal averages of the total angular momenta, < J q>cos(? qi+? q), are also presented. A brief discussion is made on the simplified Hamiltonian.

Iwata, N.; Nishikawa, M.; Shigeoka, T.

1991-09-01

207

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

PubMed Central

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

2013-01-01

208

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

SciTech Connect

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.

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

1998-06-01

209

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

NASA Astrophysics Data System (ADS)

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.

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

2013-04-01

210

Comparison of nonequilibrium processes in p+Ni and p+Au collisions at GeV energies  

SciTech Connect

The energy and angular dependence of double differential cross sections d{sup 2{sigma}}/d{Omega}dE were measured for p,d,t, {sup 3,4,6}He, {sup 6,7,8}Li, {sup 7,9,10}Be, {sup 10,11}B, and C produced in collisions of 1.2, 1.9, and 2.5 GeV protons with a Ni target. The shape of the spectra and angular distributions almost does not change whereas the absolute value of the cross sections increases by a factor {approx}1.7 for all ejectiles in this beam energy range. It was found that energy and angular dependencies of the cross sections cannot be reproduced by microscopic models of intranuclear cascade including coalescence of nucleons coupled to statistical model for evaporation of particles from excited, equilibrated residual nuclei. The inclusion of nonequilibrium processes, described by a phenomenological model of the emission from fast and hot moving sources, resulting from break up of the target nucleus, leads to very good reproduction of data. Cross sections of these processes are quite large, exhausting approximately half of the total production cross sections. Due to good reproduction of energy and angular dependencies of d{sup 2{sigma}}/d{Omega}dE it was possible to determine total production cross sections for all studied ejectiles. Results obtained in this work point to the analogous reaction mechanism for proton induced reactions on Ni target as that observed previously for Au target in the same beam energy range.

Budzanowski, A.; Kistryn, M.; Kliczewski, St.; Kozik, E. [H. Niewodniczanski Institute of Nuclear Physics PAN, Radzikowskiego 152, PL-31342 Krakow (Poland); Fidelus, M.; Jarczyk, L.; Kamys, B.; Kistryn, St.; Kowalczyk, A.; Magiera, A.; Rudy, Z.; Wojciechowski, M. [M. Smoluchowski Institute of Physics, Jagellonian University, Reymonta 4, PL-30059 Krakow (Poland); Filges, D.; Goldenbaum, F.; Machner, H. [Institut fuer Kernphysik, Forschungszentrum Juelich, D-52425 Juelich (Germany); Hodde, H. [Institut fuer Strahlen- und Kernphysik, Bonn University, D-53121 Bonn (Germany); Kulessa, P.; Pysz, K.; Siudak, R. [H. Niewodniczanski Institute of Nuclear Physics PAN, Radzikowskiego 152, PL-31342 Krakow (Poland); Institut fuer Kernphysik, Forschungszentrum Juelich, D-52425 Juelich (Germany); Piskor-Ignatowicz, B. [M. Smoluchowski Institute of Physics, Jagellonian University, Reymonta 4, PL-30059 Krakow (Poland); Institut fuer Kernphysik, Forschungszentrum Juelich, D-52425 Juelich (Germany)

2010-09-15

211

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

E-print Network

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.

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

212

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

SciTech Connect

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.

Sisourat, Nicolas; Dubois, Alain [Laboratoire de Chimie Physique - Matiere et Rayonnement, UMR 7614, UPMC Universite Paris 6, 11 rue Pierre et Marie Curie, F-75231 Paris Cedex 05 (France); LCPMR, UMR 7614, CNRS, F-75005 Paris (France); Pilskog, Ingjald [Laboratoire de Chimie Physique - Matiere et Rayonnement, UMR 7614, UPMC Universite Paris 6, 11 rue Pierre et Marie Curie, F-75231 Paris Cedex 05 (France); Department of Physics and Technology, University of Bergen, N-5007 Bergen (Norway)

2011-11-15

213

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)

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.

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

1972-01-01

214

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

SciTech Connect

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.

Newton, M.D. [Brookhaven National Lab., Upton, NY (United States). Dept. of Chemistry; Cave, R.J. [Harvey Mudd Coll., Claremont, CA (United States). Dept. of Chemistry

1996-02-01

215

Volume 107. number 2 CHEMICAL PHYSICS LETTERS 1.5 !day 1983 REACTION RATE FOR ISOMERIZATION IN A MOLECULAR BEAM  

E-print Network

rare of the concentration can be geatcr than that. BTST, predicted by transition state theory of strong collisions the long-time decay rate of the concentration provides no information about the intra- molecular rate process, but at low collision ntcs it is sensitive to the non-erpodic dynamics. In this short

Berne, Bruce J.

216

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

SciTech Connect

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.

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

2011-12-31

217

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

E-print Network

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

Maruyama, Shigeo

218

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

Microsoft Academic Search

The hippocampus plays a central role in memory consolidation, a process for converting short-term memory into cortically stored, long-lasting memory in the mammalian brain. Here, we review recent data and discuss the ‘synaptic re-entry reinforcement’ (SRR) hypothesis, which can account for the role of the hippocampus in memory consolidation at both the molecular and systems levels. The central idea of

Gayle M. Wittenberg; Joe Z. Tsien

2002-01-01

219

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

SciTech Connect

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.

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

1999-10-31

220

All-dry processible and PAG-attached molecular glasses for improved lithographic performance  

NASA Astrophysics Data System (ADS)

As the semiconductor industry moves forward, resolution limits are being pushed to the sub-30 nm regime. In order to meet these demands, radical new resist design and processes must be explored. We have developed a molecular glass system for all-dry processing conditions. Physical vapor deposition (PVD) has been used for film formation onto silicon wafers. PVD deposits a uniform film of controlled thickness free from impurities that are often introduced by casting solvents used in traditional spin coating methods. Thermal development is used as an alternative to processing in solvents in order to prevent resist swelling and pattern collapse by capillary forces. The deposited molecule is designed to crosslink upon E-beam irradiation without additives, and therefore form a homogeneous, single component film. PAG-attached molecular glasses have been synthesized in order to promote film homogeneity as well. By tethering PAG directly to the molecular glass core, issues such as PAG aggregation can be remedied. Acid migration, which increases blur and LER, can also be hindered.

Krysak, Marie; Kolb, Tristan; Neuber, Christian; Schmidt, Hans-Werner; Ober, Christopher K.

2010-04-01

221

Angular distribution of ? electrons emitted in collisions of 1.0-MeV/u Fq+ (q=4,6,8,9) with molecular hydrogen  

NASA Astrophysics Data System (ADS)

The angular distribution, as well as the energy distribution of ? electrons produced in collisions of 1.0-MeV/u Fq+ (q=4,6,8,9) ions with molecular hydrogen, have been studied for laboratory observation angles (?L) from 0° to 70° with respect to the beam direction. The measurements are in fair agreement with the impulse approximation calculations which use the quantal elastic electron-ion differential scattering cross sections folded with the Compton profile of the target electrons. We observe that the energy of the centroid of the binary-encounter-electron (BEE) peak is projectile charge state, q, and laboratory angle, ?L, dependent. Moreover, at 0°, an enhancement of the ratio of the observed double differential cross section for nonbare projectiles to that for the bare ion projectiles, ?(q+)/?(9+), is observed, contrary to the q2 scaling predicted by a first Born calculation for ionization. This ratio ?(q+)/?(9+) decreases nonotonically with increasing ?L, and becomes smaller than one for ?L>=30°.

Liao, C.; Richard, P.; Grabbe, S. R.; Bhalla, C. P.; Zouros, T. J. M.; Hagmann, S.

1994-08-01

222

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

PubMed

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

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

2014-12-01

223

Influence of the rotational energy of the molecular perturber on the Rb(5P)-H2,D2 fine structure changing collisions  

NASA Astrophysics Data System (ADS)

A crossed beam apparatus has been used to study the Rb(5P1/2 ? 5P3/2) fine-structure-changing (FSC) transitions induced by D2 and H2 molecules. The rotational temperature of the molecular perturber and the relative energy ER of the colliding atom-molecule pair were varied independently. The observed FSC cross section for H2 remains almost unchanged as the rotational temperature is varied. On the contrary, the rotational temperature of D2 results, in some cases, in a rather distinct variation of the FSC cross section; this is most pronounced for ER˜0.08 eV and Trot(D2)<200 K. Reference is made to the theoretical model of Hickman; it accounts well for the general trend in the cross section measured with H2. The results for D2-Rb collisions imply that the various rotational levels of D2 do not seem to contribute equally to the observed FSC cross sections. This work supports the assumption that for D2 molecules in the rotational level J=2 (and probably also J=3), the FSC cross section is larger than for D2 in its other rotational levels.

Cuvellier, J.; Mestdagh, J. M.; Ferray, M.; de Pujo, P.

1983-09-01

224

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs  

NASA Astrophysics Data System (ADS)

We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a many-body potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and metals using EAM potentials are presented for both Intel CPUs and Nvidia GPUs. As an example the crystallization rate of the supercooled Al melt is computed.

Morozov, I. V.; Kazennov, A. M.; Bystryi, R. G.; Norman, G. E.; Pisarev, V. V.; Stegailov, V. V.

2011-09-01

225

Bond formation in C+59 - C60 collisions  

NASA Astrophysics Data System (ADS)

In this work, we show that keV-ions are able to remove single carbon atoms from individual fullerenes in clusters of C60 molecules. This very efficiently leads to the formation of exotic C+119 dumbbell molecules through secondary C+59 + C60 collisions within the fragmenting cluster. Such molecular fusion processes are inherently different from those induced by photons where only products with even numbers of carbon atoms are observed. Thus, ion collisions ignite unique and hitherto overlooked secondary reactions in small aggregates of matter. This relates to the question on how complex molecules may form in e.g. space.

Zettergren, H.; Rousseau, P.; Wang, Y.; Seitz, F.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Rangama, J.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Domaracka, A.; Méry, A.; Maclot, S.; Vizcaino, V.; Schmidt, H. T.; Adoui, L.; Alcamí, M.; Tielens, A. G. G. M.; Martín, F.; Huber, B. A.; Cederquist, H.

2014-04-01

226

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

PubMed

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

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

2014-09-01

227

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

NASA Technical Reports Server (NTRS)

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.

Kang, Jongmin; Pierce, Allan D.

1990-01-01

228

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

NASA Astrophysics Data System (ADS)

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.

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

2004-06-01

229

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

NASA Astrophysics Data System (ADS)

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.

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

2004-11-01

230

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

231

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

NASA Astrophysics Data System (ADS)

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

Odaka, Shigeru; Kurihara, Yoshimasa

2012-04-01

232

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

PubMed

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

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

2009-09-01

233

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

PubMed Central

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

Sakurai, Takeshi; Namiki, Shigehiro; Kanzaki, Ryohei

2014-01-01

234

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

PubMed Central

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

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

2013-01-01

235

Interplay between computer simulation and transport theory in the analysis of ion-beam-induced collision processes in solids  

SciTech Connect

A brief summary is given of recent work on five loosely connected topics within atomic collisions in solids: (i) preferential recoil implantation in multicomponent targets, (ii) pronounced nonlinear behavior of atomic collision sequences induced by keV heavy ions, (iii) linear and nonlinear effects induced by cluster bombardment, (iv) round robin computer simulation of ejection probability in sputtering, and (v) depth of origin and angular spectrum of sputtered atoms. A common theme is the mutual stimulation between a purely numerical approach and theoretical reasoning, the relative weight of the two approaches being different from item to item.

Sigmund, P.

1989-05-01

236

X-ray emission from stellar jets by collision against high-density molecular clouds: an application to HH 248  

E-print Network

We investigate the plausibility of detecting X-ray emission from a stellar jet that impacts against a dense molecular cloud. This scenario may be usual for classical T Tauri stars with jets in dense star-forming complexes. We first model the impact of a jet against a dense cloud by 2D axisymmetric hydrodynamic simulations, exploring different configurations of the ambient environment. Then, we compare our results with XMM-Newton observations of the Herbig-Haro object HH 248, where extended X-ray emission aligned with the optical knots is detected at the edge of the nearby IC 434 cloud. Our simulations show that a jet can produce plasma with temperatures up to 10 MK, consistent with production of X-ray emission, after impacting a dense cloud. We find that jets denser than the ambient medium but less dense than the cloud produce detectable X-ray emission only at the impact onto the cloud. From the exploration of the model parameter space, we constrain the physical conditions (jet density and velocity, cloud den...

Lopez-Santiago, Javier; Orellana, Mariana; Miceli, Marco; Orlando, Salvatore; Ustamujic, Sabina; Albacete-Colombo, Juan Facundo; de Castro, Elisa; de Castro, Ana Ines Gomez

2015-01-01

237

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

PubMed Central

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

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

2005-01-01

238

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

E-print Network

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 {\\mu}s at a temperature of 100 K, which represents a lower bound to the temperature range of Earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that signif...

Pedersen, Andreas; Karssemeijer, Leendertjan; Cuppen, Herma; Jónsson, Hannes

2014-01-01

239

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

PubMed Central

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

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

2011-01-01

240

Chemi-ionization Processes. Alkali-metal Geocosmical Plasmas  

SciTech Connect

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.

Klyucharev, Andrey N.; Bezuglov, Nikolay N.; Matveev, Andrey A. [V.A. Fock Institute of Physics, Saint-Petersburg State University, Ulianovskaya 1, 198504, St. Petersburg, Petrodvorets (Russian Federation); Mihajlov, Anatolij A.; Ignjatovic, Ljubinko M. [Institute of Physics, P.O. Box 57, 11001 Belgrade (Serbia); Dimitrijevic, Milan S. [Astronomical Observatory, Volgina 7, 11160 Belgrade 74 (Serbia)

2007-09-28

241

Plane-wave-factor, molecular-state treatment of electron transfer in collisions of He/sup 2 +/ ions with H atoms  

SciTech Connect

Total cross sections are reported for electron transfer into the individual states 2s, 2p/sub 0/, and 2p/sub 1/, and into all bound states of He/sup +/ in collisions of 1- to 70-keV /sup 4/He/sup 2 +/ ions with H atoms. Following Bates and McCarroll, plane-wave factors have been fully incorporated in a coupled-molecular-state approximation. All velocity-dependent matrix elements have been evaluated as power series in the nuclear velocity. The bases used include up to 10 states 1ssigma, 2ssigma, ..., 3ddelta of the frozen HeH/sup 2 +/ molecule. Convergence of cross sections with respect to the size of the bound-state basis was studied: fewer basis functions are needed than when plane-wave factors are omitted. To test the convergence of the latter results with respect to the size of the bound-state basis, the two potentially important states 5gsigma and 5g..pi.. have been added to the previously used 20-state (1ssigma, 2ssigma, ..., 4fphi) basis, and were found to affect the cross section for transfer into all states by at most 6%. For transfer into all states, results with and without plane-wave factors converge at low energies, agreeing to within 5% at 1 keV. The agreement of the plane-wave-factor results with the experimental data for transfer into all states is excellent at /sup 4/He/sup 2 +/ energies down to 8 keV, but poor at the lower energies, where the coupled-state results are believed to be more fully converged. For capture into the 2s state, the plane-wave-factor results lie above the upper bound of the experimental values by 25% at 20 keV.

Winter, T.G.; Hatton, G.J.

1980-03-01

242

A comparative analysis of the molecular genetic processes in the pathogenesis of psoriasis and Crohn’s disease  

Microsoft Academic Search

A comparative bioinformatics analysis of the molecular genetic processes in the pathogenesis of multifactorial diseases—psoriasis\\u000a and Crohn’s disease—was performed using the results of microarray experiments deposited with the GEO DataSets database. A\\u000a number of genes and molecular genetic processes common to both pathologies were found. The involvement of several transcription\\u000a factors, including AP-1 transcription factors, in the pathogeneses of both

E. S. Piruzian; A. A. Ishkin; T. A. Nikol’skaya; R. M. Abdeev; S. A. Bruskin

2009-01-01

243

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

SciTech Connect

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

Xiao Tiejun; Song Xueyu [Department of Chemistry, Iowa State University, Ames, Iowa 50011 (United States)

2013-03-21

244

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

SciTech Connect

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.

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

245

Extending pathways and processes using molecular interaction networks to analyse cancer genome data  

PubMed Central

Background Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways. Results We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyse their enrichment in pancreatic mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes. Conclusions The proposed method for extending cellular pathways helps to explain the functions of cancer mutated genes by exploiting the synergies of canonical knowledge and large-scale interaction data. PMID:21144022

2010-01-01

246

MOLECULAR SIEVES AS CATALYSTS FOR METHANOL DEHYDRATION IN THE LPDMEtm PROCESS  

SciTech Connect

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.

Andrew W. Wang

2002-04-01

247

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

SciTech Connect

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.

Ahmadov, A. I., E-mail: ahmadov@theor.jinr.ru; Bystritskiy, Yu. M., E-mail: bystr@theor.jinr.ru; Kuraev, E. A., E-mail: kuraev@theor.jinr.ru [Joint Institute for Nuclear Research (Russian Federation)

2011-10-15

248

Half collision resonance phenomena in molecules  

SciTech Connect

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

Maximo Garcia-Sucre (Universidad Central de Venezuela, Caracas (Venezuela)); Raseev, G. (Paris-11 Univ., 91 - Orsay (France)); Ross, S.C. (New Brunswick Univ., Fredericton, NB (Canada)) (eds.)

1991-01-01

249

Thermal- and urea-induced unfolding processes of glutathione S-transferase by molecular dynamics simulation.  

PubMed

The Schistosoma juponicum 26 kDa glutathione S-transferase (sj26GST) consists of the N-terminal domain (N-domain), containing three alpha-helices (named H1-H3) and four anti-parallel beta-strands (S1-S4), and the C-terminal domain (C-domain), comprising five alpha-helices (named H4-H8). In present work, molecular dynamics simulations and fluorescence spectroscopic were used to gain insights into the unfolding process of sj26GST. The molecular dynamics simulations on sj26GST subunit both in water and in 8 M urea were carried out at 300 K, 400 K and 500 K, respectively. Spectroscopic measurements were employed to monitor structural changes. Molecular dynamics simulations of sj26GST subunit induced by urea and temperature showed that the initial unfolding step of sj26GST both in water and urea occurred on N-domain, involving the disruption of helices H2, H3 and strands S3 and S4, whereas H6 was the last region exposed to solution and was the last helix to unfold. Moreover, simulations analyses combining with fluorescence and circular dichroism spectra indicated that N-domain could not fold independent, suggesting that correct folding of N-domain depended on its interactions with C-domain. We further proposed that the folding of GSTs could begin with the hydrophobic collapse of C-domain whose H4, H5, H6 and H7 could move close to each other and form a hydrophobic core, especially H6 wrapped in the hydrophobic center and beginning spontaneous formation of the helix. S3, S4, H3, and H2 could form in the wake of the interaction between C-domain and N-domain. The paper can offer insights into the molecular mechanism of GSTs unfolding. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 247-259, 2015. PMID:25403814

Li, Jiahuang; Chen, Yuan; Yang, Jie; Hua, Zichun

2015-05-01

250

Board-invited review: Sensitivity and responses of functional groups to feed processing methods on a molecular basis.  

PubMed

In complex feed structures, there exist main chemical functional groups which are associated with nutrient utilization and availability and functionality. Each functional group has unique molecular structure therefore produce unique molecular vibration spectral profile. Feed processing has been used to improve nutrient utilization for many years. However, to date, there was little study on processing-induced changes of feed intrinsic structure and functional groups on a molecular basis within intact tissue. This is because limited research technique is available to study inherent structure on a molecular basis. Recently bioanalytical techniques: such as Synchrotron Infrared Microspectroscopy as well as Diffuse Reflectance Infrared Fourier Transform molecular spectroscopy have been developed. These techniques enable to detect molecular structure change within intact tissues. These techniques can prevent destruction or alteration of the intrinsic protein structures during processing for analysis. However, these techniques have not been used in animal feed and nutrition research. The objective of this review was show that with the advanced technique, sensitivity and responses of functional groups to feed processing on a molecular basis could be detected in my research team. These functional groups are highly associated with nutrient utilization in animals. PMID:23216994

Yu, Peiqiang

2012-01-01

251

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

SciTech Connect

The cross sections for capture, ionization, capture from pair production, and free pair production were measured for 0.96-GeV/nucleon U{sup 92+} and 0.405-, 0.96-, and 1.3-GeV/nucleon La{sup 57+} ions incident on Au, Ag, and Cu targets. The cross sections for capture from pair production, free pair production, ionization, and total capture (the sum of capture from pair production, radiative electron capture, and nonradiative capture) are analyzed as a function of collision energy, projectile, and target atomic numbers. We find that, when the collision energy is increased from 0.405 GeV/nucleon to 1.3 GeV/nucleon, the capture from pair production and the free pair production cross sections increase by almost a factor of 6, while the capture cross section decreases by two orders of magnitude. The ionization cross section is found to vary very weakly with the collision energy in the 1-GeV/nucleon energy range. We found a dependence of free pair production cross sections on the target and projectile atomic number to be close to Z{sup 2}, characteristic of an ionizationlike process. We also found a dependence of the capture from pair production cross sections on the target atomic number to be usually steeper than Z{sub t}{sup 2}, and on the projectile atomic number, somewhat steeper than the Z{sub p}{sup 5}, characteristic of a capturelike process. Theory and experiment are in some disagreement for capture from pair production, and free pair production, cross sections, but are in general agreement for the other capture processes and for ionization. {copyright} {ital 1997} {ital The American Physical Society}

Belkacem, A.; Gould, H. [Chemical Sciences Division, Building 71-259, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States)] [Chemical Sciences Division, Building 71-259, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States); Feinberg, B. [Accelerator and Fusion Research Division, Building 80-101, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States)] [Accelerator and Fusion Research Division, Building 80-101, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States); Bossingham, R. [Nuclear Science Division, Building 50A-1148, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States)] [Nuclear Science Division, Building 50A-1148, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720 (United States); Meyerhof, W.E. [Department of Physics, Stanford University, Stanford, California 94305 (United States)] [Department of Physics, Stanford University, Stanford, California 94305 (United States)

1997-10-01

252

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

PubMed Central

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

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

2013-01-01

253

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

PubMed Central

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

Little, Max A.; Jones, Nick S.

2013-01-01

254

Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes  

NASA Astrophysics Data System (ADS)

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.

Prior, Javier; Castro, Enrique; Chin, Alex W.; Almeida, Javier; Huelga, Susana F.; Plenio, Martin B.

2013-12-01

255

Acceleration of early-photon fluorescence molecular tomography with graphics processing units.  

PubMed

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

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

2013-01-01

256

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

PubMed Central

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

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

2013-01-01

257

Wavelet analysis of molecular dynamics: Efficient extraction of time-frequency information in ultrafast optical processes  

SciTech Connect

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.

Prior, Javier; Castro, Enrique [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain)] [Departamento de Física Aplicada, Universidad Politécnica de Cartagena, Cartagena 30202 (Spain); Chin, Alex W. [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom)] [Theory of Condensed Matter Group, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Almeida, Javier; Huelga, Susana F.; Plenio, Martin B. [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)] [Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm (Germany)

2013-12-14

258

Molecular characterization of arylsulfatase G: expression, processing, glycosylation, transport, and activity.  

PubMed

Arylsulfatase G (ARSG) is a recently identified lysosomal sulfatase that was shown to be responsible for the degradation of 3-O-sulfated N-sulfoglucosamine residues of heparan sulfate glycosaminoglycans. Deficiency of ARSG leads to a new type of mucopolysaccharidosis, as described in a mouse model. Here, we provide a detailed molecular characterization of the endogenous murine enzyme. ARSG is expressed and proteolytically processed in a tissue-specific manner. The 63-kDa single-chain precursor protein localizes to pre-lysosomal compartments and tightly associates with organelle membranes, most likely the endoplasmic reticulum. In contrast, proteolytically processed ARSG fragments of 34-, 18-, and 10-kDa were found in lysosomal fractions and lost their membrane association. The processing sites and a disulfide bridge between the 18- and 10-kDa chains could be roughly mapped. Proteases participating in the processing were identified as cathepsins B and L. Proteolytic processing is dispensable for hydrolytic sulfatase activity in vitro. Lysosomal transport of ARSG in the liver is independent of mannose 6-phosphate, sortilin, and Limp2. However, mutation of glycosylation site N-497 abrogates transport of ARSG to lysosomes in human fibrosarcoma cells, due to impaired mannose 6-phosphate modification. PMID:25135642

Kowalewski, Björn; Lübke, Torben; Kollmann, Katrin; Braulke, Thomas; Reinheckel, Thomas; Dierks, Thomas; Damme, Markus

2014-10-01

259

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

PubMed

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

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

2014-01-01

260

Statistical Analysis of the Processes Controlling Choline and Ethanolamine Glycerophospholipid Molecular Species Composition  

PubMed Central

The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation. PMID:22662143

Kiebish, Michael A.; Yang, Kui; Han, Xianlin; Gross, Richard W.; Chuang, Jeffrey

2012-01-01

261

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

PubMed

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

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

2014-01-21

262

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

PubMed

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

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

2014-08-01

263

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

NASA Astrophysics Data System (ADS)

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 ?s at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere.

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

2014-12-01

264

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

PubMed

Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first ?-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design applications. PMID:25240418

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

2015-02-16

265

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

NASA Astrophysics Data System (ADS)

Context. Circumstellar disks are known to contain a significant mass in dust ranging from micron to centimeter size. Meteorites are evidence that individual grains of those sizes were collected and assembled into planetesimals in the young solar system. Aims: We assess the efficiency of dust collection of a swarm of non-drifting planetesimals with radii ranging from 1 to 103 km and beyond. Methods: We calculate the collision probability of dust drifting in the disk due to gas drag by planetesimal accounting for several regimes depending on the size of the planetesimal, dust, and orbital distance: the geometric, Safronov, settling, and three-body regimes. We also include a hydrodynamical regime to account for the fact that small grains tend to be carried by the gas flow around planetesimals. Results: We provide expressions for the collision probability of dust by planetesimals and for the filtering efficiency by a swarm of planetesimals. For standard turbulence conditions (i.e., a turbulence parameter ? = 10-2), filtering is found to be inefficient, meaning that when crossing a minimum-mass solar nebula (MMSN) belt of planetesimals extending between 0.1 AU and 35 AU most dust particles are eventually accreted by the central star rather than colliding with planetesimals. However, if the disk is weakly turbulent (? = 10-4) filtering becomes efficient in two regimes: (i) when planetesimals are all smaller than about 10 km in size, in which case collisions mostly take place in the geometric regime; and (ii) when planetary embryos larger than about 1000 km in size dominate the distribution, have a scale height smaller than one tenth of the gas scale height, and dust is of millimeter size or larger in which case most collisions take place in the settling regime. These two regimes have very different properties: we find that the local filtering efficiency xfilter,MMSN scales with r- 7/4 (where r is the orbital distance) in the geometric regime, but with r- 1/4 to r1/4 in the settling regime. This implies that the filtering of dust by small planetesimals should occur close to the central star and with a short spread in orbital distances. On the other hand, the filtering by embryos in the settling regime is expected to be more gradual and determined by the extent of the disk of embryos. Dust particles much smaller than millimeter size tend only to be captured by the smallest planetesimals because they otherwise move on gas streamlines and their collisions take place in the hydrodynamical regime. Conclusions: Our results hint at an inside-out formation of planetesimals in the infant solar system because small planetesimals in the geometrical limit can filter dust much more efficiently close to the central star. However, even a fully-formed belt of planetesimals such as the MMSN only marginally captures inward-drifting dust and this seems to imply that dust in the protosolar disk has been filtered by planetesimals even smaller than 1 km (not included in this study) or that it has been assembled into planetesimals by other mechanisms (e.g., orderly growth, capture into vortexes). Further refinement of our work concerns, among other things: a quantitative description of the transition region between the hydro and settling regimes; an assessment of the role of disk turbulence for collisions, in particular in the hydro regime; and the coupling of our model to a planetesimal formation model. Appendices are available in electronic form at http://www.aanda.org

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

2014-12-01

266

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

PubMed Central

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

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

2013-01-01

267

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

PubMed

The most recent method of fungal chitosan purification, i.e., two steps of dilute sulfuric acid treatment, pretreatment of cell wall at room temperature for phosphate removal and extraction of chitosan from the phosphate free cell wall at high temperature, significantly reduces the chitosan molecular weight. This study was aimed at improvement of this method. In the pretreatment step, to choose the best conditions, cell wall of Rhizopus oryzae, containing 9% phosphate, 10% glucosamine, and 21% N-acetyl glucosamine, was treated with sulfuric, lactic, acetic, nitric, or hydrochloric acid, at room temperature. Sulfuric acid showed the best performance in phosphate removal (90%) and cell wall recovery (89%). To avoid depolymerisation of chitosan, hot sulfuric acid extraction was replaced with lactic acid treatment at room temperature, and a pure fungal chitosan was obtained (0.12 g/g cell wall). Similar pretreatment and extraction processes were conducted on pure shrimp chitosan and resulted in a chitosan recovery of higher than 87% while the reduction of chitosan viscosity was less than 15%. Therefore, the sulfuric-lactic acid method purified the fungal chitosan without significant molecular weight manipulation. PMID:24211428

Naghdi, Mitra; Zamani, Akram; Karimi, Keikhosro

2014-02-01

268

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

PubMed

In the following study we investigated the utility of molecular genetic testing of the DNA extracted from routinely stained and processed smears from uveal melanoma (UM). Smears from five uveal melanoma cell lines and 12 primary tumors were prepared and stained with Papanicolaou and Romanowsky stains. Genotyping was carried out utilizing 14 microsatellite markers on chromosomes 3, 6 and 8. Mutational screening for alterations in GNAQ and GNA11 genes was carried out by restriction fragment length polymorphism. The results were compared to those obtained through direct sequencing of frozen tumor tissues. High quality DNA was extracted from the stained slides with no difference in the efficiency of DNA extraction between the two staining techniques. The extracted DNA was of adequate quality for genotyping and mutational screening. DNA extracted from approximately 200 tumor cells is sufficient for reproducible testing of allelic imbalances and for studying the common somatic mutations in GNAQ and GNA11 genes. In conclusion, we presented the feasibility of utilizing routinely stained cytology smears from UM for molecular genetic testing. The DNA obtained is of sufficient quality to carry out genotyping for markers on chromosome 3, 6 and 8, as well as screening for somatic mutations in GNAQ and GNA11 genes. PMID:21945171

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

2011-11-01

269

Electron spin resonance studies on reduction process of nitroxyl spin radicals used in molecular imaging  

SciTech Connect

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.

Dhas, M. Kumara; Benial, A. Milton Franklin, E-mail: miltonfranklin@yahoo.com [Department of Physics, NMSSVN College, Nagamalai, Madurai-625019, Tamilnadu (India); Jawahar, A. [Department of Chemistry, NMSSVN College, Nagamalai, Madurai-625019, Tamilnadu (India)

2014-04-24

270

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

NASA Astrophysics Data System (ADS)

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.

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

2008-07-01

271

Mapping Variable Ring Polymer Molecular Dynamics: A Path-Integral Based Method for Nonadiabatic Processes  

E-print Network

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

Ananth, Nandini

2013-01-01

272

On the use of graphics processing units (GPUs) for molecular dynamics simulation of spherical particles  

NASA Astrophysics Data System (ADS)

General-purpose computation on Graphics Processing Units (GPU) on personal computers has recently become an attractive alternative to parallel computing on clusters and supercomputers. We present the GPU-implementation of an accurate molecular dynamics algorithm for a system of spheres. The new hybrid CPU-GPU implementation takes into account all the degrees of freedom, including the quaternion representation of 3D rotations. For additional versatility, the contact interaction between particles is defined using a force law of enhanced generality, which accounts for the elastic and dissipative interactions, and the hard-sphere interaction parameters are translated to the soft-sphere parameter set. We prove that the algorithm complies with the statistical mechanical laws by examining the homogeneous cooling of a granular gas with rotation. The results are in excellent agreement with well established mean-field theories for low-density hard sphere systems. This GPU technique dramatically reduces user waiting time, compared with a traditional CPU implementation.

Hidalgo, R. C.; Kanzaki, T.; Alonso-Marroquin, F.; Luding, S.

2013-06-01

273

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

274

Collision Animations  

NSDL National Science Digital Library

This series of interactive Flash animation explores all aspects of the India-Eurasian continental collision. Animations show the motion of the two continents, the growth of the Himalayas, earthquakes resulting from their collision, and the incredible rate of erosion of the newly formed mountains.

University of Leeds School of Earth and Environment

275

High Energy Collision of Particles in the Vicinity of Extremal Black Holes in Higher Dimensions: Banados-Silk-West Process as Linear Instability of Extremal Black Holes  

E-print Network

We study high energy particle collisions around the higher dimensional black holes. It is shown that the center of mass energy can be arbitrarily large in the vicinity of the event horizon like the Banados, Silk and West (BSW) process in four dimensions if the following two conditions are satisfied: (i) the horizon is extremal and (ii) the parameters of either of the two colliding particles are fine-tuned, which is called a critical particle condition. We also show that a test particle which satisfies the critical particle condition can reach the event horizon from a distant region for a simple case. Finally, we discuss the relation between the BSW process and the linear instability of test fields around the extremal black holes, the latter of which has been recently found by Aretakis.

Naoki Tsukamoto; Masashi Kimura; Tomohiro Harada

2014-01-06

276

High Energy Collision of Particles in the Vicinity of Extremal Black Holes in Higher Dimensions: Banados-Silk-West Process as Linear Instability of Extremal Black Holes  

E-print Network

We study high energy particle collisions around the higher dimensional black holes. It is shown that the center of mass energy can be arbitrarily large in the vicinity of the event horizon like the Banados, Silk and West (BSW) process in four dimensions if the following two conditions are satisfied: (i) the horizon is extremal and (ii) the parameters of either of the two colliding particles are fine-tuned, which is called a critical particle condition. We also show that a test particle which satisfies the critical particle condition can reach the event horizon from a distant region for a simple case. Finally, we discuss the relation between the BSW process and the linear instability of test fields around the extremal black holes, the latter of which has been recently found by Aretakis.

Tsukamoto, Naoki; Harada, Tomohiro

2014-01-01

277

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

E-print Network

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

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

2012-01-01

278

ABILITY TO PREDICT MOLECULAR ROTATIONVIBRATION LINE SHAPES  

E-print Network

for molecular collision dynamics on an accurate intermolecular potential energy surface. For some simple of current capabilities. INTRODUCTION The theory of line shapes in molecular vibration­rotation spectra has semiclassical (classical path) collision dynamics, solved the collision dynamics using second­order perturbation

279

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

PubMed Central

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

de Storme, Nico; Geelen, Danny

2014-01-01

280

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

SciTech Connect

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.

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

2011-01-01

281

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

E-print Network

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 th...

Erdmann, Thorsten; Schwarz, Ulrich S

2013-01-01

282

Event characterization in (very) asymmetric collisions  

NASA Astrophysics Data System (ADS)

Event-by-event reconstruction of the collision geometry using some incarnation of the Glauber-model is a widely accepted method in studying heavy ion collisions. While there is no known problem with the procedure when applied to the collision of two large ions, we will argue that in very asymmetric collisions, like p(d)+A with at least one hard scattering process occuring the event geometry deduced with the simple Glauber-model may be biased.

David, Gabor

2015-03-01

283

Event characterization in (very) asymmetric collisions  

E-print Network

Event-by-event reconstruction of the collision geometry using some incarnation of the Glauber-model is a widely accepted method in studying heavy ion collisions. While there is no known problem with the procedure when applied to the collision of two large ions, we will argue that in very asymmetric collisions, like $p(d)$+A with at least one hard scattering process occuring the event geometry deduced with the simple Glauber-model may be biased.

G. David

2014-09-24

284

Tuning ultracold collisions of excited rotational dipolar molecules  

NASA Astrophysics Data System (ADS)

We investigate the ultracold collisions of rotationally excited dipolar molecules in free-space, taking the hetero-nuclear bi-alkali molecule of KRb as an example. We show that we can sharply tune the elastic, inelastic and reactive rate coefficients of lossy molecular collisions when a second rotationally excited colliding channel crosses the threshold of the initial colliding channel, with the help of an applied electric field, as found by Avdeenkov et al for non-lossy molecules (Phys. Rev. A 73 022707). We can increase or decrease the inelastic and reactive processes whether the second channel is above or below the initial channel. This is seen for both bosonic and fermionic molecules. Additionally, we include the electric quadrupole and octopole moment to the dipole moment in the expression of the long-range multipole–multipole interaction. We found that for processes mediated by the incident channel, such as elastic and reactive collisions, the inclusion of quadrupole and octopole moments is not important at ultralow energies. The moments are important for processes mediated by state-to-state transitions like inelastic collisions.

Wang, Gaoren; Quéméner, Goulven

2015-03-01

285

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

SciTech Connect

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.

Levine, Benjamin G., E-mail: ben.levine@temple.ed [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA (United States); Stone, John E., E-mail: johns@ks.uiuc.ed [Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL (United States); Kohlmeyer, Axel, E-mail: akohlmey@temple.ed [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA (United States)

2011-05-01

286

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

PubMed Central

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

Stone, John E.; Kohlmeyer, Axel

2011-01-01

287

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

PubMed

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

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

2011-05-01

288

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

NASA Astrophysics Data System (ADS)

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.

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

2011-05-01

289

Supersonic cloud collision. I.  

NASA Astrophysics Data System (ADS)

Context: It has long been suggested that shocks might play an important role in altering the form of the interstellar medium (ISM). Shocks enhance gas density and sufficiently dense regions may become self gravitating. Potential star-forming clouds within larger molecular clouds, move randomly at supersonic speeds and a collision between them, is highly inelastic. Aims: Depending on the precollision velocity, colliding molecular clouds produce a slab that is either shock-compressed or pressure-confined. In a sequel of two Papers (I and II), we simulate molecular cloud collision and investigate the dynamical evolution of such slabs. Shocked slabs appear susceptible to hydrodynamic instabilities and, in the present Paper (I), we study the effect of strong shear between slab layers on the dynamic evolution of a shock compressed gas slab. Head-on and off-centre cloud collisions have been examined in this work. Self gravity is included in all our simulations. Methods: Simulations presented were performed using the smoothed particle hydrodynamics (SPH) numerical scheme. Individual, precollision clouds are modelled as pressure-confined Bonnor-Ebert spheres. However, for simplicity the thermodynamic details of the problem are simplified and the gas temperature is evolved simply by a barytropic equation of state. Obviously, the gas suffers to some extent from thermal inertial effects. However, we note that the dynamical timescale is much smaller than the local sound crossing time so that any such effects should have minimum influence. Results: Strong shocks are highly radiative. Thus a highly supersonic cloud collision produces a cold, roughly isothermal shock compressed gas slab. We find that the shocked slab is susceptible to dynamical instabilities like the gravitational instability, Kelvin-Helmholtz (KH) instability and the non linear thin shell instability (NTSI). Rapid growth of instabilities within the slab produces structure in it. The NTSI competes with the gravitational instability and the fate of the shocked slab apparently depends on the relative dominance of either of the two instabilities. Dominance of the NTSI causes turbulent mixing between slab layers and dissipates internal energy. Eventually the slab collapses to form a thin elongated body, aligned with the collision axis, and star formation may commence in it. Our hydrodynamical models discussed here suggest that, high-velocity cloud collisions may be a viable mechanism for the formation of observed filamentary structure in the ISM.

Anathpindika, S.

2009-09-01

290

Cosmic Collisions  

NSDL National Science Digital Library

This Web site, created to complement the Museum's Cosmic Collisions space show, takes a look at the hypersonic impacts that drive the dynamic and continuing evolution of the universe. The site includes a one-minute QuickTime preview of the space show, a collection of 26 scientific simulations and visualizations, a look at the fusion of cutting-edge astrophysics research and state-of-the-art science visualization expertise that went into creating Cosmic Collisions and other information.

291

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

PubMed

Dopamine, as a universal material for surface treatment, can effectively improve the surface performance of aramid fibers. However, directly processing the surface of aramid fibers using dopamine currently incurs a high cost. To seek dopamine substitutes, one must first explore the adhesion mechanism responsible for binding the dopamine to the surface of the fiber. In this study, we construct an all-atomic molecular dynamics model of an aramid fiber before and after surface modification using dopamine. A force field based on condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) is used. Using it, we analyze the surface adhesion mechanism of polydopamines aggregated by 21 kinds of molecular structures typically found on the surface of aramid fibers. The results show that a clear and smooth interface is formed between the polydopamine nanofilm layer and the surface of the aramid fiber. The high atomic density of the polydopamine in the small interface region is found to be conducive to noncovalent bonds of polydopamines with the surface of the aramid fiber. In addition, we investigate the works of adhesion of the 21 molecular structures typically found on the surface of aramid fibers. The results suggest that the work of adhesion of 5,6-indolequinone is the highest, followed by annular eumelanin molecules with annular planar structure. Straight-chain shaped dimers proved to be the molecules with the highest adhesion ability of the dihydroxyindole chain oligomers. Therefore, there is reason to suppose that more molecular structures (as above) can be formed by processing the surface of aramid fibers using dopamine by controlling the processing conditions. These molecular structures help improve the adhesion ability of the dopamine on the surface of the aramid fiber. Additionally, if these polydopamine molecules with high adhesion ability can be synthesized on a large scale, then new surface-processing materials are possible. PMID:25275919

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

2014-10-22

292

ROLE OF COMPUTATIONAL APPROACHES TO ENZYME STRUCTURE AND FUNCTION IN THE STUDY OF MOLECULAR PROCESSES IN BIOLOGY: AN INTRODUCTION  

EPA Science Inventory

The paper describes the current role of computational approaches in the study of enzyme structure and function. The computational simulation of the molecular processes in enzymes with known structures that are amenable to direct experimentation has enormous value for the further ...

293

Adaptive binary splitting for efficient RFID tag anti-collision  

Microsoft Academic Search

Tag collision arbitration for passive RFID tags is a significant issue for fast tag identification. This letter presents a novel tag anti-collision scheme called adaptive binary splitting (ABS). For reducing collisions, ABS assigns distinct timeslots to tags by using information obtained from the last identification process. Our performance evaluation shows that ABS outperforms other tree based tag anti-collision protocols.

Jihoon Myung; Wonjun Lee; J. Srivastava

2006-01-01

294

Uncovering Molecular Relaxation Processes with Nonlinear Spectroscopies in the Deep UV  

NASA Astrophysics Data System (ADS)

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.

West, Brantley Andrew

295

Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations  

NASA Astrophysics Data System (ADS)

Thermal conductivity is a very important property of a material both for testing theoretical models and for designing better practical devices such as more efficient thermoelectrics, and accurate and efficient calculations of thermal conductivity are very desirable. In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme, where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme, where a whole block is used for one particle and each thread in the block calculates one or several pair forces between the particle associated with the given block and its neighbor particle(s) associated with the given thread. For both schemes, two different classical potentials, namely, the Lennard-Jones potential and the rigid-ion potential are implemented. While the thread-scheme performs a little better for relatively large systems, the block-scheme performs much better for relatively small systems. The relative performance of the block-scheme over the thread-scheme also increases with the increasing cutoff radius. We validate the implementation by calculating lattice thermal conductivities of solid argon and lead telluride. The efficiency of our code makes it very promising to study thermal conductivity properties of more complicated materials, especially, materials with interesting nanostructures.

Fan, Zheyong; Siro, Topi; Harju, Ari

2013-05-01

296

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

PubMed

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

Cortés-Francisco, Nuria; Caixach, Josep

2013-09-01

297

Novel in situ activity assays for the quantitative molecular analysis of neurodegenerative processes in the retina.  

PubMed

The mechanisms of neuronal cell death are still only poorly understood, which has hindered the advancement of therapies for many currently untreatable neurodegenerative diseases. This calls for the development of new methods which reveal critical molecular mechanisms of the celldeath machinery with both high sensitivity and cellular resolution. Using animal models for hereditary neurodegeneration in the retina, we have developed or adapted different biochemical assays to determine the enzymatic activities of calpain, poly-ADP-ribose-polymerase (PARP), and histone deacetylase (HDAC) directly and in situ. Additionally, the enzymatic activity of cGMP-dependent protein kinase (PKG) was assessed indirectly using in situ immunohistological techniques to detect PKG-activity-dependent products. Combining these assays with in situ cell death markers revealed close temporospatial correlations, suggesting causal connections between the PKG, HDAC, PARP and calpain activities and neuronal cell death. Using different pharmacological and genetic manipulations, causality could indeed be demonstrated. Surprisingly, the often dramatic rises in metabolic activities didnot match by corresponding increases in expression, highlighting the importance of analyses of protein activities at the cellular level. The above mentioned studies identified a number of metabolic processes previously unknownto be involved in inherited retinal degeneration. Comparing different animal retinal degeneration models uncovered striking similarities in enzymatic activities, suggesting a generality of the destructive pathways. Taken together, these findings provided a number of novel targets for neuroprotection and as such opened up new perspectives for the therapy of hereditary neurodegeneration in the retina and possibly other parts of the central nervous system. PMID:24934347

Ekström, P A R; Ueffing, M; Zrenner, E; Paquet-Durand, F

2014-01-01

298

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

E-print Network

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.

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

2013-10-17

299

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

NASA Astrophysics Data System (ADS)

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

Tian, Ziqi; Wen, Jin; Ma, Jing

2013-07-01

300

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

SciTech Connect

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.

Erdmann, Thorsten; Albert, Philipp J.; Schwarz, Ulrich S. [BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany and Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg (Germany)

2013-11-07

301

Energetics of particle collisions near dirty rotating extremal black holes: Banados-Silk-West effect versus Penrose process  

E-print Network

If two particles collide near the horizon of a rotating extremal black hole, under certain conditions the energy E_{c.m.} in the center-of-mass frame can grow without limit (the so-called Banados-Silk-West effect). We consider collisions that produce two other particles. We show that for a generic dirty (surrounded by matter) black hole, there exist upper bounds on the energy and mass of product particles which can be detected at infinity. As a result, the positive energy gain is possible but is quite modest. It mainly depends on two numbers in which near-horizon behavior of the metric is encoded. The obtained results suggest astrophysical limits on the possibility of observation of the products of the collisional Banados-Silk-West effect. These results are consistent with recent calculations for the Kerr metric, extending them to generic dirty black holes. It is shown that for dirty black holes there are types of scenarios of energy extraction impossible in the Kerr case.

O. B. Zaslavskii

2012-10-07

302

Repeatability and reproducibility of thermal field-flow fractionation in molecular weight determination of processed natural rubber.  

PubMed

The purpose of this study is (1) to determine the repeatability and reproducibility of thermal field-flow fractionation (ThFFF) in measuring the molecular weight of compounded natural rubber, and (2) to examine the correlation between the molecular weights obtained from ThFFF and the rheological data. 8 batches of compounded natural rubber were obtained from a thermo-mechanical mastication process, and were analyzed by ThFFF in a designed testing sequence. ThFFF analysis showed the compounded natural rubbers range in weight-average molecular weight (M(w)) from 143,000 to 360,000. By taking into account both the short term variability (repeatability) as well as the long term variability (reproducibility) of the instrument, ThFFF was shown to be able to distinguish between samples differing by as little as 21,000 in M(w) and 15,600 in number-average molecular weight, M(n) (based on cis-polyisoprene calibration); and thus is a useful tool for the molecular weight analysis of natural rubber-related materials. It was also found that the rheological data (G' and tan delta) measured on both the virgin and the compounded natural rubber correlated well with the molecular weights obtained from ThFFF when normalized. PMID:16496053

Kim, Won-Suk; Eum, Chul Hun; Molnár, Attila; Yu, Jong-Sung; Lee, Seungho

2006-03-01

303

Molecular nanotechnology  

Microsoft Academic Search

Molecular nanotechnology is an interdisciplinary field combining the sciences of molecular chemistry and physics with the engineering principles of mechanical design, structural analysis, computer science, electrical engineering, and systems engineering. Molecular manufacturing is a method conceived for the processing and rearrangement of atoms to fabricate custom products. It relies on the use of a large number of molecular robotic subsystems

D. R. Forrest

2001-01-01

304

Antihydrogen - Hydrogen Collisions  

NASA Astrophysics Data System (ADS)

Recently, both the ATRAP (G. Gabrielse et al., PRL 89 213404, (2002)) and ATHENA (M. Amoretti et al., Nature 419 (2002)) experiments at the CERN anti-proton decelerator have successfully created and detected low temperature antihydrogen atoms in the laboratory. Present efforts are directed toward the goal of trapping and cooling the antihydrogen into the ultra-cold regime in order to enable tests, of unprecedented accuracy, for some of the most fundamental symmetries of matter and anti-matter. Several methods for cooling have been proposed. Here we discuss the feasibility of cooling antihydrogen via its contact with ultra-cold matter, in particular hydrogen. The cooling efficiency is determined by the collision properties of this system. Annihilation of the leptons, the proton and antiproton, as well as re-arrangements into protonium and positronium during a collision conspire to limit the utility of sympathetic cooling. In this talk we will discuss the various collision processes and present calculated collision data in order to assess the viability of sympathetic cooling of antimatter in contact with matter. We will also discuss properties of the novel, unstable, exotic molecule (B. Zygelman et al., PRA 69, 042715 (2004)) that has been predicted as a possible by-product in a collision of antihydrogen with an hydrogen atom. Collaborators in this study include, A. Dalgarno, P. Froelich, S. Jonsell and A. Saenz. Partial support was provided by an NSF grant to the Harvard-MIT CUA where the author was a Visiting Scientist.

Zygelman, Bernard

2005-05-01

305

Theoretical atomic collision physics  

SciTech Connect

The theoretical atomic physics at Rice University focuses on obtaining a better understanding of the mechanisms that control inelastic collisions between excited atoms and atoms, molecules and ions. Particular attention is given to systems and processes that are of potential importance to advanced energy technologies. In the current year, significant progress has been made in quantitative studies of: quenching of low-Rydberg Na atoms in thermal energy collisions with He, Ne and Ar atoms; selective excitation resulting from charge transfer in collisions of highly stripped ions of He, Li, C, and with Li, Na and He atoms and H{sub 2} molecules at keV energies; differential elastic and single, and double electron transfer in He{sup ++} collisions with He at keV energies; inelastic electron-transfer in ultra-low-energy-energy (T=8 to 80K) collisions between {sup 3}He{sup +} and {sup 4}He and {sup 4}He{sup +} and {sup 3}He; a formalism for ionization by electron impact of ions in dense, high temperature plasmas.

Lane, N.F. (Rice Univ., Houston, TX (USA) Rice Univ., Houston, TX (USA). Quantum Inst.)

1990-01-01

306

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

PubMed

In seasonally ice-covered seas and along the margins of perennial ice pack, i.e., in regions with medium ice concentrations, the ice cover typically consists of separate floes interacting with each other by inelastic collisions. In this paper, hitherto unexplored analogies between this type of ice cover and two-dimensional granular gases are used to formulate a model of ice dynamics at the floe level. The model consists of (i) momentum equations for floe motion between collisions, formulated in the form of a Stokes-flow problem, with floe-size-dependent time constant and equilibrium velocity, and (ii) a hard-disk collision model. The numerical algorithm developed is suitable for simulating particle-laden flow of N disk-shaped floes with arbitrary size distributions. The model is applied to study clustering phenomena in sea ice with power-law floe-size distribution. In particular, the influence of the average ice concentration A on the formation and characteristics of clusters is analyzed in detail. The results show the existence of two regimes, at low and high ice concentrations, differing in terms of the exponents of the cluster-size distribution and of the size of the largest cluster. PMID:22181470

Herman, Agnieszka

2011-11-01

307

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...

308

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

ERIC Educational Resources Information Center

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…

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

2010-01-01

309

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

PubMed Central

Background Campylobacter is a major cause of human disease worldwide and poultry are identified as a significant source of this pathogen. Most disease in humans is associated with the consumption of contaminated poultry or cross-contamination with other foods. The primary drugs of choice for treatment of human campylobacteriosis include erythromycin and ciprofloxacin. In this study, we investigated the prevalence of resistance to erythromycin and ciprofloxacin in Campylobacter isolates recovered from turkey carcasses at two processing plants in the Upper Midwest US. Further analysis of a subset of isolates was carried out to assess resistance and genotype profiles. Results Campylobacter isolates from plant A (n = 439; including 196 C. coli and 217 C. jejuni) and plant B (n = 362, including 281 C. coli and 62 C. jejuni) were tested for susceptibility to ciprofloxacin and erythromycin using agar dilution. C. coli were more frequently resistant than C. jejuni in both plants, including resistance to ciprofloxacin (28% of C. jejuni and 63% of C. coli, plant B; and 11% of C. coli, plant A). Erythromycin resistance was low among C. jejuni (0% plant A and 0.3% plant B) compared to C. coli (41%, plant A and 17%, plant B). One hundred resistant and susceptible isolates were selected for additional antimicrobial susceptibility testing, restriction fragment length polymorphism analysis of the flaA gene (fla typing), and pulsed-field gel electrophoresis (PFGE). Fla-PFGE types obtained (n = 37) were associated with a specific plant with the exception of one type that was isolated from both plants. C. coli isolates (n = 65) were grouped into 20 types, while C. jejuni isolates (n = 35) were grouped into 17 types. Most isolates with identical fla-PFGE patterns shared identical or very similar antimicrobial resistance profiles. PFGE alone and composite analysis using fla-PFGE with resistance profiles separated C. jejuni and C. coli into distinct groups. Conclusion Ciprofloxacin and erythromycin resistance in Campylobacter recovered from processed turkey occurred more frequently among C. coli than C. jejuni. Fla-PFGE types were associated with a particular species, antimicrobial resistance profiles, and a specific plant. Molecular subtyping in this study provided more information about the relationships among antimicrobial-resistant Campylobacter at the processing level. PMID:19772592

2009-01-01

310

Structure and evolution of the Magnitogorsk forearc basin: Identifying upper crustal processes during arc-continent collision in the southern Urals  

NASA Astrophysics Data System (ADS)

The southern Urals of Russia contain a well-preserved example of a Paleozoic arc-continent collision in which the intraoceanic Magnitogorsk volcanic arc and its forearc basin sediments accreted to the East European Craton during the Devonian. The Magnitogorsk arc records the evolution from incipient intraoceanic subduction to a mature arc, and by comparing its surface geological features with those in active arc-continent collision settings it is possible to identify upper crustal processes that were active in the southern Urals. The arc edifice can be divided into western and eastern volcanic fronts that were active during different stages of arc evolution and for which two distinct phases of forearc basin development can be recognized. The late Lower to Middle Devonian Aktau Formation represents a remnant of the intraoceanic to collisional forearc basin to the Irendyk volcanic front, whereas the Middle Devonian to Lower Carboniferous Ulutau, Koltubanian, and Zilair Formations were deposited in a suture forearc basin to the east Magnitogorsk volcanic front. It was not until the Late Devonian that these two basins were joined. Structural mapping, combined with reflection seismic profiling, shows these basins to be affected by open, nonlinear, volcanic basement-cored synsedimentary folds. The Karamalytash anticline appears to have the geometry of a growth fold that formed during deposition of sediments in the suture forearc basin. The forearc region is affected by minor thrusting that involves the volcanic basement, although it is not clear if these thrusts reactivate preexisting trench-parallel faults. Synsedimentary deformation, slumping, and olistostrome development were common throughout the suture forearc basin history but were especially widespread during the Late Devonian, when the full thickness of the continental crust is interpreted as having arrived at the subduction zone.

Brown, D.; Alvarez-Marrón, J.; PéRez-Estaún, A.; Puchkov, V.; Gorozhanina, Y.; Ayarza, P.

2001-06-01

311

Model approach for low-energy inelastic atomic collisions and application to Al+H and Al++H-  

NASA Astrophysics Data System (ADS)

A model approach is derived for estimates of cross sections and rate coefficients in low-energy inelastic collisions of hydrogen atoms and negative ions with other atoms and positive ions, which are of astrophysical interests. The approach is based on the asymptotic method for electronic molecular structure determination and on the branching probability current method for a nonadiabatic nuclear dynamical treatment. The derived approach is applied to low-energy Al + H and Al+ + H- inelastic collisions. It is shown that the processes with the largest values of cross sections and rates are the excitation and de-excitation ones between the Al(3d) and Al(4p) states in collisions with H, as well as the ion-pair formation and the mutual neutralization processes between these states and the ionic state; the second largest cross sections correspond to the similar processes involving the Al(4s) state. The mechanisms of the processes are discussed in detail.

Belyaev, Andrey K.

2013-11-01

312

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

PubMed

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

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

2012-01-01

313

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

NASA Astrophysics Data System (ADS)

It is the purpose of this study to demonstrate that the molecular scale reaction mechanisms describing calcite precipitation and calcium isotope fractionations under highly controlled laboratory conditions also reproduce field scale measurements of ?44Ca in groundwater systems. We present data collected from an aquifer during active carbonate mineral precipitation and develop a reactive transport model capturing the observed chemical and isotopic variations. Carbonate mineral precipitation and associated fluid ?44Ca data were measured in multiple clogged well bores during organic carbon amended biogenic reduction of a uranium contaminated aquifer in western Colorado, USA. Secondary mineral formation induced by carbonate alkalinity generated during the biostimulation process lead to substantial permeability reduction in multiple electron-donor injection wells at the field site. These conditions resulted in removal of aqueous calcium from a background concentration of 6 mM to <1 mM while ?44Ca enrichment ranged from 1‰ to greater than 2.5‰. The relationship between aqueous calcium removal and isotopic enrichment did not conform to Rayleigh model behavior. Explicit treatment of the individual isotopes of calcium within the CrunchFlow reactive transport code demonstrates that the system did not achieve isotopic reequilibration over the time scale of sample collection. Measured fluid ?44Ca values are accurately reproduced by a linear rate law when the Ca2+:CO32- activity ratio remains substantially greater than unity. Variation in the measured ?44Ca between wells is shown to originate from a difference in carbonate alkalinity generated in each well bore. The influence of fluid Ca2+:CO32- ratio on the precipitation rate and ?44Ca is modeled by coupling the CrunchFlow reactive transport code to an ion by ion growth model. This study presents the first coupled ion-by-ion and reactive transport model for isotopic enrichment and demonstrates that reproducing field-scale ?44Ca enrichment in groundwater where Ca2+:CO32- approaches unity is only accomplished by utilizing such a coupled modeling approach.

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

2013-10-01

314

Advective collisions  

E-print Network

Small particles advected in a fluid can collide (and therefore aggregate) due to the stretching or shearing of fluid elements. This effect is usually discussed in terms of a theory due to Saffman and Turner [J. Fluid Mech., 1, 16-30, (1956)]. We show that in complex or random flows the Saffman-Turner theory for the collision rate describes only an initial transient (which we evaluate exactly). We obtain precise expressions for the steady-state collision rate for flows with small Kubo number, including the influence of fractal clustering on the collision rate for compressible flows. For incompressible turbulent flows, where the Kubo number is of order unity, the Saffman-Turner theory is an upper bound.

B. Andersson; K. Gustavsson; B. Mehlig; M. Wilkinson

2007-02-13

315

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

PubMed Central

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

Destro, M T; Leitão, M F; Farber, J M

1996-01-01

316

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

PubMed

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

Destro, M T; Leitão, M F; Farber, J M

1996-02-01

317

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

SciTech Connect

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.

Tang Haibin; Cheng Jiao; Liu Chang [School of Astronautics, Beijing University of Aeronautics and Astronautics, Beijing 100191 (China); York, Thomas M. [Ohio State University, Columbus, Ohio 43235 (United States)

2012-07-15

318

High energy collision of particles in the vicinity of extremal black holes in higher dimensions: Bañados-Silk-West process as linear instability of extremal black holes  

NASA Astrophysics Data System (ADS)

We study high energy particle collisions around higher dimensional black holes. It is shown that the center of mass energy can be arbitrarily large in the vicinity of the event horizon like the Bañados, Silk and West (BSW) process in four dimensions if the following two conditions are satisfied: (i) the horizon is extremal and (ii) the parameters of either of the two colliding particles are fine-tuned, which is called a critical particle condition. We also show that a test particle which satisfies the critical particle condition can reach the event horizon from a distant region for a simple case. Finally, we discuss the relation between the BSW process and the linear instability of test fields around extremal black holes, the latter of which has been recently found by Aretakis [Commun. Math. Phys. 307, 17 (2011); Ann. Inst. Henri Poincaré 12, 1491 (2011); J. Funct. Anal. 263, 2770 (2012); arXiv:1206.6598; Classical Quantum Gravity 30, 095010 (2013); Phys. Rev. D 87, 084052 (2013)].

Tsukamoto, Naoki; Kimura, Masashi; Harada, Tomohiro

2014-01-01

319

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

SciTech Connect

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

Alekseev, V. A. [Department of Physics, St. Petersburg State University, Peterhof 198504 (Russian Federation); Grosser, J.; Hoffmann, O. [Institut fuer Gravitationsphysik, Leibniz Universitaet Hannover, 30167 Hannover (Germany); Rebentrost, F. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany)

2008-11-28

320

Geochemical Interpretation of Collision Volcanism  

NASA Astrophysics Data System (ADS)

Collision volcanism can be defined as volcanism that takes place during an orogeny from the moment that continental subduction starts to the end of orogenic collapse. Its importance in the Geological Record is greatly underestimated as collision volcanics are easily misinterpreted as being of volcanic arc, extensional or mantle plume origin. There are many types of collision volcanic province: continent-island arc collision (e.g. Banda arc); continent-active margin collision (e.g. Tibet, Turkey-Iran); continent-rear-arc collision (e.g. Bolivia); continent-continent collision (e.g. Tuscany); and island arc-island arc collision (e.g. Taiwan). Superimposed on this variability is the fact that every orogeny is different in detail. Nonetheless, there is a general theme of cyclicity on different time scales. This starts with syn-collision volcanism resulting from the subduction of an ocean-continent transition and continental lithosphere, and continues through post-collision volcanism. The latter can be subdivided into orogenic volcanism, which is related to thickened crust, and post-orogenic, which is related to orogenic collapse. Typically, but not always, collision volcanism is preceded by normal arc volcanism and followed by normal intraplate volcanism. Identification and interpretation of collision volcanism in the Geologic Record is greatly facilitated if a dated stratigraphic sequence is present so that the petrogenic evolution can be traced. In any case, the basis of fingerprinting collision terranes is to use geochemical proxies for mantle and subduction fluxes, slab temperatures, and depths and degrees of melting. For example, syn-collision volcanism is characterized by a high subduction flux relative to mantle flux because of the high input flux of fusible sediment and crust coupled with limited mantle flow, and because of high slab temperatures resulting from the decrease in subduction rate. The resulting geochemical patterns are similar regardless of collision type with extreme LILE and significant HFSE enrichment relative to MORB and with large negative Nb-Ta and Ti anomalies. Post-collision volcanism is usually ascribed to combinations of slab detachment, delamination, and slab roll back (orogenic) and extension (post-orogenic). The magma source is typically conductively-heated, sub-continental mantle lithosphere with composition and depth of melting depending on the nature and evolution of the collision zone in question. Geochemical patterns may be similar to those of syn-collision basalts or of intraplate, continental basalts - or transitional between these. This variability in space and time, though problematic for geochemical fingerprinting, can give clues to the polarity and development of the collision zone, for example by highlighting the distribution of subduction-modified mantle lithosphere and hence of pre-collision subduction zones. One characteristic common to this setting is a high crustal input resulting from the presence of a hot, thick 'crustal chemical filter' which is evident on geochemical projections that highlight AFC-type processes. Using this, and other, geochemical features it is possible to develop methodologies to at least partly see through the complexity of collision terranes.

Pearce, Julian

2014-05-01

321

Continental collisions and seismic signature  

NASA Astrophysics Data System (ADS)

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.

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

1991-04-01

322

Invisible Collisions  

NSDL National Science Digital Library

This activity relates an elastic collision to the change in a satellite’s or spacecraft’s speed and direction resulting from a planetary fly-by, often called a “gravity assist” maneuver. Both hands-on and online interactive methods are used to explore these topics.

Keri Hallau

2009-01-01

323

Laser modification of ultracold atomic collisions: Theory  

Microsoft Academic Search

Specific molecular mechanisms are proposed for associative ionization collisions of ultracold sodium atoms in a hybrid optical trap. When an intense, strongly detuned optical trap laser is on, the ionization rate is modulated by molecular bound-state resonances which are strongly affected by field dressing. When the weak, slightly detuned optical molasses lasers are on to provide cooling, an excitation mechanism

Paul S. Julienne; Robert Heather

1991-01-01

324

Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete Pseudopolydora vexillosa.  

PubMed

Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/?-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts/proteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes. PMID:23294167

Chandramouli, Kondethimmahalli H; Sun, Jin; Mok, Flora Sy; Liu, Lingli; Qiu, Jian-Wen; Ravasi, Timothy; Qian, Pei-Yuan

2013-03-01

325

Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae  

PubMed Central

Background Virus-like particles (VLP) have an increasing range of applications including vaccination, drug delivery, diagnostics, gene therapy and nanotechnology. These developments require large quantities of particles that need to be obtained in efficient and economic processes. Production of VLP in yeast is attractive, as it is a low-cost protein producer able to assemble viral structural proteins into VLP. However, to date only single-layered VLP with simple architecture have been produced in this system. In this work, the first steps required for the production of rotavirus-like particles (RLP) in S. cerevisiae were implemented and improved, in order to obtain the recombinant protein concentrations required for VLP assembly. Results The genes of the rotavirus structural proteins VP2, VP6 and VP7 were cloned in four Saccharomyces cerevisiae strains using different plasmid and promoter combinations to express one or three proteins in the same cell. Performance of the best constructs was evaluated in batch and fed-batch cultures using a complete synthetic media supplemented with leucine, glutamate and succinate. The strain used had an important effect on recombinant protein concentration, while the type of plasmid, centromeric (YCp) or episomal (YEp), did not affect protein yields. Fed-batch culture of the PD.U-267 strain resulted in the highest concentration of rotavirus proteins. Volumetric and specific productivities increased 28.5- and 11-fold, respectively, in comparison with batch cultures. Expression of the three rotavirus proteins was confirmed by immunoblotting and RLP were detected using transmission electron microscopy. Conclusions We present for the first time the use of yeast as a platform to express multilayered rotavirus-like particles. The present study shows that the combined use of molecular and bioprocess tools allowed the production of triple-layered rotavirus RLP. Production of VLP with complex architecture in yeasts could lead to the development of new vaccine candidates with reduced restrictions by regulatory agencies, using the successful experience with other yeast-based VLP vaccines commercialized worldwide. PMID:21569612

2011-01-01

326

Vibrationally-resolved Charge Transfer for Proton Collisions with CO  

NASA Astrophysics Data System (ADS)

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

Lin, Chih-Yuan; Stancil, Phillip; Li, Y.; Gu, J. P.; Liebermann, H. P.; Buenker, Robert; Kimura, Mineo

2007-06-01

327

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

SciTech Connect

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.

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

1993-06-01

328

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

E-print Network

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.

David d'Enterria; Jean-Philippe Lansberg

2010-01-11

329

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

SciTech Connect

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.

Chen Zhaoquan [College of Electrical and Information Engineering, Anhui University of Science and Technology, Huainan, Anhui 232001 (China); State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, Liaoning 116024 (China); State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Ye Qiubo [College of Electrical and Information Engineering, Anhui University of Science and Technology, Huainan, Anhui 232001 (China); Communications Research Centre, 3701 Carling Ave., Ottawa K2H 8S2 (Canada); Xia Guangqing [State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian, Liaoning 116024 (China); Hong Lingli; Hu Yelin; Zheng Xiaoliang; Li Ping [College of Electrical and Information Engineering, Anhui University of Science and Technology, Huainan, Anhui 232001 (China); Zhou Qiyan [College of Electrical and Information Engineering, Anhui University of Science and Technology, Huainan, Anhui 232001 (China); State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Hu Xiwei; Liu Minghai [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)

2013-03-15

330

Collision induced ultraviolet structure in nitrogen radar REMPI spectra.  

PubMed

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(1)?g ? X(1)?g(+) electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a(?1)?g(+) electronic state. PMID:25554145

McGuire, S; Miles, R

2014-12-28

331

Collision induced ultraviolet structure in nitrogen radar REMPI spectra  

NASA Astrophysics Data System (ADS)

We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a1?g ? X 1 ?g + electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a ? 1 ?g + electronic state.

McGuire, S.; Miles, R.

2014-12-01

332

Chemistry 231 Fall 2013 Chemistry 231, Chemical Kinetics and Molecular Reaction Dynamics  

E-print Network

, collision theory, transition state theory and the theory of unimolecular reactions will be covered ­ Collision theory and the rate constant October 17 Lecture 7. Kinematics and Dynamics of Classical Collisions of molecular reaction dynamics, an understanding of the kinematics of atomic and molecular collisions

Continetti, Robert E.

333

Ultrafiltration processes for removing humic substances: effect of molecular weight fractions and PAC treatment  

Microsoft Academic Search

The role of humic substances in general and different molecular weight fractions of humic substances in particular on the membrane performance in terms of quality (chlorination byproducts) and quantity (permeate flux) is unclear. One of the goals of the present study is to evaluate the effect of fractionated humic substances on the ultrafiltration (UF) performance. A commercial humic solution was

Cheng-Fang Lin; Yuh-Jay Huang; Oliver J Hao

1999-01-01

334

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

ERIC Educational Resources Information Center

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…

Kelly, Resa M.; Jones, Loretta L.

2008-01-01

335

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles  

Microsoft Academic Search

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for devel- oping analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES

Carol Friedman; Pauline Kra; Hong Yu; Michael Krauthammer; Andrey Rzhetsky

2001-01-01

336

Statistical Analysis of the Processes Controlling Choline and Ethanolamine Glycerophospholipid Molecular Species Composition  

Microsoft Academic Search

The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical

Kourosh Zarringhalam; Lu Zhang; Michael A. Kiebish; Kui Yang; Xianlin Han; Richard W. Gross; Jeffrey Chuang

2012-01-01

337

Ion Collisions with Water Molecules: A Time-Dependent Density Functional Theory Approach  

NASA Astrophysics Data System (ADS)

Collisions of simple ions from water molecules in the energy range of 10-5000 keV/amu are considered within an independent electron model. The basis generator method applied in the past successfully to ion-atom collisions is adapted to deal with molecular targets. Cross sections for single- and multiple-electron processes (capture and transfer to the continuum) are obtained directly from solving time-dependent Kohn-Sham-type orbital equations and using a Slater determinant based analysis. Fragmentation yields are predicted on the basis of a semi-phenomenological model which uses the calculated cross sections as input. Comparison with experiment is made for proton and He+He+ impact collisions.

Kirchner, Tom; Murakami, Mitsuko; Horbatscha, Marko; Lüddeb, Hans Jürgen

2013-06-01

338

Formations of Dumbbell C118 and C119 inside Clusters of C60 Molecules by Collision with ? Particles  

NASA Astrophysics Data System (ADS)

We report highly selective covalent bond modifications in collisions between keV alpha particles and van der Waals clusters of C60 fullerenes. Surprisingly, C119+ and C118+ are the dominant molecular fusion products. We use molecular dynamics simulations to show that C59+ and C58+ ions—effectively produced in prompt knockout processes with He2+—react rapidly with C60 to form dumbbell C119+ and C118+. Ion impact on molecular clusters in general is expected to lead to efficient secondary reactions of interest for astrophysics. These reactions are different from those induced by photons.

Zettergren, H.; Rousseau, P.; Wang, Y.; Seitz, F.; Chen, T.; Gatchell, M.; Alexander, J. D.; Stockett, M. H.; Rangama, J.; Chesnel, J. Y.; Capron, M.; Poully, J. C.; Domaracka, A.; Méry, A.; Maclot, S.; Schmidt, H. T.; Adoui, L.; Alcamí, M.; Tielens, A. G. G. M.; Martín, F.; Huber, B. A.; Cederquist, H.

2013-05-01

339

Dependence of collision-induced dissociation energy on molecular degrees of freedom as a means to assess relative binding affinity in multivalent complexes.  

PubMed

In collision-induced dissociation mass spectrometry experiments, the collision energy required for dissociation linearly depends on the degrees of freedom in the precursor ion. The magnitude of the slope of this relationship previously has been shown to qualitatively correlate to the relative binding strength of a noncovalently bound, monovalent complex. The goal of the work presented here is to determine if a similar methodology can be applied for assessing relative binding strengths in multivalent species. We have tested the method on complexes formed from 18-crown-6 and a variety of protonated, primary alkylamines, [C(n)H(2n+1)NH(3)](+) (n=9, 12, 14, 16 and 18) and alkyldiamines, [H(3)NC(n)H(2n)NH(3)](2+) (n=3, 5, 6, 9 and 12), and compared our results with dissociation energies calculated using density functional theory at the B3LYP/6-31G* level. We found that the method correctly assessed the stronger crown ether/headgroup interaction in the two divalent species (1:1 and 2:1 complexes formed from the diaminoalkanes) compared with the weaker interaction in the monovalent species (1:1 complexes formed from mono-aminoalkanes). However, the experimental method could not distinguish between the binding strengths of the two divalent complexes, perhaps because their calculated dissociation energies were quite similar. Our preliminary results suggest that this method could potentially be used for a quick and simple analysis of binding strengths in multivalent species if the binding strengths of the species are significantly different from one another. PMID:21766373

Huffman, Carmen L; Williams, Melissa Lee; Benoist, D Michelle; Overstreet, Richard E; Jellen-McCullough, Emily E

2011-08-30

340

Chemical composition and molecular structure of polysaccharide-protein biopolymer from Durio zibethinus seed: extraction and purification process  

PubMed Central

Background The biological functions of natural biopolymers from plant sources depend on their chemical composition and molecular structure. In addition, the extraction and further processing conditions significantly influence the chemical and molecular structure of the plant biopolymer. The main objective of the present study was to characterize the chemical and molecular structure of a natural biopolymer from Durio zibethinus seed. A size-exclusion chromatography coupled to multi angle laser light-scattering (SEC-MALS) was applied to analyze the molecular weight (Mw), number average molecular weight (Mn), and polydispersity index (Mw/Mn). Results The most abundant monosaccharide in the carbohydrate composition of durian seed gum were galactose (48.6-59.9%), glucose (37.1-45.1%), arabinose (0.58-3.41%), and xylose (0.3-3.21%). The predominant fatty acid of the lipid fraction from the durian seed gum were palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid (C18:2). The most abundant amino acids of durian seed gum were: leucine (30.9-37.3%), lysine (6.04-8.36%), aspartic acid (6.10-7.19%), glycine (6.07-7.42%), alanine (5.24-6.14%), glutamic acid (5.57-7.09%), valine (4.5-5.50%), proline (3.87-4.81%), serine (4.39-5.18%), threonine (3.44-6.50%), isoleucine (3.30-4.07%), and phenylalanine (3.11-9.04%). Conclusion The presence of essential amino acids in the chemical structure of durian seed gum reinforces its nutritional value. PMID:23062269

2012-01-01

341

Molecular-level processes governing the interaction of contaminants with iron and manganese oxides. 1997 annual progress report  

SciTech Connect

'The central tenet of this proposal is that a fundamental understanding of specific mineral surface-site reactivities will substantially improve reactive transport models of contaminants in geologic systems, and will allow more effective remediation schemes to be devised. Most large-scale, macroscopic models employ global chemical reaction kinetics and thermochemistry. However, such models do not incorporate molecular-level input critical to the detailed prediction of how contaminants interact with minerals in the subsurface. A first step leading to the incorporation of molecular-level processes in large-scale macroscopic models is the ability to understand which molecular-level processes will dominate the chemistry at the microscopic grain level of minerals. To this end, the research focuses on the fundamental mechanisms of redox chemistry at mineral surfaces. As much of this chemistry in sediments involves the Fe(III)/Fe(II) and Mn(IV)/Mn(II) couples, the authors focus on mineral phases containing these species. Of particular interest is the effect of the local coordination environment of Fe and Mn atoms on their reactivity toward contaminant species. Studies of the impact of local atomic structure on reactivity in combination with knowledge about the types and amounts of various surfaces on natural grain- size minerals provide the data for statistical models. These models in turn form the basis of the larger-scale macroscopic descriptions of reactivity that are needed for reactive transport models. A molecular-level understanding of these mechanisms will enhance the ability to design much greater performance efficiency, cost effectiveness, and remediation strategies that have minimal negative impact on the local environment. For instance, a comprehensive understanding of how minerals that contain Fe(II) reduce oxyanions and chlorinated organics should enable the design of other Fe(II)-containing remediation materials in a way that is synergistic with existing minerals in the subsurface environment.'

Chambers, S.A. [Pacific Northwest National Lab., Richland, WA (US); Brown, G. [Stanford Univ., CA (US). Dept. of Geological and Environmental Sciences

1997-06-01

342

Molecular analysis of Salmonella serotypes at different stages of commercial turkey processing  

Technology Transfer Automated Retrieval System (TEKTRAN)

Salmonella isolates were collected from two commercial turkey processing plants (A and B) located in different US geographical locations. Isolates recovered at different stages of processing were subjected to two genotype techniques (polyacrylamide gel electrophoresis [PAGE] and denatured gradient ...

343

Collision Broadening Of Line Spectrum In Sonoluminescence  

SciTech Connect

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.

Li Chaohui [Department of Physics, Tsinghua University, Beijing 100084 (China); An Yu [Department of Physics, Tsinghua University, Beijing 100084 (China); Institute of Acoustics, Chinese Academy of Science, Beijing 100080 (China)

2008-06-24

344

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

E-print Network

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...

Bandyopadhyay, Anirban; Pati, Ranjit

2008-01-01

345

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

346

Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process.  

PubMed

We present here a review of the mechanistic studies of the Wacker process stressing the long controversy about the key reaction steps. We give an overview of the previous experimental and theoretical studies on the topic. Then we describe the importance of the most recent Ab Initio Molecular Dynamics (AIMD) calculations in modelling organometallic reactivity in water. As a prototypical example of homogeneous catalytic reactions, the Wacker process poses serious challenges to modelling. The adequate description of the multiple role of the water solvent is very difficult by using static quantum chemical approaches including cluster and continuum solvent models. In contrast, such reaction systems are suitable for AIMD, and by combining with rare event sampling techniques, the method provides reaction mechanisms and the corresponding free energy profiles. The review also highlights how AIMD has helped to obtain a novel understanding of the mechanism and kinetics of the Wacker process. PMID:24654007

Stirling, András; Nair, Nisanth N; Lledós, Agustí; Ujaque, Gregori

2014-07-21

347

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

PubMed Central

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

Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

2014-01-01

348

From Molecular Structure to Global Processes : NMR Spectroscopy in Analytical/Environmental Chemistry  

NASA Astrophysics Data System (ADS)

NMR Spectroscopy is arguably the most powerful tool to elucidate structure and probe molecular interactions. A range of NMR approaches will be introduced with emphasis on addressing and understanding structure and reactivity of soil organic matter at the molecular level. The presentation will be split into three main sections. The first section will look at evidence from advanced NMR based approaches that when considered synergistically describes the major structural components in soil organic matter. Multidimensional NMR spectroscopy (1-3D NMR), automated pattern matching, spectral simulations, diffusion NMR and hybrid-diffusion NMR will be introduced in context of molecular structure. Finally the structural components in soil will be contrasted to those found in aquatic dissolved organic matter. Secondly molecular interactions of natural organic matter will be considered. Advanced structural studies have provided detailed spectral assignments which in turn permit the reactivity of various soil components to be elucidated. Aggregation and self-association of soil and dissolved organic matter will be discussed along with the structural components likely responsible for aggregation/colloid formation. Interactions of soil organic matter with anthropogenic chemicals will also be considered and NMR techniques based on "Saturation Transfer Difference" introduced. These techniques are extremely powerful and can be used to both; describe mechanistically how anthropogenic chemicals sorb to whole soils and identify the structural components (lignin, protein, cellulose, etc..) that are responsible for the binding/sorption in soil. In the last section, the "big questions" and challenges facing the field will be considered along with some novel experimental NMR based approaches that should, in future, assist in providing answers to these questions.

Simpson, A.

2009-04-01

349

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

NASA Technical Reports Server (NTRS)

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

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

2006-01-01

350

Theoretical Studies of Molecular Dynamical Processes on Solid Surfaces and in the Gas Phase  

NASA Astrophysics Data System (ADS)

Scope and method of study. The purpose of this study was to develop detailed potential-energy surfaces able to describe the molecular systems in the gas-phase or the interactions of molecular systems with solid surfaces. The approach followed was to use parametrized functions of the internal coordinates to fit the geometrical, thermochemical, spectroscopic and kinetic data available for the system of interest. These potential-surfaces have been further used in connection with trajectory methods and Monte Carlo calculations to investigate the molecular dynamics of several molecular systems. Findings and conclusions. Specific potential -energy surfaces for H atoms interaction with the Si(111) -(7times7) surface, for bicyclo(2.1.0)pentane, 1,3-cyclopentadiyl radical, 2,3-diazabicyclo(2.2.1)hept -2-ene and the diazenyl biradical have been developed. Diffusion of H atoms on the Si(111)-(7times7) reconstructed surface has been investigated using the Monte Carlo variational-phase-space theory method. The calculated diffusion coefficients at different temperatures are of the form D=0.023 exp(-1.54 eV/kT) cm^2/s. The type of statistics obeyed by skeletal ring inversion of bicyclo(2.1.0)-pentane has been investigated based on projection methods and molecular dynamics simulations. The results of trajectory calculations, power spectra and the calculated intramolecular vibrational rates for the energy flow out of the flap mode support the statistical character of the ring inversion in bicyclo(2.1.0)-pentane. The thermal decomposition of 2,3-diazabicyclo-(2.2.1)hept-2-ene has been investigated in the energy range of 60-175 kcal/mol. It was found that the reaction takes place with a preference for inversion of configuration in the reaction products. The exo/endo ratio of bicyclo(2.1.0)pentane isomers was found to vary between 1.8-2.2 for the energy range considered. The stepwise dissociation of the C-N bond was found to be the predominant mechanism which characterizes the nitrogen elimination from the parent molecule. The energy dependence of the rate coefficients, power spectra calculations and energy partitioning among products support a global statistical behavior.

Sorescu, Dan Constantin

351

Molecular fountain.  

SciTech Connect

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.

Strecker, Kevin E.; Chandler, David W.

2009-09-01

352

Thermal Decoupling of Molecular-Relaxation Processes from the Vibrational Density of States at Terahertz Frequencies in Supercooled Hydrogen-Bonded Liquids  

E-print Network

Thermal Decoupling of Molecular-Relaxation Processes from the Vibrational Density of States at Terahertz Frequencies in Supercooled Hydrogen-Bonded Liquids Juraj Sibik, † Stephen R. Elliott, ‡ and J. Axel Zeitler* ,† †Department of Chemical...

Sibik, Juraj; Elliott, Stephen R.; Zeitler, J. Axel

2014-05-20

353

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

SciTech Connect

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.

Rozsalyi, E.; Vibok, A. [Department of Theoretical Physics, University of Debrecen, P.O. Box 5, H-4010 Debrecen (Hungary); Bene, E. [Institute of Nuclear Research, Hungarian Academy of Sciences, P.O. Box 51, H-4001 Debrecen (Hungary); Halasz, G. J. [Department of Information Technology, University of Debrecen, P.O. Box 12, H-4010 Debrecen (Hungary); Bacchus-Montabonel, M. C. [Laboratoire de Spectrometrie Ionique et Moleculaire, Universite de Lyon (Lyon I), CNRS-UMR5579, 43 Bd. du 11 Novembre 1918, F-69622 Villeurbanne Cedex (France)

2011-05-15

354

Rigid body constraints in HOOMD-Blue, a general purpose molecular dynamics code on graphics processing units  

NASA Astrophysics Data System (ADS)

Rigid body constraints are commonly used in a wide range of molecular modeling applications from the atomistic scale, modeling the bonds in molecules such as water, carbon dioxide, and benzene, to the colloidal scale, modeling macroscopic rods, plates and patchy nanoparticles. While the parallel implementations of rigid constraints for molecular dynamics simulations for distributed memory clusters have poor performance scaling, on shared memory systems, such as multi-core CPUs and many-core graphics processing units (GPUs), rigid body constraints can be parallelized so that significantly better performance is possible. We have designed a massively parallel rigid body constraint algorithm and implemented it in HOOMD-Blue, a GPU-accelerated, open-source, general purpose molecular dynamics simulation package. For typical simulations, the GPU implementation running on a single NVIDIA^ GTX 480 card is twice as fast as LAMMPS running on 32 CPU cores. In the HOOMD-blue code package, rigid constraints can be used seamlessly with non-rigid parts of the system and with different integration methods, including NVE, NVT, NPT, and Brownian Dynamics. We have also incorporated the FIRE energy minimization algorithm, reformulated to be applicable to mixed systems of rigid bodies and non-rigid particles.

Nguyen, Trung D.; Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

2011-03-01

355

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)

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.

Avakyan, Sergei

2010-05-01

356

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

SciTech Connect

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.

Su Jun [College of Nuclear Science and Technology, Beijing Normal University, 100875 Beijing (China); Beijing Radiation Center, Beijing 100875 (China); Zhang Fengshou [College of Nuclear Science and Technology, Beijing Normal University, 100875 Beijing (China); Beijing Radiation Center, Beijing 100875 (China); Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator of Lanzhou, Lanzhou 730000 (China); Bian Baoan [School of Science, Jiangnan University, Wuxi, Jiangsu 214122 (China)

2011-01-15

357

Tight-Binding Quantum Chemical Molecular Dynamics Study on Depth Profile Prediction in Low Energy Boron Implantation Process  

NASA Astrophysics Data System (ADS)

Creation of shallow junction for the future generation LSI is a crucial step in semiconductor industry and low-energy boron implantation process is considered to be a key technology. In this study, we have statistically investigated the effects of orientation of implantation on the dynamic behavior of boron implantation process into hydrogen-terminated Si(001) 2× 1 surface by using our original tight-binding quantum chemical molecular dynamics method, which is over 5,000 times faster than conventional first-principle molecular dynamics method. It was found that depth profile of boron implantation can be controlled by orientation of boron implantation and the shallowest implantation depth was obtained in the case of tilt angle equal to 7° among the investigated tilt angles of 0°, 7°, 15°, 22.5°, 30° and 45° at the initial boron energy of 100 eV. At the boron implantation process of over 1 keV energy the tilt angle of 7° has been employed experimentally and the same tilt angle was predicted to be the best even at low-energy region of 100 eV. Furthermore, we investigated the effect of rotation angle on the depth profile and at all the investigated tilt angles the average implantation depth becomes shallower for rotation angle of 45° that is along < 011> direction, than for rotation angle of 0° that is along < 001>. Hence, the shallowest depth profile was obtained in the case of tilt angle of 7° and rotation angle of 45°, where the distribution of intruded boron atom was more concentrated than for the same tilt angle but rotation angle of 0°. The effect of tilt and rotation angles on the boron implantation process has not been clarified experimentally at low-energy boron implantation process of less than 1 keV and hence we concluded that theoretical optimization of low-energy boron implantation process has been succeeded by means of our original tight-binding quantum chemical molecular dynamics method.

Tsuboi, Hideyuki; Sagawa, Ai; Iga, Hideki; Sasata, Katsumi; Masuda, Tsuyoshi; Koyama, Michihisa; Kubo, Momoji; Broclawik, Ewa; Yabuhara, Hidehiko; Miyamoto, Akira

2005-04-01

358

Integrated Collision Avoidance System for Air Vehicle  

NASA Technical Reports Server (NTRS)

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.

Lin, Ching-Fang (Inventor)

2013-01-01

359

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

NASA Astrophysics Data System (ADS)

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.

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

360

Analyzing Collisions in Terms of Newton's Laws  

NASA Astrophysics Data System (ADS)

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?"

Roeder, John L.

2003-02-01

361

Dynamics of the baseball-bat collision  

Microsoft Academic Search

A model is developed for the collision between the baseball and bat, taking into account the transverse bending vibrations of the bat. By coupling the flexible bat to the ball via a parametrized force that each mutually exerts on the other, a complete description of the collision process is obtained, including the exit speed of the ball vf. It is

Alan M. Nathan

2000-01-01

362

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...

363

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...

364

Photophysical processes of triplet states and radical ions in pure and molecularly doped polymers. Final report  

SciTech Connect

Both the past and current objectives are to learn how to control the rate and direction of triplet exciton migration in both pure and molecularly doped polymer systems. Since triplet excimers are efficient traps for migrating excitons, a secondary objective has been to characterize these excimers with a view toward their use as rate modifiers or excited state quenchers. Further objectives included those stated above as past and current objectives but with an additional goal. The authors learned that fluid solutions of many of the nitrogen containing chromophores with which they work produce both radical cations and anions upon excimer laser excitation. They also learned that a phosphorus analogue behaves similarly. At this time the mechanism of charge generation in these systems is not well established but they do know that the electronically excited states and radical ions can potentially interconvert. They wanted to find out whether or not the pure or molecularly doped polymer systems could be used in a step-wise sequence involving light absorption followed by charge generation. All of their activities are oriented toward the potential end use of polymeric systems in the conversion of light energy to perform various types of useful work.

Burkhart, R.D.

1998-01-01

365

Changes in Molecular Characteristics of Cereal Carbohydrates after Processing and Digestion  

PubMed Central

Different extraction, purification and digestion methods were used to investigate the molecular properties of carbohydrates in arabinoxylan and ?-glucan concentrates, dietary fiber (DF) rich breads and ileum content of bread fed pigs. The breads studied were: a low DF wheat bread (WF), whole meal rye bread (GR), rye bread with kernels (RK), wheat bread supplemented with wheat arabinoxylan concentrate (AX) and wheat bread supplemented with oat ?-glucan concentrate (BG). The weight average molecular weight (Mw) of extractable carbohydrates in ?-glucan concentrate decreased eight-fold after inclusion in the BG bread when exposed to in vitro digestion, while the Mw of purified extractable carbohydrates in AX bread was reduced two-fold, and remained almost unaffected until reaching the terminal ileum of pigs. Similarly, the Mw of purified extractable carbohydrates in GR and RK bread was not significantly changed in the ileum. The AX bread resulted in the highest concentration of dissolved arabinoxylan in the ileum among all the breads that caused a substantial increased in ileal AX viscosity. Nevertheless, for none of the breads, the Mw of extractable carbohydrates was related neither to the bread extract nor ileal viscosity. PMID:23222731

Kasprzak, Miros?aw Marek; Lærke, Helle Nygaard; Knudsen, Knud Erik Bach

2012-01-01

366

Time-dependent density-functional theory for molecular processes in strong fields: Study of multiphoton processes and dynamical response of individual valence electrons of N2 in intense laser fields  

E-print Network

We present a time-dependent density-functional theory (TDDFT) with proper asymptotic long-range potential for nonperturbative treatment of multiphoton processes of many-electron molecular systems in intense laser fields. ...

Chu, Xi; Chu, Shih-I

2001-11-14

367

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

NASA Technical Reports Server (NTRS)

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

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

1985-01-01

368

Supercritical fluid processing of polymer thin films: an X-ray study of molecular-level porosity.  

PubMed

This paper reviews our recent experimental results that address the effects of solvent density inhomogeneities in supercritical carbon dioxide (scCO(2)) on polymer thin film processing. The key phenomenon is excess sorption of CO(2) molecules into polymer thin films even when the bulk miscibility with CO(2) is very poor. We have found that the amount of the excess sorption is attributed to the large density fluctuations in scCO(2) near the critical point. Further, taking advantage of the vitrification process of polymer chains through quick evaporation of CO(2), we can preserve the "expanded" structures as they are. The resultant films have large degree of molecular-level porosity that is very useful in producing coatings with low dielectric constants, enhanced adhesion, and metallization properties. These characteristics can be achieved in an environmentally "green" manner, without organic solvents, and are not specific to any class of polymers. PMID:17239334

Koga, Tadanori; Jerome, J; Rafailovich, M H; Chu, B; Douglas, J; Satija, S

2006-12-21

369

Introduction to the study of collisions between heavy nuclei  

SciTech Connect

Current investigations concerning the collisions of nuclei governed by small de Broglie wavelengths are reviewed. The wave packets localize nuclei in regions small compared to their diameters. Cross sections are examined for potential scattering, elastic scattering, quasi-molecular states, peripheral particle-transfer reactions, fusion, and deep inelastic collisions. Theories of fusion and deep inelastic collisions are summarized. This paper is in the nature of a review-tutorial. 45 references, 51 figures, 2 tables. (RWR)

Bayman, B.F.

1980-01-01

370

Mass transfer of SCWO processes: Molecular diffusion and mass transfer coefficients of inorganic nitrate species in sub- and supercritical water  

SciTech Connect

Molecular diffusion coefficients of lithium-, sodium-, potassium-, cesium-, calcium-, and strontium nitrate in subcritical water were determined by analysis of Taylor dispersion profiles. Pressures ranged from 300 to 500 bar at temperatures ranging from 25{degrees}C to 300{degrees}C. The reported diffusion values were determined at infinite dilution. Molecular diffusion coefficients were 10 to 20 times faster in near-critical subcritical water than in water at ambient temperature and pressure (ATP). These findings implied that the diffusion rates were more liquid like than they were gas like, hence experimental results were correlated with diffusion models for liquids. The subcritical diffusion data presented in this work, and supercritical diffusion results published elsewhere were correlated with hydrodynamic diffusion equations. Both the Wilke-Chang correlation and the Stokes-Einstein equation yielded predictions within 10% of the experimental results if the structure of the diffusing species could be estimated. The effect of the increased diffusion rates on mass transfer rates in supercritical water oxidation applications was quantified, with emphasis on heterogeneous oxidation processes. This study and results published elsewhere showed that diffusion limited conditions are much more likely to be encountered in SCWO processes than commonly acknowledged.

Goemans, M.G.E.; Gloyna, E.F. [Univ. of Texas, Austin, TX (United States). Dept. of Civil Engineering; Buelow, S.J. [Los Alamos National Lab., NM (United States)

1996-04-01

371

Cloud-cloud collision as a trigger of the high-mass star formation; a molecular line study in RCW120  

E-print Network

RCW120 is a Galactic HII region which has a beautiful infrared ring. Previous studies on RCW120 provided a wealth of information on the second generation star formation, but the origin of the exciting O star located inside the ring structure has not been focused so far. Our new CO observations performed with the NANTEN2, Mopra, and ASTE telescopes have revealed that two molecular clouds with a velocity separation 20km/s are both physically associated with RCW120. The cloud at -8km/s apparently traces the infrared ring, while the other cloud at -28km/s is mainly distributed just outside the opening of the infrared ring, interacting with the HII region as supported by high kinetic temperature of the molecular gas and by the complementary distribution with the ionized gas. A spherically expanding shell driven by the HII region is usually discussed as the origin of the observed ring structure in RCW120. In this model, the neutral material which surrounds the HII region is expected to have an expanding motion. Our...

Torii, 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

2015-01-01

372

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....

373

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

NASA Technical Reports Server (NTRS)

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.

Luther, George W., III

1987-01-01

374

Systems- and Molecular-Level Elucidation of Signaling Processes Through Chemistry  

NSDL National Science Digital Library

Complete understanding of the molecular mechanisms of signal transduction is a major focus of research in the postgenomic era. Efforts to realize this goal have benefited from interdisciplinary approaches, specifically through the development of new technologies. Several groups have now described new chemical strategies to probe signaling with broadly different degrees of focus. The first report employs an enzymatic tagging strategy to monitor global proteolytic cleavage events that occur during apoptosis. The second study illustrates a general method to functionally characterize a specific kinase through the identification of its substrates. Finally, the third report describes a synthetic route to generate ubiquitinated proteins and demonstrates the utility of protein chemistry in understanding the detailed biochemical mechanisms of signaling. Together, these papers highlight the power of chemical tools to examine specific networks, thereby expanding our understanding of signaling pathways.

Kyle P. Chiang (The Rockefeller University; Laboratory of Synthetic Protein Chemistry REV)

2008-10-21

375

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

SciTech Connect

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.

Walsh, S.P.

1992-01-01

376

GoSynthetic database tool to analyse natural and engineered molecular processes  

PubMed Central

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

Liang, Chunguang; Krüger, Beate; Dandekar, Thomas

2013-01-01

377

Structure and evolution of the Magnitogorsk forearc basin: Identifying upper crustal processes during arc-continent collision in the southern Urals  

Microsoft Academic Search

The southern Urals of Russia contain a well-preserved example of a Paleozoic arc-continent collision in which the intraoceanic Magnitogorsk volcanic arc and its forearc basin sediments accreted to the East European Craton during the Devonian. The Magnitogorsk arc records the evolution from incipient intraoceanic subduction to a mature arc, and by comparing its surface geological features with those in active

D. Brown; J. Alvarez-Marrón; A. Pérez-Estaún; V. Puchkov; Y. Gorozhanina; P. Ayarza

2001-01-01

378

Spontaneous ultraweak photon emission imaging of oxidative metabolic processes in human skin: effect of molecular oxygen and antioxidant defense system  

NASA Astrophysics Data System (ADS)

All living organisms emit spontaneous ultraweak photon emission as a result of cellular metabolic processes. In this study, the involvement of reactive oxygen species (ROS) formed as the byproduct of oxidative metabolic processes in spontaneous ultraweak photon emission was studied in human hand skin. The effect of molecular oxygen and ROS scavengers on spontaneous ultraweak photon emission from human skin was monitored using a highly sensitive photomultiplier tube and charged coupled device camera. When spontaneous ultraweak photon emission was measured under anaerobic conditions, the photon emission was decreased, whereas under hyperaerobic condition the enhancement in photon emission was observed. Spontaneous ultraweak photon emission measured after topical application of glutathione, ?-tocopherol, ascorbate, and coenzyme Q10 was observed to be decreased. These results reveal that ROS formed during the cellular metabolic processes in the epidermal cells play a significant role in the spontaneous ultraweak photon emission. It is proposed that spontaneous ultraweak photon emission can be used as a noninvasive tool for the temporal and spatial monitoring of the oxidative metabolic processes and intrinsic antioxidant system in human skin.

Rastogi, Anshu; Pospíšil, Pavel

2011-09-01

379

Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast ?-relaxation is followed by a much slower ?-relaxation. There is a little change in the structural properties in the ?-relaxation region, while major configuration rearrangements occurred in the ?-relaxation range and the crystallization process was completed at the end of ?-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.

Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou

2014-10-01

380

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

SciTech Connect

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.

Otec, Roman; /Prague, Tech. U.

2006-09-01

381

Analysis of discharge characteristics of the inertial electrostatic confinement fusion using a particle code with Monte Carlo collision scheme  

Microsoft Academic Search

In this paper, we study the mechanism of a self-maintaining discharge in the Inertial Electrostatic Confinement Fusion (IECF) with D2 gas. We developed a 1-D particle code with Monte Carlo collision scheme including atomic and molecular processes of ion, energetic neutral, and electron impact based on the PDS-1 code. Also we developed the energy dependent transparency model of the cathode,

Takuya Sakai; Kazuyuki Noborio; Y. Yamamoto

2002-01-01

382

PLANT SEEDS: AN EXCITING MODEL SYSTEM FOR DISSECTING MOLECULAR AND CELLULAR REGULATION OF METABOLIC PROCESSES  

Microsoft Academic Search

Metabolic processes are regulated by complex networks of interacting mechanisms that utilize various cellular machineries. Such complex networks may be well exemplified by the synthesis, accumulation, and degradation of storage proteins in developing and germinating seeds. Our laboratories are using plant seeds as a model system for studying the regulation of production of the essential amino acid lysine, the control

GAD GALILI; GUILIANG TANG; XIAOHONG ZHU; RACHEL AMIR; HANNA LEVANONY; GALIA SHY; ELIOT M. HERMANb

2000-01-01

383

Molecular Epidemiological Survey of Listeria monocytogenes in Seafoods and Seafood-Processing Plants  

Microsoft Academic Search

To evaluate the role of seafoods in the epidemiology of human listeriosis and the role of the processing environment as a source of Listeria monocytogenes in seafood products, 305 L. monocytogenes isolates were characterized by multilocus enzyme electrophoresis using 21 genetic loci and restriction enzyme analysis of total DNA. Forty-four isolates were recovered from patients in Norway; 93 were isolated

L. M. Rorvik; BRIT AASE; TORILL ALVESTAD; DOMINIQUE A. CAUGANT

2000-01-01

384

Molecular systems biology: data-flow diagram modeling of process in protein  

Microsoft Academic Search

In this paper, we introduce a new method of modeling tool for a biological process - central dogma. The data-flow diagram is used as a representation of the whole data input and output, which enables us to simulate, analyze, and manipulate (in the future) at our disposal. From DNA to protein via RNA is the one of most well-known biological

J. W. Yeol; I. Barjis; Y. S. Ryu

2005-01-01

385

Functional Genomics Approach for Identification of Molecular Processes Underlying Neurodegenerative Disorders in Prion Diseases  

PubMed Central

Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders leading to death. These include Cresutzfeldt-Jakob disease (CJD), familial, sporadic and variant CJD and kuru in humans; and animal TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) of mule deer and elk, and transmissible mink encephalopathy. All these TSEs share common pathological features such as accumulation of mis-folded prion proteins in the central nervous system leading to cellular dysfunction and cell death. It is important to characterize the molecular pathways and events leading to prion induced neurodegeneration. Here we discuss the impact of the functional genomics approaches including microarrays, subtractive hybridization and microRNA profiling in elucidating transcriptional cascades at different stages of disease. Many of these transcriptional changes have been observed in multiple neurodegenerative diseases which may aid in identification of biomarkers for disease. A comprehensive characterization of expression profiles implicated in neurodegenerative disorders will undoubtedly advance our understanding on neuropathology and dysfunction during prion disease and other neurodegenerative disorders. We also present an outlook on the future work which may focus on analysis of structural genetic variation, genome and transcriptome sequencing using next generation sequencing with an integrated approach on animal and human TSE related studies. PMID:23372423

Basu, Urmila; Guan, Le Luo; Moore, Stephen S

2012-01-01

386

Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units  

NASA Astrophysics Data System (ADS)

Molecular dynamics (MD) methods compute the trajectory of a system of point particles in response to a potential function by numerically integrating Newton's equations of motion. Extending these basic methods with rigid body constraints enables composite particles with complex shapes such as anisotropic nanoparticles, grains, molecules, and rigid proteins to be modeled. Rigid body constraints are added to the GPU-accelerated MD package, HOOMD-blue, version 0.10.0. The software can now simulate systems of particles, rigid bodies, or mixed systems in microcanonical (NVE), canonical (NVT), and isothermal-isobaric (NPT) ensembles. It can also apply the FIRE energy minimization technique to these systems. In this paper, we detail the massively parallel scheme that implements these algorithms and discuss how our design is tuned for the maximum possible performance. Two different case studies are included to demonstrate the performance attained, patchy spheres and tethered nanorods. In typical cases, HOOMD-blue on a single GTX 480 executes 2.5-3.6 times faster than LAMMPS executing the same simulation on any number of CPU cores in parallel. Simulations with rigid bodies may now be run with larger systems and for longer time scales on a single workstation than was previously even possible on large clusters.

Nguyen, Trung Dac; Phillips, Carolyn L.; Anderson, Joshua A.; Glotzer, Sharon C.

2011-11-01

387

Binary cluster collision dynamics and minimum energy conformations  

NASA Astrophysics Data System (ADS)

The collision dynamics of one Ag or Cu atom impinging on a Au12 cluster is investigated by means of DFT molecular dynamics. Our results show that the experimentally confirmed 2D to 3D transition of Au12?Au13 is mostly preserved by the resulting planar Au12Ag and Au12Cu minimum energy clusters, which is quite remarkable in view of the excess energy, well larger than the 2D-3D potential barrier height. The process is accompanied by a large s-d hybridization and charge transfer from Au to Ag or Cu. The dynamics of the collision process mainly yields fusion of projectile and target, however scattering and cluster fragmentation also occur for large energies and large impact parameters. While Ag projectiles favor fragmentation, Cu favors scattering due to its smaller mass. The projectile size does not play a major role in favoring the fragmentation or scattering channels. By comparing our collision results with those obtained by an unbiased minimum energy search of 4483 Au12Ag and 4483 Au12Cu configurations obtained phenomenologically, we find that there is an extra bonus: without increase of computer time collisions yield the planar lower energy structures that are not feasible to obtain using semi-classical potentials. In fact, we conclude that phenomenological potentials do not even provide adequate seeds for the search of global energy minima for planar structures. Since the fabrication of nanoclusters is mainly achieved by synthesis or laser ablation, the set of local minima configurations we provide here, and their distribution as a function of energy, are more relevant than the global minimum to analyze experimental results obtained at finite temperatures, and is consistent with the dynamical coexistence of 2D and 3D liquid Au clusters conformations obtained previously.

Muñoz, Francisco; Rogan, José; Valdivia, J. A.; Varas, A.; Kiwi, Miguel

2013-10-01

388

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

NASA Technical Reports Server (NTRS)

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.

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

2002-01-01

389

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

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.

López, E.; Lucas, J. M.; Andrés, J. de; Albertí, M.; Aguilar, A., E-mail: a.aguilar@ub.edu [Departament de Química Física, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona (Spain); Bofill, J. M. [Departament de Química Orgànica, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona (Spain); Bassi, D. [Dipartimento di Fisica, Università degli Studi di Trento, 38123 Povo-Trento (Italy)

2014-10-28

390

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

SciTech Connect

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.

Annapureddy, Harsha V.; Dang, Liem X.

2012-12-07

391

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes  

PubMed Central

TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe ‘equivalog’ families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at and . PMID:17151080

Selengut, Jeremy D.; Haft, Daniel H.; Davidsen, Tanja; Ganapathy, Anurhada; Gwinn-Giglio, Michelle; Nelson, William C.; Richter, Alexander R.; White, Owen

2007-01-01

392

The calculation of product quantum state distributions and partial cross-sections in time-dependent molecular collision and photodissociation theory  

Microsoft Academic Search

A new method of analyzing the results of multidimensional time-dependent quantum dynamical wavepacket calculations in terms of the product quantum state distributions is presented. The method requires knowledge only of the time-dependent projection coefficients of the wavepacket onto individual product quantum states along a cut in the exit valley of the photodissociation or reaction process. The squares of the Fourier

Gabriel G. Balint-Kurti; Richard N. Dixon; C. Clay Marston; A. J. Mulholland

1991-01-01

393

Uncovering molecular relaxation processes with nonlinear spectroscopies in the deep UV  

NASA Astrophysics Data System (ADS)

Nonlinear laser spectroscopies in the deep UV spectral range are motivated by studies of biological systems and elementary processes in small molecules. This perspective article discusses recent technical advances in this area with a particular emphasis on diffractive optic based approaches to four-wave mixing spectroscopies. Applications to two classes of systems illustrate present experimental capabilities. First, experiments on DNA components at cryogenic temperatures are used to uncover features of excited state potential energy surfaces and vibrational cooling mechanisms. Second, sub-200 fs internal conversion processes and coherent wavepacket motions are investigated in cyclohexadiene and ?-terpinene. Finally, we propose new experimental directions that combine methods for producing few-cycle UV laser pulses in noble gases with incoherent detection methods (e.g., photoionization) in experiments with time resolution near a singlefemtosecond. These measurements are motivated by knowledge of extremely fast non-adiabatic dynamics and the resolution of electronic wavepacket motions in molecules.

West, Brantley A.; Molesky, Brian P.; Giokas, Paul G.; Moran, Andrew M.

2013-09-01

394

The changes of membrane performance with polyamide molecular structure in the reverse osmosis process  

Microsoft Academic Search

In order to develop high performance membranes for the reverse osmosis process, thin film composite membranes were prepared by the interfacial polymerization with various acyl chloride solutions and amine solutions containing poly(m-aminostyrene), (PmAS). PmAS was prepared by reducing poly(m-nitrostyrene) that was obtained by the free radical polymerization of 3-nitrostyrene. The results related to changes in the membrane performance with interfacial

C. K Kim; J. H Kim; I. J Roh; J. J Kim

2000-01-01

395

High-speed atomic force microscopy shows dynamic molecular processes in photoactivated bacteriorhodopsin  

Microsoft Academic Search

Dynamic changes in protein conformation in response to external stimuli are important in biological processes, but it has proved difficult to directly visualize such structural changes under physiological conditions. Here, we show that high-speed atomic force microscopy can be used to visualize dynamic changes in stimulated proteins. High-resolution movies of a light-driven proton pump, bacteriorhodopsin, reveal that, upon illumination, a

Mikihiro Shibata; Hayato Yamashita; Takayuki Uchihashi; Hideki Kandori; Toshio Ando

2010-01-01

396

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

Microsoft Academic Search

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. mono- cytogenescontaminationpatternsin3Latin-stylefresh- cheese processing plants togain a better understanding of L. monocytogenes contamination sources in the man- ufacture of these cheeses. Over a 6-mo period, 246 envi- ronmental samples

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

2004-01-01

397

Metamorphism and Continental Collision  

NSDL National Science Digital Library

Physical Geology students are required to understand the processes involved in plate tectonics. They are expected to know the geologic differences between continents and ocean basins and should be able to recall and use simple geologic terms to describe geologic processes and events. This activity is designed to improve student comprehension of the varied Earth materials and complex processes involved in plate collisions. The activity synthesizes material covered during the first eight weeks of Physical Geology on plate tectonics, rock types, volcanoes, and Earth's composition. The instructor introduces the exercise to the students as a component of the college's Critical Thinking Initiative. The "hook" for the students is that the exercise represents a chance for self-appraisal of course content and understanding prior to the next semester test. The grading rubric for the lab is discussed with the students in terms of the Bloom Pyramid so that they can assess their level of progress in the course.

Kenneth Howard

398

Melt spinning of poly( l\\/ d)lactide 96\\/4: Effects of molecular weight and melt processing on hydrolytic degradation  

Microsoft Academic Search

This study focused on determining the effects of molecular weight on the degradation of polylactide 96l\\/4d in melt spinning and the effects of melt processing on hydrolytic degradation. Three polylactides with different inherent viscosities were melt spun, and the fibres were studied in vitro. Results showed that during melt spinning high-molecular-weight polylactide degraded because polymer chains were subject to high

K. Paakinaho; V. Ellä; S. Syrjälä; M. Kellomäki

2009-01-01

399

Experimental study of {mu}-atomic and {mu}-molecular processes in pure helium and deuterium-helium mixtures  

SciTech Connect

We present experimental results of {mu}-atomic and {mu}-molecular processes induced by negative muons in pure helium and helium-deuterium mixtures. The experiment was performed at the Paul Scherrer Institute (Switzerland). We measured relative intensities of muonic x-ray K series transitions in ({mu}{sup 3,4}He){sup *} atoms in pure helium as well as in helium-deuterium mixtures. The d{mu}{sup 3}He radiative decay probabilities for two different helium densities in D{sub 2}+{sup 3}He mixture were also determined. Finally, the q{sub 1s}{sup He} probability for a d{mu} atom formed in an excited state to reach the ground state was measured and compared with theoretical calculations using a simple cascade model.

Bystritsky, V.M.; Boreiko, V.F.; Gerasimov, V.V.; Pavlov, V.N.; Sandukovsky, V.G.; Stolupin, V.A.; Volnykh, V.P. [Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Czaplinski, W.; Popov, N.P.; Wozniak, J. [AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, PL-30059 Cracow (Poland); Filipowicz, M. [AGH University of Science and Technology, Faculty of Fuels and Energy, PL-30059 Cracow (Poland); Huot, O.; Knowles, P.E.; Schaller, L.A.; Schneuwly, H. [Department of Physics, University of Fribourg, CH-1700 Fribourg (Switzerland); Mulhauser, F. [University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

2005-03-01

400

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

NASA Astrophysics Data System (ADS)

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.

Deratzou, Susan

401

Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials  

SciTech Connect

The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.

Prasad, Manish; Conforti, Patrick F.; Garrison, Barbara J. [Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

2007-08-28

402

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

SciTech Connect

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.

Walewski, L. [Warsaw University; Krachtus, D [University of Heidelberg; Fischer, S. [University of Heidelberg; Smith, Jeremy C [ORNL; Bala, P. [Institute of Physics, Nicolaus Copernicus University, Toru?, Poland; Lesyng, B. [Warsaw University

2005-09-01

403

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

NASA Astrophysics Data System (ADS)

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.

Kohler, Felix; Rohrbach, Alexander

2015-01-01

404

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

NASA Astrophysics Data System (ADS)

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.

Spatz, Joachim

2013-03-01

405

Molecular processes underlying the floral transition in the soybean shoot apical meristem.  

PubMed

The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem. The flowering process is of vital importance for agriculture, but the associated events or regulatory pathways in the SAM are not well understood, especially at a system level. To address this issue, we have used a GeneChip containing 37 744 probe sets to generate a temporal profile of gene expression during the floral initiation process in the SAM of the crop legume, soybean (Glycine max). A total of 331 transcripts displayed significant changes in their expression profiles. The in silico and RT-PCR analysis on differentially regulated transcripts implies the intriguing involvement of sugar, auxin or abscisic acid (ABA) in events prior to the induction of floral homeotic transcripts. The novel involvement of ABA in the floral transition is further implicated by immunoassay, suggesting an increase in ABA levels in the SAM during this developmental transition. Furthermore, in situ localization, together with in silico data demonstrating a marked enhancement of abiotic stress-related transcripts, such as trehalose metabolism genes in SAMs, points to an overlap of abiotic stress and floral signalling pathways. PMID:18980639

Wong, Chui E; Singh, Mohan B; Bhalla, Prem L

2009-03-01

406

Morphological and molecular analysis of the collagen fibers in inflammatory process  

NASA Astrophysics Data System (ADS)

Collagen makes up one third of the total protein in humans, being formed by the connection of three polypeptide chains arranged in a triple helix. This protein has fundamental importance in the formation of extracellular matrix of connective tissue. This study aimed to analyze the structural changes of collagen, which are resulting from inflammatory processes in oral mucosa, and to make the comparative analysis between the histopathology and the Raman spectra. The samples of tissues with inflammatory fibrous hyperplasia (IFH) and normal mucosa (NM) were evaluated by Raman Spectroscopy, hematoxylin-eosin and Massons trichrome stain. The histological analysis in both stains showed differences in collagen fibers, which was presented as thin fibers and arranged in parallel direction in NM and as collagen fibers are thick, mature and not organized, showing that these types of stain show morphological changes of collagen in IFH. The Raman Spectroscopy discriminate the groups of NM and IFH based on vibrational modes of proline, hydroxiproline and CH3, CH2. The histological stains only shows information from morphological data, and can be complemented by Raman spectra. This technique could demonstrate that inflammatory process caused some changes in collagen structure which is related to aminoacids such as proline and hidroxyproline.

de Carvalho, Luis