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1

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

2

Tight-binding molecular-dynamics simulation of buckyball collisions  

Microsoft Academic Search

The collisions between C[sub 60] molecules are studied by tight-binding molecular-dynamics simulations. We observe three different regimes of behavior as the collisions become more and more energetic: bouncing, fusion, and fragmentation. The critical energies for fusion and fragmentation as well as details of the energy transfer during the collision process for the bouncing regime are investigated. The collisions at several

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

1993-01-01

3

Aligned molecular collisions and a stereodynamical mechanism for selective chirality  

Microsoft Academic Search

Investigations of the stereodynamics of elementary processes provide the background for perspective demonstration of the manifestation\\u000a of chiral effects in molecular collisions. Advances in experimental vacuum technology allow the generation of molecular beams\\u000a containing oriented molecules. Here, we focus on collisional alignment, a molecular polarization phenomenon occurring in supersonic\\u000a expansions of gaseous mixtures. The underlying physical mechanisms, relevant gas-phase experiments

Vincenzo Aquilanti; Gaia Grossi; Andrea Lombardi; Glauciete S. Maciel; Federico Palazzetti

2011-01-01

4

Electronic nonadiabaticity in collinear reactive molecular collisions  

SciTech Connect

Several aspects of electronic nonadiabaticity in collinear reactive molecular collisions are investigated. A two-surface, nonadiabatically coupled, model problem (loosely based on the F + H{sub 2} system) is adapted for three case studies of differing dynamical character. The resulting state to state transition probabilities are examined as function of collision energy and also compared with single-surface calculations. Certain features of the results which are common to all three studies are identified and ascribed to reactant valley location of the nonadiabatic coupling envelope. We also attempt to shed light on the energy dependence of various off-surface to on-surface reactive probability ratios by examining the vibrational structure of the nonadiabatic coupling. A picture emerges whereby the presence or absence of alternate pathways for the electronic switching is reflected in these ratios.

Horn, T.R.; Eno, L. (Clarkson Univ., Potsdam, NY (USA)); Zimmerman, I.H. (Lawrence Livermore National Lab., CA (USA))

1989-02-23

5

Numerical analysis of nanograin collision by classical molecular dynamics  

SciTech Connect

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

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

2007-08-29

6

SPH simulations of clumps formation by dissipative collisions of molecular clouds. II. Magnetic case  

Microsoft Academic Search

We performed computer simulations of interstellar cloud-cloud collisions using the three-dimensional smoothed particle magnetohydrodynamics method. In order to study the role of the magnetic field on the process of collision-triggered fragmentation, we focused our attention on head-on supersonic collisions between two identical spherical molecular-clouds. Two extreme configurations of the magnetic field were adopted: parallel and perpendicular to the initial clouds

E. P. Marinho; C. M. Andreazza; J. R. D. Lépine

2001-01-01

7

Molecular vibrational states during a collision  

NASA Technical Reports Server (NTRS)

Alternative algebraic techniques to approximate a given Hamiltonian by a harmonic oscillator are described both for time-independent and time-dependent systems. We apply them to the description of a one dimensional atom-diatom collision. From the resulting evolution operator, we evaluate vibrational transition probabilities as well as other time-dependent properties. As expected, the ground vibrational state becomes a squeezed state during the collision.

Recamier, Jose A.; Jauregui, Rocio

1995-01-01

8

FOREWORD: Collision Processes of Metallic Ions in Fusion Plasmas  

NASA Astrophysics Data System (ADS)

On May 16-18, 1990, an Advisory Group Meeting on "Atomic and Molecular Data for Metallic Impurities in Fusion Plasmas" was organized by the Atomic and Molecular Data Unit of the International Atomic Energy Agency and held in Vienna, Austria. The objectives of the Meeting were to review the status of atomic collision data for the most important fusion plasma metallic impurities (Ti, Cr, Fe and Ni), to identify the gaps in the database in relation to the data needs of the current fusion research and reactor design work, and to report on recent original cross section calculations and measurements for the collision processes of these ions. The scope of the meeting included the following collision processes: (a) Electron collisions with Tiq+, Crq+, Feq+ and Niq+ ions (excitation, ionization, radiative and dielectronic recombination); (b) Collisions of Tiq+, Crq+, Feq+ and Niq+ ions with H, H2, and He (total and state-selective electron capture, excitation, ionization and dissociative processes with H2). The meeting was attended by fifteen participants covering almost uniformly the various collision processes, energy ranges and research methods (theoretical and experimental). In the area of electron-ion collision processes, extensive reviews of the current research and cross section data situation have been presented by Y Hahn (on radiative and dielectronic recombination), D Gregory (on excitation) and A Muller (on ionization). Contributions regarding the cross sections and/or reaction rates of many specific processes were given by N Badnell, K Berrington, M Bitter, R E H Clark, A Muller and V P Shevelko. V A Abramov provided a comparison of the electron-impact excitation data, evaluated by several groups, and demonstrated their consistency in the majority of analyzed cases. In the area of heavy-particle collision processes, the research and database situation was reviewed by H B Gilbody. Original cross section information for specific heavy-particle collision processes was presented by H Cederquist, W Fritsch, R E Olson, K Katsonis and G L Yudin. The present Topical Issue of Physica Scripta contains the contributions presented at the meeting with the exception of the presentation of V A Abramov. The reports of the Working Groups, established at the meeting to critically evaluate the available data and to identify the gaps in the database, are also included in this volume. An appropriate introductory comment by the Guest Editor on the impurity sources and the role of impurity collision processes in fusion plasmas is also added. On behalf of the International Atomic Energy Agency, I take this opportunity to thank the participants of the Advisory Group Meeting for their dedicated work and valuable contribution to this international endeavour and for their co-operativeness in the course of preparation of this volume.

Janev, R. K.

1991-01-01

9

The generalized cumulant expansion approach to stochastic reductions in molecular collision dynamics: Applications to collisional energy transfer  

Microsoft Academic Search

A generalized cumulant expansion method is developed for applying stochastic reductions to molecular collision processes. We begin by introducing an approximate partitioning of a collision system into two subsystems Sr and Si which are assumed to be weakly correlated. Cumulant expansion methods are then used to simultaneously perform a stochastic reduction over Si, and a projection of the diagonal elements

George C. Schatz

1977-01-01

10

Resonant electron-CF collision processes  

SciTech Connect

Electronic structure methods are combined with variationalfixed-nuclei electron scattering calculations and nuclear dynamicsstudies to characterize resonant vibrational excitation and electronattachment processes in collisions between low-energy electrons and CFradicals. Several low-lying negative ion states are found which give riseto strong vibrational excitation and which are expected to dominate thelow-energy electron scattering cross sections. We have also studiedseveral processes which could lead to production of negative ions (F- andC-), However, in contrast to other recent predictions, we do not find CFin itsground state to be a significant source of negative ion productionwhen interacting with thermal electrons.

Trevisan, Cynthia S.; Orel, Ann E.; Rescigno, Thomas N.

2005-03-18

11

Petascale computations for Large-scale Atomic and Molecular collisions  

E-print Network

Petaflop architectures are currently being utilized efficiently to perform large scale computations in Atomic, Molecular and Optical Collisions. We solve the Schroedinger or Dirac equation for the appropriate collision problem using the R-matrix or R-matrix with pseudo-states approach. We briefly outline the parallel methodology used and implemented for the current suite of Breit-Pauli and DARC codes. Various examples are shown of our theoretical results compared with those obtained from Synchrotron Radiation facilities and from Satellite observations. We also indicate future directions and implementation of the R-matrix codes on emerging GPU architectures.

McLaughlin, Brendan M

2014-01-01

12

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

13

The calculation of time-correlation functions for molecular collisions  

Microsoft Academic Search

A general formalism relating cross sections to collisional time-correlation functions is applied to the calculation of energy transfer in molecular collisions. Basic aspects of the formalism are reviewed, followed by a detailed description of methods suitable for the calculation of quantal state-to-state cross sections. These methods are particularly useful in the description of scattering by large systems, or of systems

Eduardo Vilallonga; David A. Micha

1992-01-01

14

Optimal separable bases and molecular collisions  

SciTech Connect

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

Poirier, L.W. [Univ. of California, Berkeley, CA (United States)]|[Lawrence Berkeley National Lab., CA (United States)

1997-12-01

15

Collision dynamics of the associative ionization process arising from collisions between two excited sodium 3p atoms  

SciTech Connect

Associative ionization (AI) in collisions between Na(3p) atoms, Na(3p) + Na(3p) ..-->.. Na/sub 2//sup +/ + e/sup -/ was studied in detail in a crossed-atomic-beam apparatus. The primary object of the work is to determine the mechanisms by which the AI reactive collision process takes place. First studied was the collision energy dependence of the AI cross section. The accessed collision energy spans more than two orders of magnitude, from subthermal (20 K) to suprathermal (2230K) regions. The author oriented the spins of Na(3p) atoms and measured the separate AI excitation functions for singlet and triplet manifolds of Na/sub 2/ molecular states contributing to AI. Secondly, it was discovered that the AI depends strongly on p-lobe alignment. The anisotropy in AI cross sections grows rapidly with collision velocity and AI increasingly flavors ..gamma gamma.. p-orbital alignment over all other configurations. The results suggest the dominance of ..sigma.. states in the AI reaction. Thirdly, the measurements show that AI produces vibrationally excited Na/sub 2//sup +/ with a distribution increasing approximately linearly with vibrational level. The analysis of the rotational energy distribution indicates a short-range opacity function for AI with a maximum impact parameter of 2 A. Fourthly, evidence was found of the preference for ..gamma gamma.. orbital symmetry in Al reactive collisions. A semiclassical model for AI was formulated and successfully interpreted the battery of experimental results.

Wang, M.X.

1986-01-01

16

Taming molecular collisions using electric and magnetic fields.  

PubMed

The motion of molecules that possess a permanent electric or magnetic dipole moment can be manipulated using electric or magnetic fields. Various devices have been developed over the last few decades to deflect or focus molecules, to orient them in space, and to decelerate or accelerate them. These precisely controlled molecules are ideal starting points for scattering experiments that reveal the quantum mechanical nature of molecular interactions. In this Tutorial Review, we present an overview of the various manipulation tools, discuss how they can be used to advantage in molecular beam scattering experiments, and review recent progress in this field. We describe a selection of benchmark experiments that illustrate the unique possibilities that are available nowadays to study molecular collisions under controlled conditions. PMID:25115818

Brouard, Mark; Parker, David H; van de Meerakker, Sebastiaan Y T

2014-11-01

17

Electron loss from multiply protonated lysozyme ions in high energy collisions with molecular oxygen.  

PubMed

We report on the electron loss from multiply protonated lysozyme ions Lys-Hn(n)+ (n = 7 - 17) and the concomitant formation of Lys-Hn(n+1)+. in high-energy collisions with molecular oxygen (laboratory kinetic energy = 50 x n keV). The cross section for electron loss increases with the charge state of the precursor from n = 7 to n = 11 and then remains constant when n increases further. The absolute size of the cross section ranges from 100 to 200 A2. The electron loss is modeled as an electron transfer process between lysozyme cations and molecular oxygen. PMID:11506221

Hvelplund, P; Nielsen, S B; Sørensen, M; Andersen, J U; Jørgensen, T J

2001-08-01

18

Studies of fluctuation processes in nuclear collisions  

SciTech Connect

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

Ayik, S.

1992-02-01

19

ReaxFF molecular dynamics simulations of CO collisions on an O-preadsorbed silica surface.  

PubMed

A quasiclassical trajectory dynamics study was performed for carbon monoxide collisions over an oxygen preadsorbed ?-cristobalite (001) surface. A reactive molecular force field (ReaxFF) was used to model the potential energy surface. The collisions were performed fixing several initial conditions: CO rovibrational states (v?=?0-5 and j?=?0, 20, 35), collision energies (0.05 ? E(col) ? 2.5 eV), incident angles (?(v)?=?0°, 45°) and surface temperatures (T(surf)?=?300 K, 900 K). The principal elementary processes were the molecular reflection and the non-dissociative molecular adsorption. CO? molecules were also formed in minor extension via an Eley-Rideal reaction although some of them were finally retained on the surface. The scattered CO molecules tend to be translationally colder and internally hotter (rotationally and vibrationally) than the initial ones. The present study supports that CO?+?O(ad) reaction should be less important than O?+?O(ad) reaction over silica for similar initial conditions of reactants, in agreement with experimental data. PMID:24633769

Gamallo, Pablo; Prats, Hèctor; Sayós, Ramón

2014-04-01

20

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

21

A collision process responsible for widespread formation of H anions  

NASA Astrophysics Data System (ADS)

The hydride ion H- is widely understood to play a major role in many processes important for physics, cosmology, astrophysics and chemistry. Here we report that H- ions can be formed by collision-induced fragmentation of molecules containing hydrogen and heavier nuclei. We observed H- emission from OH+ + Ar and OH+ + acetone collisions at the energy of 7 keV. Our data reveal a process of electron-grabbing by fast hydrogen fragments emitted in hard collisions with large momentum transfer between atomic cores.

Juhász, Zoltán; Sulik, Béla; Kovács, Sándor T. S.; Lattouf, Elie; Rangama, Jimmy; Bene, Erika; Huber, Bernd; Frémont, François; Méry, Aiain; Poully, Jean-Christophe; Rousseau, Patrick; Herczku, Péter; Chesnel, Jean-Yves

2014-04-01

22

Excitation and charge transfer in He/sup +/ + H collisions. A molecular approach including two-electron translation factors  

SciTech Connect

In a previous paper we have pointed out that the common-translation-factor (CTF) method is the only one which, at present, and within the framework of the molecular model of atomic collisions, can be shown to be both convergent and computationally fast, even for many-electron systems. In this Communication we check that this second statement is correct, presenting, for the first time, a molecular calculation involving two-electron translation factors, for He/sup +/ + H collisions. A careful study of the sensitivity of the calculated cross sections to the choice of the CTF is performed, and conclusions on that sensitivity are drawn, for several types of processes.

Errea, L.F.; Mendez, L.; Riera, A.

1983-06-01

23

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

NASA Astrophysics Data System (ADS)

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

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

2014-07-01

24

Fundamental electron collision processes relevant to low-temperature plasmas  

SciTech Connect

This paper attempts to elucidate the mutually beneficial interaction between electron collision physics and the physics and chemistry that govern the properties of low temperature plasmas, in particular technologically relevant low-temperature processing plasmas. We hope to demonstrate how recent developments in collision physics contributed to an improved understanding of the fundamental collision processes in low-temperature plasmas, how they made possible more sophisticated modelling efforts of such plasmas and how they advanced the development of more sensitive plasma diagnostics techniques. At the same time, we hope to show how some of the many unanswered questions and challenges faced by the plasma processing community have stimulated new developments and novel approaches in atomic and electron collision physics. {copyright} {ital 1996 American Institute of Physics.}

Becker, K.H. [Physics Department, City College of C.U.N.Y., Convent Avenue and 138th Street, New York, New York 10031-9198 (United States)

1996-03-01

25

Multichannel quantum defect theory for cold molecular collisions  

SciTech Connect

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

Croft, James F. E.; Wallis, Alisdair O. G.; Hutson, Jeremy M.; Julienne, Paul S. [Department of Chemistry, Durham University, South Road, Durham DH1 3LE (United Kingdom); Joint Quantum Institute, NIST and the University of Maryland, Gaithersburg, Maryland 20899-8423 (United States)

2011-10-15

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

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

PubMed

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

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

2013-01-28

28

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

NASA Astrophysics Data System (ADS)

A significant process in the formation of the unique atmosphere of Io, a Jovian moon, is collision-induced dissociation of sulfur dioxide. The direct simulation Monte Carlo method (DSMC) is used to model the rarefied gas dynamics of the Ionian atmosphere. However, there is a lack of reliable reaction and collision cross sections needed for hypervelocity conditions. In this work, collisions between SO2 and O were studied using molecular dynamics/quasi-classical trajectories methods with the potential of Murrell and a force field for reactive systems (ReaxFF). Dissociation to SO was found to be the significant reacting process, but at higher collision energies, complete atomization of SO2 was found to frequently occur. In contrast, dissociation to O2 was found to be mostly negligible and formation of SO3 occurred only at low impact velocities. The chemistry and collision models developed from the Murrell and ReaxFF methods were implemented in DSMC simulations and compared to the baseline DSMC collision and reaction models. It was found that the selection of both the dissociation reaction cross section and the non-reactive collision model has a significant effect on the counterflow, shock gas dynamic structure.

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

2013-01-01

29

Effect of laser frequency on a collision-induced radiative process  

NASA Astrophysics Data System (ADS)

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

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

1981-11-01

30

Interchange of Translational, Rotational and Vibrational Energy in Molecular Collisions  

Microsoft Academic Search

The change in internal energy of molecules upon collisions has been analysed. Formulae, (26) to (27-C), for the effective cross section of inelastic collisions have been obtained as functions of known properties of the molecules, subject to certain conditions. These conditions are: the atoms which come into contact during collision must belong to the first row of the periodic table;

Clarence Zener

1931-01-01

31

A one-body transport model of fluctuation processes in nuclear collisions  

SciTech Connect

Many aspects of a many-body system can be described in terms of one- body transport models in which the system at any time is characterized by its single-particle density rather than by the full many-body information. In these one-body models evaluation of the single-particle density is determined by a transport equation which contains the self-consistent mean-field potential and a collision term due to binary two-body collisions. Recently, this approach in a semi-classical limit with a Boltzmann-Uehling-Uhlenbeck (BUU) form of a collision term has been applied to nuclear collisions at intermediate energies. Common to all one-body models, only the average effects of two-body collisions are retained in the equation of motion and higher order correlations are entirely neglected. This approximation corresponds to an ensemble averaging which is evident, for example, from the molecular chaos assumption'' introduced in derivation of Boltzmann equation. As a result, these one-body models determine the ensemble averaged single-particle density and cannot provide a description for the fluctuation processes in nuclear collisions. On the other hand, at low and intermediate energies dynamical fluctuations are substantial due to large available phase space for decay into many final states. Therefore, it is of great interest to improve one-body transport models by incorporating dynamical fluctuations due to high order correlations into the equation of motion. 5 refs., 3 figs.

Ayik, S. (Tennessee Technological Univ., Cookeville, TN (USA)); Gregoire, C.; Suraud, E.; Stryjewski, J.; Belkacem, M. (Grand Accelerateur National d'Ions Lourds (GANIL), 14 - Caen (France))

1990-01-01

32

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

33

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

34

Collision Avoidance for Unmanned Aircraft using Markov Decision Processes  

E-print Network

Collision Avoidance for Unmanned Aircraft using Markov Decision Processes Selim Temizer , Mykel J. Kochenderfer , Leslie P. Kaelbling§ , Tom´as Lozano-P´erez¶ , and James K. Kuchar Before unmanned aircraft can attention in recent years. However, unmanned aircraft are not currently permitted access to civil airspace

Lozano-Perez, Tomas

35

Electron-Nitrogen Collision Processes Relevant to Planetary Atmospheres  

NASA Astrophysics Data System (ADS)

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

Johnson, Paul

2011-06-01

36

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

37

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

38

Dynamics of persistent collision complexes in molecular beam reactive scattering  

Microsoft Academic Search

New microcanonical theories for the angular distributions of reactive scattering arising from long-lived collision complexes and their application to a wide range of transition state geometries are reviewed. Transition states formed at the top of centrifugal barriers on potential energy surfaces without a potential energy barrier are well described by symmetric top transition states, provided that the loosening of bending

Roger Grice

1995-01-01

39

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

40

Atomic Site-Sensitive Processes in Low Energy Ion-Dimer Collisions  

NASA Astrophysics Data System (ADS)

Electron capture processes for low energy Ar9+ ions colliding with Ar2 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.

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

41

Calculations of fast ion collisions with multi-center molecular targets  

NASA Astrophysics Data System (ADS)

The theoretical treatment of ion-molecule collisions is challenging for several reasons: the systems have many degrees of freedom, a rather complex geometry, and the electron dynamics might be nonperturbative and involve electron-electron interaction effects. However, the interest in accurate calculations has been growing recently. An important reason for this development is the relevance of ion-molecule collisions for a number of fields, such as atmospheric science, and the understanding of radiation damage of biological tissue. We have developed a new approach to meet these challenges [1]. It disregards rovibrational motion, but it does address the multi-center geometry of the system and the generally nonperturbative nature of the electron dynamics. The key ingredients are an expansion of the initially populated molecular orbitals in terms of a single-center basis and a spectral representation of the molecular Hamiltonian. This facilitates a separation of molecular geometry and collision dynamics and makes it possible to use well-established ion-atom methods with relatively minor modifications. We have extended our basis generator method to deal with the collision dynamics and report on results for ionization and fragmentation of water molecules by proton and He^+ ion impact over wide ranges of collision energies. For the case of He^+ impact this will include a discussion of effects due to the presence of the projectile electron. [4pt] [1] H. J. Lüdde et al., Phys. Rev. A 80, 060702(R) (2009)

Kirchner, Tom

2011-06-01

42

Cloud-cloud collision in the Sgr B2 molecular cloud complex  

NASA Astrophysics Data System (ADS)

We present results from a high-resolution wide-field imaging observation of the central molecular zone (CMZ) in H13CO+ J = (1 - 0) and SiO v=0, J = (2-1) emission lines by using the Nobeyama 45-m telescope in order to depict the high-density molecular gas mass distribution and explore molecular gas affected by interstellar shocks. We found a candidate for ongoing cloud-cloud collision in the Sgr B2 complex. This is identified as a hollow paraboloid-like structure in the l-b-v data cube of both emission lines. The central part of the feature is denser and warmer than the outer envelope and contains a vast amount of shocked molecular gas. These properties are consistent with those expected from simulations of cloud-cloud collisions in the CMZ.

Tsuboi, Masato; Miyazaki, Atsushi; Handa, Toshihiro

2014-05-01

43

Neighbor list collision-driven molecular dynamics simulation for nonspherical hard particles. I. Algorithmic details  

Microsoft Academic Search

In this first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of non-spherical particles, within a parallelepiped simulation domain, under both periodic or hard-wall boundary conditions. The algorithm extends previous event-driven molecular dynamics algorithms for spheres, and is most efficient when applied to systems of particles with relatively

Aleksandar Donev; Salvatore Torquato; Frank H. Stillinger

2005-01-01

44

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

NASA Technical Reports Server (NTRS)

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

Hutchinson, M.; George, T. F.

1981-01-01

45

Collisions of low-energy antiprotons with molecular hydrogen: ionization, excitation and stopping power  

NASA Astrophysics Data System (ADS)

A time-dependent coupled-channel approach was used to calculate ionization, excitation, and energy-loss cross sections as well as energy spectra for antiproton and proton collisions with molecular hydrogen for impact energies 8 < E < 4000 keV.

Lühr, Armin; Saenz, Alejandro

2009-11-01

46

Mountain building processes during continent continent collision in the Uralides  

NASA Astrophysics Data System (ADS)

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

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

2008-08-01

47

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

48

Cold state-selected molecular collisions and reactions.  

PubMed

Over the past decade, and particularly the past five years, a quiet revolution has been building at the border between atomic physics and experimental quantum chemistry. The rapid development of techniques for producing cold and even ultracold molecules without a perturbing rare-gas cluster shell is now enabling the study of chemical reactions and scattering at the quantum scattering limit with only a few partial waves contributing to the incident channel. Moreover, the ability to perform these experiments with nonthermal distributions comprising one or a few specific states enables the observation and even full control of state-to-state collision rates in this computation-friendly regime: This is perhaps the most elementary study possible of scattering and reaction dynamics. PMID:24423374

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

2014-01-01

49

Atomic site sensitive processes in low energy ion-dimer collisions  

E-print Network

Electron capture processes for low energy Ar9+ ions colliding on Ar2 dimer targets are investigated, focusing attention on charge sharing as a function of molecule orientation and impact parameter. A preference in charge-asymmetric dissociation channels is observed, with a strong correlation between the projectile scattering angle and the molecular ion orientation. The measurements provide here clear evidences that projectiles distinguish each atom in the target and, that electron capture from near-site atom 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 a new insight into the dynamics of the collision by providing, for the di erent electron capture channels, the two-dimensional probability maps p(~b), where ~b is the impact parameter vector in the molecular frame.

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

2014-05-12

50

FOREWORD: Topical issue on collision processes of Be and B atoms and ions in fusion plasmas  

NASA Astrophysics Data System (ADS)

The present topical issue of Physica Scripta contains the results of a concerted effort to review and expand the cross section data information for collision processes of beryllium and boron atoms and ions in a thermonuclear fusion plasma. These two chemical species are present as dominant impurities in the plasmas of several presently operating large tokamak devices and are anticipated to be among the most abundant impurities in the next generation fusion reactor experiments. Beryllium is attractive as a plasma facing reactor material because of its low atomic number (i.e. low potential for radiative plasma power losses), excellent gettering properties with respect to oxygen (unavoidably present in any fusion plasma) and adequate thermo-mechanical and erosion properties when exposed to plasma energy and particle fluxes. Boron, on the other hand, is frequently used as a dopand in carbon-based plasma facing materials to improve their erosion, hydrogen retention and (some) thermo-mechanical properties. The beryllium and boron atoms enter the plasma edge as a result of plasma-wall interaction and in the course of their penetration into the hot plasma regions become progressively ionized. The variety of collision processes of beryllium and boron atoms and ions with other plasma constituents is very large. In the hot plasma regions, the most important among them are the electron-impact excitation, ionization and recombination. In the cold plasma edge regions which support thermodynamical coexistence of both neutral and ionized species, apart from electron-impact excitation and ionization of neutral Be and B atoms, coffision processes of low charged Be and B ions with the neutral atomic and molecular hydrogen and helium (such as momentum transfer, excitation, ionization and charge exchange) are also important. The inelastic collision processes between Beq+, Bq+ ions and H, He neutrals are particularly important when energetic neutral hydrogen and helium beams are injected into the plasma for heating and diagnostic purposes. The above mentioned collision processes between Be and B atoms and ions and other dominant plasma constituents play a prominent role in determining the transport of these impurity ions in the plasma and their radiating properties. The cross section information on these processes is also essential in the spectroscopic plasma diagnostics based on the analysis of observed radiation from Be and B species. All the important electron and heavy-particle collision processes involving Be and B atoms and ions in a fusion plasma (except the electron-ion recombination) are being addressed in the present volume. While a number of contributions to this volume provide a critical review of already existing cross section data for certain classes of processes, most of the articles report new, previously unavailable cross section information for the studied processes. The present volume of Physica Scripta is, therefore, a significant step towards a better understanding of the collision physics of Be and B ions in fusion plasmas and towards establishing a comprehensive cross section database for their collision processes. It is a great pleasure to express my deep appreciation to all contributors to the present volume for their dedicated effort and friendly cooperation during all stages of its preparation.

Janev, R. K.

1996-01-01

51

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

SciTech Connect

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

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

1984-10-01

52

Stochastic theory of molecular collisions. II. Application to atom--vibrotor collisions. [Energy-conserving classical path model, Fokker-Planck equation coefficients  

Microsoft Academic Search

In this work stochastic theory is applied to the treatment of atom--vibrotor collisions. This is an extension of a previous paper which described molecular collisions by a Pauli master equation or a Fokker--Planck equation. In this framework an energy conserving classical path model is explored, and methods for solving the equations numerically are discussed. The coefficients of the Fokker--Planck equation

S. D. Augustin; H. Rabitz

1977-01-01

53

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

Microsoft Academic Search

The vibrational to translational (VâT) 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

P. M. Y

1991-01-01

54

Electronic excitation of H[sub 2] in slow collisions with molecular ions  

SciTech Connect

Excitation of molecular hydrogen has been studied in 1.8-keV collisions with molecular projectile ions H[sub 2][sup +], N[sub 2][sup +], CO[sup +], O[sub 2][sup +], and CO[sub 2][sup +] by means of energy-loss spectrometry using a high-resolution ion translational-energy spectrometer. Excitation of the target H[sub 2] is observed only in the case of collisions with [ital H][sub 2][sup +]. Oscillator strengths for electronic transitions to various electronic states are determined by simulating the measured energy-loss spectra with calculations using calculated Franck-Condon overlap integrals. Excitation of the projectile ions is observed in the case of collisions with N[sub 2][sup +] and CO[sup +] projectiles. Neither projectile excitation nor target excitation is observed when experiments are carried out with O[sub 2][sup +] and CO[sub 2][sup +] projectiles. The results obtained in the present study are interpreted as a manifestation of wave-function-overlap effects involving the highest occupied molecular orbitals of the target and projectile ions.

Krishnamurthy, M.; Gross, P.; Mathur, D. (Tata Institute of Fundamental Research, Homi Bhabha Road, Bombay 400005 (India))

1994-09-01

55

Electron capture and deprotonation processes observed in collisions between Xe8+ and multiply protonated cytochrome-C  

NASA Astrophysics Data System (ADS)

Electron-transfer processes in interaction between highly charged ions and multiply protonated proteins have been studied. Collisions between Xe8+ at 96 keV and protonated cytochrome-C at selected charge state (q from 15+ to 19+) result in mass spectra composed mainly of intact molecular ions. From the spectra, single and double electron capture processes by Xe8+ from the protonated molecular ions were identified and the relative cross sections were measured. An unexpected process, the deprotonation process, was also observed. It is tentatively attributed to the loss of a proton induced by the strong electric field carried by the projectile ion in long-distance collisions. Upon charge variation of the molecular target from 15 to 19, the single and double electron capture cross sections remain nearly constant, while the relative cross section of the deprotonation process increases dramatically from 0.8% (±0.1%) to 17% (±1%). This strong charge dependency is explained by the decrease of the proton affinities with the charge. This proton removal process has not been observed previously. It seems to be specific to the long-distance Coulomb interactions between protons bound along the protein chain and the highly charged atomic ions.

Martin, S.; Ortega, C.; Chen, L.; Brédy, R.; Vernier, A.; Dugourd, P.; Antoine, R.; Bernard, J.; Reitsma, G.; Gonzalez-Magaña, O.; Hoekstra, R.; Schlathölter, T.

2014-01-01

56

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between CN and C4H6.  

PubMed

Collision reactions between cyano radical (CN) and dimethylacetylene (C4H6) are thought to occur in the atmosphere of Saturn's moon Titan. However, it is difficult to reproduce reactions occurring in unique environments to study their dynamical processes. In this study, collision reactions between CN and C4H6 were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short-time Fourier transform analysis of velocity autocorrelation functions obtained by the AIMD simulations, which has been recently developed by our research group, was performed to examine the nonequilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states. PMID:15688439

Tamaoki, Mari; Yamauchi, Yusuke; Nakai, Hiromi

2005-04-15

57

BioCD : An Efficient Algorithm for Self-collision and Distance Computation between Highly Articulated Molecular Models  

Microsoft Academic Search

This paper describes an efficient approach to (self) collision detection and distance computations for complex ar- ticulated mechanisms such as molecular chains. The proposed algorithm called BioCD is particularly designed for sampling- based motion planning on molecular models described by long kinematic chains possibly including cycles. The algorithm con- siders that the kinematic chain is structured into a number of

Vicente Ruiz De Angulo; Juan Cortés; Thierry Siméon

2005-01-01

58

The Atomic and Molecular Universe: Collisions in Hot Plasmas to the Building Blocks of Life  

NASA Astrophysics Data System (ADS)

Basic atomic and molecular collision phenomena are operative at the core of an enormous range of astrophysical plasmas, including the interstellar medium (ISM), protostellar regions, stars, our Sun, and planetary atmospheres, ionospheres, & magnetospheres. Laboratory measurements of cross sections and lifetimes are needed to establish plasma charge-state distributions. A required database includes absolute electron- impact excitation, ionization, and recombination cross sections in highly-charged ions (HCIs); photoionization cross sections; and absolute single- and multiple charge-exchange cross sections between a neutral target and an HCI, as when a solar/stellar wind meets a circumstellar cloud or passing comet to generate X- rays via charge exchange. Since satellites and spacecraft often detect photons from the astronomical object, the infrared-to-X- ray emissions are governed by a balance between collisional excitation and radiative decay, so that accurate lifetimes, branching fractions, and Einstein A and B coefficients are also needed. On yet another level, observations in the infrared-to- millimeter wave region from, for example, the Green Bank Telescope, Spitzer, Sofia, Herschel, and the James Webb Telescope provide information on molecular formation in the ISM and protostellar regions. Over 144 atomic, molecular, and ionic species have been identified to date. Recent laboratory results will be given on formation of some of these polyatomic molecules in superthermal, ground-state H- and O-atom collisions with simple, grain-adsorbed species, and results compared to the impressive array of space spectroscopic data.

Chutjian, Ara

2010-03-01

59

Bibliography of atomic and molecular processes, 1983  

NASA Astrophysics Data System (ADS)

This annotated bibliography includes 1762 citations 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.

1984-10-01

60

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

61

Chemical Potential Jump During Evaporation of a Bose Gas with Variable Molecular Collision Frequency  

NASA Astrophysics Data System (ADS)

Evaporation of a binary mixture is considered for the case when the evaporating component is a Bose gas. An analytical solution of the problem of the chemical potential jump of a Bose gas is obtained for the case when the molecular collision frequency of the evaporating component is a variable quantity. The dependence of the coefficient of the chemical potential jump on the evaporation coefficient is investigated. The concentration of the evaporating component is assumed to be much less than that of the carrier gas. A graphical study of the coefficient of the chemical potential jump is presented.

Bedrikova, E. A.; Latyshev, A. V.

2014-09-01

62

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

63

Half-Collision Dynamics of Excited Metal Atom Quenching Processes  

NASA Astrophysics Data System (ADS)

Half-collision studies of the quenching of excited states of Zn by Xe and Cd by H_2, CH_4 and i-C_4H _{10} have been undertaken and have provided information concerning the role of alignment of the excited metal atom p-orbital as well as other dynamical information and details about the potential energy surfaces (curves) involved in the quenching process. Van der Waals complexes of a single metal atom with a rare gas atom or quencher molecule are prepared using a supersonic expansion of the metal vapor, carrier gas and quencher gas. To provide a more detailed understanding of van der Waals bonding involving closed shell metal atoms, spectroscopic investigations of the MgcdotNe, Zncdot Ar and ZncdotKr C ^1Pi_1 and X^1 Sigma_0^+ states as well as the ZncdotXe D^1Sigma _0^+ and X^1Sigma _0^+ states via laser induced fluorescence have also been performed. No fluorescence is observed from the Zn cdotXe C^1Pi_1 state which predissociates to Zn(4s4p^3 P_{rm J}) + Xe, permitting the C state to be characterized via a Zn(4s4p^3P_2) "action spectrum." Modeling of the deeply bound C state and the shallow D state using Morse potentials suggests that the long range tail of the C state curve crosses the inner wall of the D state curve. For the CdcdotCH _4 and CdcdotC _4H_{10} complexes, fluorescence is not observed from either the C or D states. However, Cd(5s5p^3P _{rm J}) action spectra are obtained for C and D state excitation. A Cd(5s5p ^3P_0) action spectrum is observed as a result of CdcdotCH _4 A and B state excitation. Rotational structure is observed in the vibrational bands and has permitted characterization of the Cdcdot CH_4 X and A states within a pseudodiatomic approximation and provided evidence for hindered rotation of the methane molecule. When CdcdotH_2 or CdcdotD_2 is excited to the red of the Cd(5s5p^1 P_1 >=ts 5s5s^1S_0) atomic transition, fluorescence is again absent while Cd(5s5p ^3P_{rm J}) action spectra are observed. The observation in the spectra of vibrational structure, which is superimposed on a continuum, suggests that two processes lead to predissociation. The vibrational structure observed is not consistent with an excited state bound solely by van der Waals forces. It is proposed that the vibrational motion in this state results from the coupling of symmetric stretch and bending vibrations in a C_{rm 2v} geometry.

Wallace, Ingvar Axel, II

64

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

NASA Astrophysics Data System (ADS)

The interaction-induced absorption by collisional pairs of H{_2} molecules is an important opacity source in the atmospheres of various types of planets and cool stars, such as late stars, low-mass stars, brown dwarfs, cool white dwarf stars, the ambers of the smaller, burnt out main sequence stars, exoplanets, etc., and therefore of special astronomical interest The emission spectra of cool white dwarf stars differ significantly in the infrared from the expected blackbody spectra of their cores, which is largely due to absorption by collisional H{_2}-H{_2}, H{_2}-He, and H{_2}-H complexes in the stellar atmospheres. Using quantum-chemical methods we compute the atmospheric absorption from hundreds to thousands of kelvin. Laboratory measurements of interaction-induced absorption spectra by H{_2} pairs exist only at room temperature and below. We show that our results reproduce these measurements closely, so that our computational data permit reliable modeling of stellar atmosphere opacities even for the higher temperatures. First results for H_2-He complexes have already been applied to astrophysical models have shown great improvements in these models. L. Frommhold, Collision-Induced Absorption in Gases, Cambridge University Press, Cambridge, New York, 1993 and 2006 X. Li, K. L. C. Hunt, F. Wang, M. Abel, and L. Frommhold, Collision-Induced Infrared Absorption by Molecular Hydrogen Pairs at Thousands of Kelvin, Int. J. of Spect., vol. 2010, Article ID 371201, 11 pages, 2010. doi: 10.1155/2010/371201 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Collision-induced absorption by H{_2} pairs: From hundreds to thousands of Kelvin, J. Phys. Chem. A, 115, 6805-6812, 2011} L. Frommhold, M. Abel, F. Wang, M. Gustafsson, X. Li, and K. L. C. Hunt, "Infrared atmospheric emission and absorption by simple molecular complexes, from first principles", Mol. Phys. 108, 2265, 2010 M. Abel, L. Frommhold, X. Li, and K. L. C. Hunt, Infrared absorption by collisional H_2-He complexes at temperatures up to 9000 K and frequencies from 0 to 20000 cm-1, J. Chem. Phys., 136, 044319, 2012 D. Saumon, M. S. Marley, M. Abel, L. Frommhold, and R. S. Freedman, New H_2 collision-induced absorption and NH_3 opacity and the spectra of the coolest brown dwarfs, Astrophysical Journal, 2012

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

2012-06-01

65

Molecular dissolution processes in lipid bilayers: A molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

A thorough understanding of the effects of chain ordering on solute partitioning and transport across biomembranes requires a detailed account of various dissolution processes in lipid bilayers. In this study, the dissolution properties and related molecular processes for noble gases in the alkyl chain region of lipid bilayers were obtained by means of molecular dynamics simulation. The excess chemical potential exhibits a plateau value in the ordered peripheral region followed by a steep decline near the center of the bilayer. The strong entropic effects as manifested by the larger Barclay-Butler constants than commonly encountered in hydrocarbon solvents indicate that solute partitioning into membranes is driven primarily by changes of lipid chain conformation or/and an extra confinement of solute in the bilayer interior. Solute partitioning into lipid bilayers is analyzed in terms of two contributions: (1) the free energy for cavity creation to accommodate a solute, which is analyzed by scaled particle theory; and (2) the interaction energy between the inserted solute and surrounding molecules in the bilayer. The unfavorable free energy for cavity creation is found to be primarily responsible for the substantial decrease of solubility into the membranes from that into a hydrocarbon solvent (dodecane) when the solute size is increased. The observed linear decrease of the excess chemical potential with solute surface area arises from linear but opposite dependencies of the reversible work for cavity creation and the intermolecular interaction energy on solute surface area and may be described by an anisotropic surface-tension model.

Xiang, Tian-xiang; Anderson, Bradley D.

1999-01-01

66

Electron capture in low energy collisions of N{sup 2+} with molecular hydrogen  

SciTech Connect

Ab initio CI adiabatic potentials and dipole moment matrix elements for the triatomic dication NH{sub 2}{sup 2+} in the collinear, asymmetric arrangement have been calculated. A diabatic description of the collision process is obtained by a unitary transformation in a representation that diagonalizes the dipole moment matrix. Neglecting H{sub 2} orientation and rotation, cross sections for the charge transfer process N{sup 2+} + H{sub 2}(v=0) {r_arrow} N{sup +} + H{sub 2}{sup +}(v{prime}) are determined with a close-coupled quantal method. Results will be compared to recent measurements.

Stancil, P.C.; Zygelman, B. [Univ. of Nevada, Reno, NV (United States); Kirby, K.

1996-05-01

67

Formation of giant molecular clouds in global spiral structures: The role of orbital dynamics and cloud-cloud collisions  

NASA Technical Reports Server (NTRS)

The different roles played by orbital dynamics and dissipative cloud-cloud collisions in the formation of giant molecular clouds (GMCs) in a global spiral structure are investigated. The interstellar medium (ISM) is simulated by a system of particles, representing clouds, which orbit in a spiral-perturbed, galactic gravitational field. The overall magnitude and width of the global cloud density distribution in spiral arms is very similar in the collisional and collisionless simulations. The results suggest that the assumed number density and size distribution of clouds and the details of individual cloud-cloud collisions have relatively little effect on these features. Dissipative cloud-cloud collisions play an important steadying role for the cloud system's global spiral structure. Dissipative cloud-cloud collisions also damp the relative velocity dispersion of clouds in massive associations and thereby aid in the effective assembling of GMC-like complexes.

Roberts, W. W., Jr.; Stewart, G. R.

1987-01-01

68

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

E-print Network

governing the capture reactions of light nu- clei and of very heavy ions have been determined. RotatingRotating hyperdeformed quasi-molecular states formed in capture of light nuclei and in collision of very heavy ions G. Royer1, E. Zarrouk1, J. Gaudillot1, C. Beck2 and W. von Oertzen3 1Laboratoire

Boyer, Edmond

69

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

2005-12-30

70

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

Microsoft Academic Search

A new concept is proposed, according to which the plasma and collision processes accompanying hypervelocity impacts of meteorites can contribute to the arising of the conditions on early Earth, which are necessary for the appearance of primary forms of living matter. It was shown that the processes necessary for the emergence of living matter could have started in a plasma

G. Managadze

2010-01-01

71

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

72

Molecular Dynamics simulations of polymer/post collisions with explicit hydrodynamic interactions.  

NASA Astrophysics Data System (ADS)

Micro-- or nano--scopic arrays of posts, made using either microlithography or magnetically self--assembled arrays of ferro--fluids represent a promising new media for the electrophoretic separation of DNA. In order to optimize these systems we require a better understanding of the underlying mechanisms involved in separation. In light of this we carry out a systematic examination of the collision of polymers with fixed posts using large scale Molecular Dynamics simulations. These simulations explicitly include solvent, i.e., hydrodynamic interactions, in order to gain a better understanding of polymer dynamics involved in these media. In particular we examine the effects of field strength on polymer deformation, mean extension and escape time. Also we examine the effects of hydrodynamic interactions on the escape of polymers from entangled states and mean escape times of polymers as a function of molecular weight. We compare the results from the MD simulations with theoretical predictions for the escape time of a polymer derived within a non--local friction model.

Kenward, Martin; Slater, Gary W.

2003-03-01

73

Stationary Point Process, Palm measure and collision risk  

E-print Network

stationary process is made. We show in this paper that the Poisson hypothesis is not necessary, at least,b](Tn) and Tn = inf{t : N(-,t]) = n}. We say that the point process is stationary if the joint probability, the shift mapping t defined on the probability space by N(t,I) = N(,I +t). Therefore, the point process

Paris-Sud XI, Université de

74

TCP (truncated Compound Poisson) Process for Multiplicity Distributions in High Energy Collisions  

Microsoft Academic Search

On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, we obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The TCP

Prem P. Srivastava

1990-01-01

75

TCP (truncated compound Poisson) process for multiplicity distributions in high energy collisions  

Microsoft Academic Search

On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, the authors obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The

Srivastave

1990-01-01

76

Self-similarity in random collision processes Daniel ben-Avraham,1  

E-print Network

Self-similarity in random collision processes Daniel ben-Avraham,1 Eli Ben-Naim,2 Katja Lindenberg and nonlocal equation t F k,t F k,t F pk,t F qk,t . 3 This closed equation is amenable to analytical treatment

Lindenberg, Katja

77

Studies of fluctuation processes in nuclear collisions. Progress report, March 1, 1995--March 31, 1996  

SciTech Connect

This progress report studies of fluctuation processes in nuclear collisions discusses the following topics: quantal effects on growth of instabilities in nuclear matter; collisional damping of giant resonances in a non-Markovian approach; and medium-modified interaction induced by fluctuations.

Ayik, S.

1996-03-01

78

Laboratory studies of atomic collision processes of importance in planetary atmospheres  

NASA Technical Reports Server (NTRS)

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

Stebbings, R. F.; Smith, K.

1985-01-01

79

Effects of molecular rotation in low-energy electron collisions of H3+.  

PubMed

Measurements on the energetic structure of the dissociative recombination rate coefficient in the millielectronvolt range are described for H3+ ions produced in the lowest rotational levels by collisional cooling and stored as a fast beam in the magnetic storage ring TSR (Test Storage Ring). The observed resonant structure is consistent with that found previously at the storage ring facility CRYRING in Stockholm, Sweden; theoretical predictions yield good agreement on the overall size of the rate coefficient, but do not reproduce the detailed structure. First studies on the nuclear spin symmetry influencing the lowest level populations show a small effect different from the theoretical predictions. Heating processes in the residual gas and by collisions with energetic electrons, as well as cooling owing to interaction with cold electrons, were observed in long-time storage experiments, using the low-energy dissociative recombination rate coefficient as a probe, and their consistency with the recent cold H3+ measurements is discussed. PMID:17015371

Wolf, Andreas; Kreckel, H; Lammich, L; Strasser, D; Mikosch, J; Glosík, J; Plasil, R; Altevogt, S; Andrianarijaona, V; Buhr, H; Hoffmann, J; Lestinsky, M; Nevo, I; Novotny, S; Orlov, D A; Pedersen, H B; Terekhov, A S; Toker, J; Wester, R; Gerlich, D; Schwalm, D; Zajfman, D

2006-11-15

80

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

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

Nuclear collision processes around the Bragg peak in proton therapy  

Microsoft Academic Search

In the physical processes of proton interaction in bio-materials, most of the proton energy is transferred to electrons. Ionization\\u000a and excitation occur most frequently around the Bragg peak region, where nuclear reactions also exist. In this study, we investigated\\u000a the processes of energy deposition by considering interactions including the nuclear reactions between protons and water molecules\\u000a by a Monte Carlo

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

2010-01-01

83

Absorption measurements of alkali-metal resonance lines broadened by He and molecular hydrogen collisions  

NASA Astrophysics Data System (ADS)

The optical and near-infrared spectroscopic observations of cool brown dwarfs exhibit very prominent signatures of sodium and potassium resonance lines. The atmospheres of these objects are mainly composed of molecular hydrogen and helium and the collisions of these species with the alkali-metal atoms induce broadening of the K and Na resonance lines by as much as 100 nm either side of the line core. Particularly important are the far line wings, where satellite features which are usually very temperature-sensitive may appear due to extrema in the difference potentials. These features are highly sensitive to pressure and temperature, whereas their position and shape depend critically on the details in the interaction potentials. Accurate line profiles can serve as valuable diagnostics of the physical characteristics of brown dwarfs and extrasolar giant planets. Experimental determinations of the far wings are indispensable in validating the theoretical models. We report here our measurements of the absorption coefficients for pressure broadening in the far wings of the 4s-4p and 4s-5p doublet lines of potassium atoms in the presence of helium and hydrogen gas at temperatures around 900 K. Supported in part by NASA grant NNG06GF06G.

Shindo, F.; Babb, J.; Kirby, K.

2007-06-01

84

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

85

On a Qualitative Difference between the Dynamics of Particle Production in Soft and Hard Processes of High Energy Collisions  

E-print Network

The qualitative difference between the anomalous scaling properties of hadronic final states in soft and hard processes of high energy collisions is studied in some detail. It is pointed out that the experimental data of e^+e^- collisions at $E_{cm}=$91.2 GeV from DELPHI indicate that the dynamical fluctuations in e^+e^- collisions are isotropical, in contrast to the anisotropical fluctuations oberserved in hadron-hadron collision experiments. This assertion is confirmed by the Monte Carlo simulation using the Jetset7.4 event generator.

Liu Feng; Liu Fuming; Liu Lianshou

1998-12-10

86

Molecular structure based estimation of properties for process design  

Microsoft Academic Search

This paper presents an analysis of molecular structure based methods for estimation of properties from a process\\/product design point of view. Properties are classified as primary (dependent only on the molecular structure) and secondary (dependent on the molecular structure and other variables\\/properties). Estimation methods are classified as “reference” (accurate but computationally expensive) and “approximate” (limited application range but computationally simple).

Rafiqul Gani; Leonidas Constantinou

1996-01-01

87

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 to recycle hydrogen, and how to remove heat from the plasma. Cooling is required both to extract heat to run transfer, hydrogen and impurity radiation, ionization, and elastic collisions between the recycling gas

88

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

NASA Astrophysics Data System (ADS)

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

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

2004-11-01

89

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.

90

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

SciTech Connect

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

Crandall, D.H.

1982-01-01

91

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

92

Lepton-Pair Production in Relativistic Ion Collisions and Its Correspondence to the Crossing Process  

SciTech Connect

Using the Sudakov technique, we sum the perturbation series for the process 3 {yields} 3 and obtain the compact analytical expression for the amplitude of this process, which takes into account all possible Coulomb interactions between colliding particles. Comparing it to the amplitude of the lepton-pair production in heavy-ion collisions, i.e., in the process 2 {yields} 4, we show that the amplitudes obtained in the high-energy limit lose the crossing-symmetry property (which holds only on the Born level)

Bartos, E. [Department of Theoretical Physics, Comenius University, Bratislava (Slovakia); Gevorkyan, S.R. [Yerevan Physics Institute, Yerevan (Armenia); Kuraev, E.A. [Joint Institute for Nuclear Research, Dubna, Moscow oblast, 141980 (Russian Federation)

2004-10-01

93

The kinetic one-dimensional equation with frequency of collisions, affine depending on the module molecular velocity  

E-print Network

The one-dimensional kinetic equation with integral of collisions type BGK (Bhatnagar, Gross and Krook) and frequency of collisions affine depending on the module of molecular velocity is constructed. Laws of preservation of number of particles, momentum and energy at construction equation are used. Separation of variables leads to the characteristic equation. The system of the dispersion equations is entered. Its determinant is called as dispersion function. It is investigated continuous and discrete spectra of the characteristic equation. The set of zero of the dispersion equation makes the discrete spectrum of the characteristic equation. The eigen solutions of the kinetic equation corresponding to discrete spectrum are found. The solution of the characteristic equation in space of the generalized functions leads to eigen functions corresponding to the continuous spectrum. Results of the spent analysis in the form of the theorem about structure of the general solution of the entered kinetic equation are formulated.

A. L. Bugrimov; A. V. Latyshev; A. A. Yushkanov

2014-03-09

94

Molecular dynamics simulations of collision-induced desorption. I. Low coverage N2 on Ru,,001...  

E-print Network

by the details of the corrugation of the Ru­N2 PES. It is concluded that the simple hard cube­hard sphere model of the collider. It is predicted that half of the collision energy is transferred to the solid and the other half and temperature conditions ex- pose adsorbates on solid surfaces to collisions with gas at- oms and molecules

Asscher, Micha

95

Theoretical investigation of the electron capture and loss processes in the collisions of He2+ + Ne.  

PubMed

Based on the time-dependent density functional theory, a method is developed to study ion-atom collision dynamics, which self-consistently couples the quantum mechanical description of electron dynamics with the classical treatment of the ion motion. Employing real-time and real-space method, the coordinate space translation technique is introduced to allow one to focus on the region of target or projectile depending on the actual concerned process. The benchmark calculations are performed for the collisions of He(2+) + Ne, and the time evolution of electron density distribution is monitored, which provides interesting details of the interaction dynamics between the electrons and ion cores. The cross sections of single and many electron capture and loss have been calculated in the energy range of 1-1000 keV/amu, and the results show a good agreement with the available experiments over a wide range of impact energies. PMID:24007011

Hong, Xuhai; Wang, Feng; Jiao, Yalong; Su, Wenyong; Wang, Jianguo; Gou, Bingcong

2013-08-28

96

H(D) -> D(H) + Cu(111) collision system: Molecular dynamics study of surface temperature effects  

PubMed Central

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London–Eyring–Polanyi–Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. PMID:21528959

Vurdu, Can D.; Guvenc, Ziya B.

2011-01-01

97

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

98

Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions  

NASA Technical Reports Server (NTRS)

The quantum mechanical problem of reactive or nonreactive scattering of atoms and molecules is formulated in terms of square-integrable basis sets with variational expressions for the reactance matrix. Several formulations involving expansions of the wave function (the Schwinger variational principle) or amplitude density (a generalization of the Newton variational principle), single-channel or multichannel distortion potentials, and primitive or contracted basis functions are presented and tested. The test results, for inelastic and reactive atom-diatom collisions, suggest that the methods may be useful for a variety of collision calculations and may allow the accurate quantal treatment of systems for which other available methods would be prohibitively expensive.

Schwenke, David W.; Haug, Kenneth; Zhao, Meishan; Truhlar, Donald G.; Sun, Yan

1988-01-01

99

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

100

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

101

Diffusion ionization of the Rydberg diatomic quasi-molecular complex formed upon collisions of rubidium atoms  

Microsoft Academic Search

The problem of impact ionization of two Rb atoms, one of which belongs to the Rydberg P series and the other of which is in the ground state, is studied and solved with the use of the methods of stochastic dynamics\\u000a for description of the path instability of a Rydberg electron in a collision diatomic complex. The actual potential of

N. N. Bezuglov; V. M. Borodin; V. Grushevskii; A. N. Klyucharev; K. Michulis; F. Fuzo; M. Allegrini

2003-01-01

102

Correlated detection of neutral and charged fragments in collision induced fragmentation of molecular clusters  

E-print Network

the dissociation of protonated water clusters at 8keV. I Collision Induced Dissociation of protonated hydrogen neutral and charged fragments. This work focuses on the dissociation induced by collisional excitation of protonated hydrogen clusters at 60keV/amu with helium targets and that of protonated water clusters at 8ke

Paris-Sud XI, Université de

103

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

E-print Network

excitation is the main mechanism in CID at kiloelectronvolt incident energy. Vibrational excitation also was the dominant excitation mechanism at kiloelectronvolt translational energy and that vibrational excitation via mechanism, i.e., vibrational excitation dominating at low collision energy and electronic excitation at high

Kim, Myung Soo

104

Molecular Thermodynamics for Chemical Process Design  

ERIC Educational Resources Information Center

Discusses that aspect of thermodynamics which is particularly important in chemical process design: the calculation of the equilibrium properties of fluid mixtures, especially as required in phase-separation operations. (MLH)

Prausnitz, J. M.

1976-01-01

105

Double Electron Processes in Low Energy Isotope Bare Ions 13C6+ with Helium Collisions  

NASA Astrophysics Data System (ADS)

The isotopic bare ion 13C6+ was employed to collide with helium at 4.15-11.08 keV/u. The relative partial cross sections were measured by position-sensitive and time-of-flight coincident techniques. It is shown that the direct-ionization (DI) process can be completely ignored in this region, the transfer ionization (TI) process is the most important double-electron channel, and the probability of the pure double-electron capture (DC) process is quite small. The cross-section ratio of the total double-electron (DE) process (i.e. DC+TI) to the single-electron capture (SC) process is experimentally determined to be approximately a constant of 0.09±0.03 in this region, and this value is obviously smaller than the predictions of the classical over-barrier models and the semi-empirical scaling laws. It is found that the cross-section ratio of pure DC to DE decreases obviously as the projectile velocity increases. Because the pure DC process only comes from the radiation de-excitation following the DC process and are competed by the TI process (comes from the auto-ionization following the DC process), this implies that the population of the two captured electrons depends distinctly on the collision velocity. Comparison with works on Ar16+-He by Wu et al. [Phys. Rev. A 48 (1993) 3617] reveals that the strong projectile-dependent character of the pure DC process exists.

Yu, De-Yang; Cai, Xiao-Hong; Lu, Rong-Chun; Shao, Cao-Jie; Lu, Jun; Ruan, Fang-Fang; Zhang, Hong-Qiang; Cui, Ying; Xu, Xu; Shao, Jian-Xiong; Ding, Bao-Wei; Yang, Zhi-Hu; Chen, Xi-Meng

2005-06-01

106

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

E-print Network

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. Futhermore, 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$^\\circ$. Distinct structures observed in the cross sections gauge the quality of recent \\emph{ab initio} potential energy surfaces for NO-rare gas atom collisions with unprecedented precision.

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

2014-01-01

107

SPH simulations of clumps formation by dissipative collision of molecular clouds. I. Non magnetic case  

Microsoft Academic Search

Computer experiments of interstellar cloud collisions were performed with a new smoothed-particle-hydrodynamics (SPH) code. The SPH quantities were calculated by using spatially adaptive smoothing lengths and the SPH fluid equations of motion were solved by means of a hierarchical multiple time-scale leapfrog. Such a combination of methods allows the code to deal with a large range of hydrodynamic quantities. A

E. P. Marinho; J. R. D. Lépine

2000-01-01

108

Dissociation in molecule-surface collisions  

Microsoft Academic Search

Dissociation at surfaces is a very important process, both scientifically and technologically. Dissociative chemisorption of molecules impinging at surfaces with thermal energies forms the basis of many processes, like catalysis. In thermal collisions it is evident that the kinetic energy of the impinging molecules is insufficient to break the molecular bond. Electronic processes occurring in the close proximity of the

A. W. Kleyn

1992-01-01

109

Pulsed laser ranging techniques based on digital signal processing methods for automobile anti-collision application  

NASA Astrophysics Data System (ADS)

A 1.55 µm digital laser radar system is designed and implemented for automobile anti-collision application. In order to reduce the influence of foggy, rainy and snowy weather on laser detection, digital signal processing methods are adopted. Multi-pulse coherent average algorithm is used to improve the signal-to-noise ratio of echo by N times. The correlation detection algorithm is adopted to estimate the time-of-flight. Multi-time delayed correlating method is used to improve the time-of-flight estimation resolution. Experimental results indicate that the digital signal processing methods in this paper can reduce the influence of bad weather conditions, and obtain high range accuracy.

Sun, Zhihui; Deng, Jiahao

2008-12-01

110

Molecular determinants of human prorenin processing.  

PubMed

In humans, active renin is generated by the removal of a 43-amino acid prosegment from the zymogen prorenin. This cleavage event is highly specific, occurring at only one of the seven pairs of basic amino acids in the body of preprorenin. This cleavage site selectivity is also displayed by a number of other proteases in vitro and in mouse pituitary AtT-20 cells transfected with a human preprorenin expression vector, suggesting that specificity of cleavage is directed in part by the primary sequence, the higher order structure, or both of prorenin itself. To test this hypothesis, single amino acid mutations were introduced in the region of human preprorenin surrounding the natural cleavage site, and the resultant recombinant proteins were expressed in cultured Chinese hamster ovary and AtT-20 cells. The results suggest that amino acids in addition to the pair of basic amino acids surrounding the cleavage site affect the ability of both trypsin and the endogenous AtT-20 processing enzyme to cleave prorenin. Notably, although a proline at position -4 is essential for processing of prorenin in AtT-20 cells and is correlated with predicted formation of a beta-turn at this position, site-directed mutations suggest that this structural feature in addition to a pair of basic amino acids is not sufficient to lead to proteolytic activation of prorenin. Displacement of sequences surrounding the cleavage site to a position 10 amino acids toward the amino terminus led to partial processing of a mutated prorenin.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1452293

Chu, W N; Mercure, C; Baxter, J D; Reudelhuber, T L

1992-12-01

111

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

112

Star Formation in Disk Galaxies. I. Formation and Evolution of Giant Molecular Clouds via Gravitational Instability and Cloud Collisions  

E-print Network

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 3D adaptive mesh refinement (AMR) numerical simulations that follow both the global evolution on scales of ~20kpc and resolve down to scales ~=100cm^-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 ~140Myr a large fraction of the gas in the disk has fragmented into clouds with masses ~10^6 Msun 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, ~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.

Elizabeth J. Tasker; Jonathan C. Tan

2008-11-03

113

New process observed in collisions between highly charged protonated protein and Xe8+ Xe5+ He2+ ions  

NASA Astrophysics Data System (ADS)

Electron multicapture processes have been studied in collisions between cytochrome C protein and highly charged Xe and He projectile at keV kinetic energy range. In competition with single and double electron capture, a new and unexpected channel attributed to deprotonation process of the protein has been observed.

Martin, S.; Chen, L.; Brédy, R.; Vernier, A.; Dugourd, P.; Antoine, R.; Ortéga, C.; Ji, M.; Bernard, J.; Gonzalez Maganad, O.; Reitsma, G.; Schlathölter, T.

2014-04-01

114

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

NASA Technical Reports Server (NTRS)

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.

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

1990-01-01

115

Atom—Diatom Collision Processes: Rovibrationally Detailed Cross Sections For Models  

NASA Astrophysics Data System (ADS)

Atom-diatomic molecule collision processes are of particular importance in nonequilibrium numerical models in which rovibrational energy exchange and state-selected dissociation are taken into account by means of rate coefficients. If also translational nonequilibrium is considered, availability of large sets of cross sections is needed. To cope with this issue extended quasiclassical calculations have been performed to obtain translational energy dependent detailed data for hydrogen, nitrogen and oxygen, with particular attention devoted to computational optimization. Problems related to huge memory requirements of large cross section sets when used in numerical models can be effectively solved with an interpolation method proposed by the author, which seems to reach an optimal compromise between accuracy and amount of data storage required. Comparisons with literature are, when available, globally good. An important issue about the exclusion of rotational distribution in both vibrational energy exchange and dissociation rate coefficients is stressed. Rotational distribution can significantly change dynamical results, with obvious consequences in their applications to models, independently of its explicit or implicit consideration into models. Concerning collision induced dissociation/recombination dynamics, a strong rotational dependence is shown using two different mechanisms in the case of hydrogen.

Esposito, Fabrizio

2011-05-01

116

Dynamical dipole gamma radiation in heavy-ion collisions on the basis of a quantum molecular dynamics model  

SciTech Connect

Dynamical dipole gamma-ray emission in heavy-ion collisions is explored in the framework of the quantum molecular dynamics model. The studies are focused on systems of {sup 40}Ca bombarding {sup 48}Ca and its isotopes at different incident energies and impact parameters. Yields of gamma rays are calculated and the centroid energy and dynamical dipole emission width of the gamma spectra are extracted to investigate the properties of gamma emission. In addition, sensitivities of dynamical dipole gamma-ray emission to the isospin and the symmetry energy coefficient of the equation of state are studied. The results show that detailed study of dynamical dipole gamma radiation can provide information on the equation of state and the symmetry energy around the normal nuclear density.

Wu, H. L. [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100080 (China); Tian, W. D.; Ma, Y. G.; Cai, X. Z.; Chen, J. G.; Fang, D. Q.; Guo, W.; Wang, H. W. [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800 (China)

2010-04-15

117

Multiple electron transfer processes in collisions of N{sup 6+} and O{sup 7+} with methane  

SciTech Connect

Recent experiments on collision processes of O{sup 7+} and N{sup 6+} ions colliding with methane at the same velocity show unexpected differences in the fragmentation cross sections of the methane. Despite the expected similarity of these two processes, as both projectiles are hydrogenic, the mechanisms of electron transfer are different and lead to different fragmentation cross sections. In the present work, the collisions between N{sup 6+} and O{sup 7+} ions and methane are investigated theoretically at equal velocities corresponding to projectile energies of 30 and 35 keV, respectively. Electron-nuclear dynamics is used to study multiple electron transfer processes occurring in these collisions. Several multiple charge transfer probabilities are calculated and results, averaged over various orientations of the methane molecule, are reported. The collisions proceed in two stages: a fast stage of electron transfer from methane to the ion, and a much slower stage of breakup of the methane. We find and explain the intuitively unexpected result that the total charge transfer cross section for N{sup 6+} is slightly larger, but that the O{sup 7+} leaves the methane in a higher charged state with higher probability, leading to more fragmentation in the collisions with O{sup 7+}.

Guevara, N. L.; Teixeira, E.; Hall, B.; Deumens, E.; Oehrn, Y.; Sabin, J. R. [Quantum Theory Project, Department of Chemistry and Physics, University of Florida, Gainesville, Florida 32611-8435 (United States)

2009-12-15

118

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

119

A molecular dynamics simulation of the destruction of explosive molecules at high-velocity collisions  

Microsoft Academic Search

The infrared spectra and the energies of dissociation of R-NO2 bonds (R?C, N, and O) were calculated for explosive molecules (trinitrotoluene, hexogen, octogen, pentaerythrityl tetranitrate,\\u000a triaminotrinitrobenzene, and nitromethane). The time of kinetic energy redistribution over intramolecular vibrational modes\\u000a for these molecules (the V-V relaxation time) was calculated by the molecular dynamics simulation method. Molecular dynamics simulations were also used\\u000a to

A. A. Selezenev; A. Yu. Aleinikov; I. V. Briginas

2008-01-01

120

Nuclear de-excitation processes following medium energy heavy ion collisions  

SciTech Connect

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

Blann, M.

1986-09-01

121

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

NASA Astrophysics Data System (ADS)

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

Parsons, Neal; Levin, Deborah A.

2014-10-01

122

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

123

Molecular Evolution across the Asteraceae: Micro-and Macroevolutionary Processes  

E-print Network

in the fossil record (Gould and Eldridge 1977), key developmental innovations (Erwin 1999), and higher level microevolutionary changes would easily qualify as ``punctuations'' in the fossil record (CharlesworMolecular Evolution across the Asteraceae: Micro- and Macroevolutionary Processes Nolan C. Kane,*,1

Rieseberg, Loren

124

Nuclear and Molecular Processes in Muon-Catalyzed Fusion  

Microsoft Academic Search

The dt-alpha n continuum in the presence of the muon is studied in detail, and it is shown that the existence of extended continuum states just beneath the d + (tmu) _{1s} threshold can lead to a variety of 'pseudoresonant' fusion processes with a temperature and density dependence distinct from those leading to molecular formation. Various in-flight and pseudoresonant fusion

David Harley

1991-01-01

125

Processing of microcellular foams from polybenzobisthiazole\\/polyetherketoneketone molecular composites  

Microsoft Academic Search

This manuscript presents the results of a research project dealing with the processing of microcellular foams from molecular composites. The main goal of this work is the preparation, characterization, and evaluation of polymer-based foams. A variety of thermoplastic polymers have been evaluated with regard to the extent to which they can be formed into monolithic foams, and methods have been

S. C. Tan; Z. Bai; H. Sun; J. E. Mark; F. E. Arnold; C. Y.-C. Lee

2003-01-01

126

Unified description of transverse momentum spectrums contributed by soft and hard processes in high-energy nuclear collisions  

NASA Astrophysics Data System (ADS)

The transverse momentum spectrums of ? -, ? +, K -, K +, , and p produced in p-Pb collisions at ? s NN = 502 TeV measured by the CMS Collaboration and in Pb-Pb collisions at ? s NN = 2.76 TeV measured by the ALICE Collaboration are described by a two-component Erlang distribution. The first component corresponds to "soft" excitation process and contributes in the low transverse momentum region, which is contributed by 2-5 partons (sea quarks and gluons) with strong interactions. The second component corresponds to "hard" scattering process and contributes in the high transverse momentum region, which is contributed by 2 partons (valent quarks) with violent head-on collision. Each parton source contributes an exponential transverse momentum spectrum. Both the soft and hard processes result in an Erlang distribution. The transverse momentum spectrums of final-state charged particles are then described by the two-component Erlang distribution. The contribution ratio (30-40%) of the hard process extracted from nuclear collisions at the Large Hadron Collider is consistent with that (17-46%) obtained from other methods.

Liu, Fu-Hu; Gao, Ya-Qin; Tian, Tian; Li, Bao-Chun

2014-06-01

127

Processing of Collision Data to Support Efficient Diagnosis of Concussion in Sports Athletes  

Microsoft Academic Search

Collision\\/Contact sports persons, particularly football and hockey players are involved in very high impact collisions during play. The player may be subjected to Concussion a medical term related to the disturbance in the brain function following a blow to head or a violent impact. This Concussion may result in to Mild Traumatic Brain Injury (MTBI). Often it is difficult to

Dayananda Suratkal

2012-01-01

128

Stability of nuclei in peripheral collisions in the JAERI quantum molecular dynamics model  

SciTech Connect

The JAERI quantum molecular dynamics (JQMD) model has been successfully used for a long time now to describe many different aspects of nuclear reactions in a unified way. In some cases, however, the JQMD model cannot produce consistent results: First, it lacks a fully relativistically covariant approach to the problem of molecular dynamics; second, the quantum-mechanical ground state of nuclei cannot be faithfully reproduced in a semiclassical framework. Therefore, we introduce R-JQMD, an improved version of JQMD that also features a new ground-state initialization algorithm for nuclei. We compare the structure of the two codes and discuss whether R-JQMD can be adjusted to improve JQMD's agreement with measured heavy-ion fragmentation cross sections.

Mancusi, Davide; Niita, Koji; Maruyama, Tomoyuki; Sihver, Lembit [Nuclear Engineering, Applied Physics, Chalmers University of Technology, Gothenburg (Sweden); Research Organization for Information Science and Technology, Tokai-mura (Japan); College of Bioresource, Nihon Unniversity, Fujisawa (Japan); Nuclear Engineering, Applied Physics, Chalmers University of Technology, Gothenburg, Sweden and Department of Mathematics, Computer Science and Physics, Roanoke College, Salem, Virginia (United States)

2009-01-15

129

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

130

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

131

TCP (truncated Compound Poisson) Process for Multiplicity Distributions in High Energy Collisions  

NASA Astrophysics Data System (ADS)

On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, we obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The TCP curves are narrower than NB at high multiplicity tail, look narrower at very high energy and develop shoulders and oscillations which become increasingly pronounced as the energy grows. At lower energies the curves are very close to the NB ones. We also compare the parametrizations, by these two distributions, of the data for fixed intervals of rapidity for UA5 data and for the data (at low energy) for e+e- annihilation and pion-proton, proton-proton and muon-proton scattering. A discussion of compound Poisson distribution, expressions of reduced moments and Poisson transforms are also given. The TCP curves and curves of the reduced moments for different values of the parameters are also presented.

Srivastava, Prem P.

132

TCP (truncated compound Poisson) process for multiplicity distributions in high energy collisions  

SciTech Connect

On using the Poisson distribution truncated at zero for intermediate cluster decay in a compound Poisson process, the authors obtain TCP distribution which describes quite well the multiplicity distributions in high energy collisions. A detailed comparison is made between TCP and NB for UA5 data. The reduced moments up to the fifth agree very well with the observed ones. The TCP curves are narrower than NB at high multiplicity tail, look narrower at very high energy and develop shoulders and oscillations which become increasingly pronounced as the energy grows. At lower energies the distributions, of the data for fixed intervals of rapidity for UA5 data and for the data (at low energy) for e{sup +}e{sup {minus}} annihilation and pion-proton, proton-proton and muon-proton scattering. A discussion of compound Poisson distribution, expression of reduced moments and Poisson transforms are also given. The TCP curves and curves of the reduced moments for different values of the parameters are also presented.

Srivastave, P.P. (International Centre for Theoretical Physics, Trieste (IT))

1990-02-20

133

Charge-changing processes in collisions of heavy many-electron ions with neutral atoms  

NASA Astrophysics Data System (ADS)

Some features of charge-changing processes, namely, electron capture (EC) and electron loss (EL), are considered for heavy many-electron ions colliding with neutral atoms in a wide range of ion energy E = 10 keV/u-100 GeV/u. The discussion is based on cross-section calculations performed by available computer codes, namely, CAPTURE, DEPOSIT and RICODE. The RICODE (Relativistic Ionization CODE), which provides calculation of single-electron loss cross sections in the relativistic energy regime, was recently created on the basis of the relativistic Born approximation and is described in the Appendix A. In addition, a semi-empirical formula for single-electron loss cross sections is suggested based on properties of the Born approximation and numerical calculations by the RICODE program. To cover also the low and intermediate collision energies, EL cross sections are obtained by the recently created DEPOSIT code which provides calculation of single- and multiple-electron as well as the total cross sections. Based on the results obtained by these codes, recommended capture and loss cross sections for heavy ions like xenon, uranium and lead ions colliding with neutral atoms are presented over a wide energy range.

Shevelko, V. P.; Beigman, I. L.; Litsarev, M. S.; Tawara, H.; Tolstikhina, I. Yu.; Weber, G.

2011-06-01

134

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

SciTech Connect

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

Ayik, S.

1992-02-01

135

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

PubMed

The dissociative electron transfer from He into 10 keV H2+ was measured in a kinematically complete experiment by using the cold target recoil ion momentum spectroscopy imaging technique in combination with a highly resolving molecular fragment imaging technique. The electron transfer into the dissociative b(3)Sigma+_(u) state of H2 could be selected by kinematic conditions. We find a striking double slit interference pattern in the transverse momentum transfer which we can modify by selecting different internuclear distances. Compared to an optical double slit, interference minima and maxima are interchanged. The latter is the result of a phase shift in the electronic part of the wave function. PMID:18999747

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

2008-10-24

136

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

137

Multiple ionization and excitation processes in single ion-atom collisions  

SciTech Connect

Several experimental methods are discussed, which, by relying on intentionally imposed restrictions such as coincidence requirements and/or special detection geometries, permit measurements differential in several important collision parameters. Such multiply differential measurements are necessary for the isolation of particular excitation and ionization mechanisms and provide much more stringent tests of existing theories. Emphasis is on single collision phenomena involving primarily heavy ions at velocities comparable to K-shell velocities. (GHT)

Elston, S.B.

1980-01-01

138

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

139

Collision processes of C2,3Hy and C2,3Hy+ hydrocarbons with electrons and protons  

NASA Astrophysics Data System (ADS)

Cross sections and rate coefficients are provided for inelastic collision processes of electrons and protons with CxHy and CxHy+ (x=2,3; 1?y?2x+2) hydrocarbon species in a wide range of collision energies and plasma (gas) temperatures. The considered processes include electron-impact ionization and dissociation of CxHy, dissociative excitation, ionization and recombination of CxHy+ with electrons, and both charge transfer and atom exchange in proton channels are considered separately. The presented cross sections are based upon a critical assessment of available experimental data and upon an extensive use of a number of semi-empirical, physically well grounded cross section scaling relationships. Information is also provided for the energetics of each individual reaction channel. The cross sections and rate coefficients are presented in compact analytic forms.

Janev, R. K.; Reiter, D.

2004-02-01

140

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

141

Process for attaching molecular wires and devices to carbon nanotubes and compositions thereof  

NASA Technical Reports Server (NTRS)

The present invention is directed towards processes for covalently attaching molecular wires and molecular electronic devices to carbon nanotubes and compositions thereof. Such processes utilize diazonium chemistry to bring about this marriage of wire-like nanotubes with molecular wires and molecular electronic devices.

Tour, James M. (Inventor); Bahr, Jeffrey L. (Inventor); Yang, Jiping (Inventor)

2008-01-01

142

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

143

Numerical simulation for polymer solutions based on a hybrid computation of multi-particle collision dynamics and coarse-grained molecular dynamics  

NASA Astrophysics Data System (ADS)

Numerical simulation of the flow-induced structure of complex fluids is an important issue in the flow analysis of complex fluids. Several schemes have been proposed for coupling the macro flow computation and the micro simulation of the inner structure of complex fluids. The present study proposed a numerical model based on a hybrid computation of multi particle collision dynamics (MPCD) and coarse-grained molecular dynamics (MD). The present model can easily treat hydrodynamic interactions among polymers, which play an important role in the dynamics of polymers in non-dilute solutions. In the MPCD, a solvent is represented by point-like particles (solvent particles) that move with a continuous distribution of velocities. The MPCD algorithm consists of a streaming step and a collision step. A scheme based on the MPC-AT+a algorithm for the collision step was adopted in the present simulation. Furthermore polymers were modeled by elastic dumbbells. The movement of beads of the dumbbells was computed using a coarse-grained MD, and the interaction among beads and solvent particles were considered in the collision step. Numerical simulations of shear flows were performed to analyze the dynamics of linear polymers. The numerical results agree well with both experimental results and predictions by other numerical methods.

Yamamoto, Takehiro; Masaoka, Norichika

2014-05-01

144

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

145

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

146

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

147

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

148

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

SciTech Connect

Atomic collision processes associated with surface production of negative hydrogen ions (H{sup -}) by particle reflection at molybdenum surface immersed in hydrogen plasma have been investigated. To calculate sputtering yields of Cs, as well as energy spectra and angular distributions of reflected hydrogen atoms from molybdenum surface by H{sup +} ion and Cs{sup +} ion bombardments, a Monte Carlo simulation code ACAT (Atomic Collision in Amorphous Target) was run with the corresponding surface conditions. A fractal surface model has been developed and adopted to ACAT for evaluating the effect due to roughness of target material. The results obtained with ACAT have indicated that the retention of hydrogen atoms leads to the reduction in sputtering yields of Cs, and the surface roughness does largely affect the sputtering yields of Cs.

Kenmotsu, T.; Wada, M. [Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394 (Japan)

2012-02-15

149

Cosmic Collision  

NSDL National Science Digital Library

This Hubblesite website provides two movies about galaxy collisions. The first movie called "Cosmic Collision" details the collision of the Milky Way and the Andromeda galaxy. The second movie, "Striking Encounters", discusses the dynamics of galaxy collisions.

Space Telescope Science Institute, Formal E.; Administration, National A.

2005-04-27

150

Charge transfer processes: the role of optimized molecular orbitals.  

PubMed

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

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

2014-08-01

151

A compound poisson process for relaxing the molecular clock.  

PubMed

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages. PMID:10747076

Huelsenbeck, J P; Larget, B; Swofford, D

2000-04-01

152

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

153

Systematic Investigation of Negative Cooper-Frye Contributions in Heavy Ion Collisions Using Coarse-grained Molecular Dynamics  

E-print Network

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 $E_{\\rm lab} = 5$--$160A$ 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 i...

Oliinychenko, D; Petersen, H

2014-01-01

154

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

SciTech Connect

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

Torii, K.; Enokiya, R.; Sano, H.; Yoshiike, S.; Hanaoka, N.; Ohama, A.; Furukawa, N.; Dawson, J. R.; Moribe, N.; Oishi, K.; Nakashima, Y.; Okuda, T.; Yamamoto, H.; Kawamura, A.; Mizuno, N.; Onishi, T.; Fukui, Y. [Department of Physics and Astrophysics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Maezawa, H. [Department of Astrophysics, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan); Mizuno, A., E-mail: torii@a.phys.nagoya-u.ac.jp [Solar-Terrestrial Environment Laboratory, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan)

2011-09-01

155

Progress in stored ion beam experiments on atomic and molecular processes  

NASA Astrophysics Data System (ADS)

Stored fast ion beams in atomic and molecular collision experiments are discussed with an emphasis on electron ion interactions at low relative energies. Recent progress was obtained in electron collision spectroscopy using an electron-cooled stored ion beam and a separate electron target in the same storage ring; from a cryogenic photocathode, electron beams with internal temperatures of 5 to 10 K were produced. Results are presented for dielectronic recombination resonances, resolving the hyperfine structure of stored lithiumlike scandium ions and obtaining precise results for the fine structure splitting of these ions, and for ro-vibrational resonances in the recombination of electrons with hydrogen molecular ions, revealing sharp structures down to 2 meV. An overview of the cryogenic storage ring (CSR) project in Heidelberg is given.

Wolf, Andreas; Buhr, Henrik; Grieser, Manfred; von Hahn, Robert; Lestinsky, Michael; Lindroth, Eva; Orlov, Dmitry A.; Schippers, Stefan; Schneider, Ioan F.

2006-09-01

156

Progress in stored ion beam experiments on atomic and molecular processes  

NASA Astrophysics Data System (ADS)

Stored fast ion beams in atomic and molecular collision experiments are discussed with an emphasis on electron-ion interactions at low relative energies. Recent progress was obtained in electron collision spectroscopy using an electron-cooled stored ion beam and a separate electron target in the same storage ring; from a cryogenic photocathode, electron beams with internal temperatures of 5 to 10 K were produced. Results are presented for dielectronic recombination resonances, resolving the hyperfine structure of stored lithiumlike scandium ions and obtaining precise results for the fine structure splitting of these ions, and for ro-vibrational resonances in the recombination of electrons with hydrogen molecular ions, revealing sharp structures down to 2 meV. An overview of the cryogenic storage ring (CSR) project in Heidelberg is given.

Wolf, Andreas; Buhr, Henrik; Grieser, Manfred; von Hahn, Robert; Lestinsky, Michael; Orlov, Dmitry A.; Lindroth, Eva; Schneider, Ioan F.; Schippers, Stefan

157

Coordinate space translation technique for simulation of electronic process in the ion-atom collision  

NASA Astrophysics Data System (ADS)

Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lüdde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O(3P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results.

Wang, Feng; Hong, Xuhai; Wang, Jian; Kim, Kwang S.

2011-04-01

158

Coordinate space translation technique for simulation of electronic process in the ion-atom collision.  

PubMed

Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lu?dde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O((3)P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results. PMID:21513388

Wang, Feng; Hong, Xuhai; Wang, Jian; Kim, Kwang S

2011-04-21

159

Study of hard scattering processes in multihadron production from ?? collisions at LEP  

Microsoft Academic Search

The production of multihadronic states in ?? collisions at LEP has been studied with the DELPHI detector. The analyzed data correspond to an integrated luminosity of about 32pb-1, collected in the LEP runs of 1990–1992. Minimum bias data and a sample of events with jets at highpT have been selected under the requirement that no scattered electron or positron is

P. Abreu; W. Adam; T. Adye; E. Agasi; R. Aleksan; G. D. Alekseev; P. Allport; S. Almehed; F. M. L. Almeida Junior; S. J. Alvsvaag; U. Amaldi; A. Andreazza; P. Antilogus; W.-D. Apel; R. J. Apsimon; Y. Arnoud; B. Åsman; J.-E. Augustin; A. Augustinus; P. Baillon; P. Bambade; F. Barao; R. Barate; G. Barbiellini; D. Y. Bardin; G. J. Barker; A. Baroncelli; O. Barring; J. A. Barrio; W. Bartl; M. J. Bates; M. Battaglia; M. Baubillier; K.-H. Becks; M. Begalli; P. Beilliere; Yu. Belokopytov; P. Beltran; A. C. Benvenuti; M. Berggren; D. Bertrand; F. Bianchi; M. Bigi; M. S. Bilenky; P. Billoir; J. Bjarne; D. Bloch; J. Blocki; S. Blyth; V. Bocci; P. N. Bogolubov; T. Bolognese; M. Bonesini; W. Bonivento; P. S. L. Booth; G. Borisov; C. Bosio; B. Bostjancic; S. Bosworth; O. Botner; B. Bouquet; C. Bourdarios; T. J. V. Bowcock; M. Bozzo; S. Braibant; P. Branchini; K. D. Brand; R. A. Brenner; H. Briand; C. Bricman; L. Brillault; R. C. A. Brown; P. Bruckman; J.-M. Brunet; A. Budziak; L. Bugge; T. Buran; A. Buys; J. A. M. A. Buytaert; M. Caccia; M. Calvi; A. J. Camacho Rozas; R. Campion; T. Bamporesi; V. Canale; K. Cankocak; F. Cao; F. Carena; P. Carrilho; L. Carroll; R. Cases; M. V. Castillo Gimenez; A. Cattai; F. R. Cavallo; L. Cerrito; V. Chabaud; A. Chan; M. Chapkin; Ph. Charpentier; J. Chauveau; P. Checchia; G. A. Chelkov; L. Chevalier; P. Chliapnikov; V. Chorowicz; J. T. M. Chrin; V. Cindro; P. Collins; J. L. Contreras; R. Contri; E. Cortina; G. Cosme; F. Couchot; H. B. Crawley; D. Crennell; G. Crosetti; J. Cuevas Maestro; S. Czellar; E. Dahl-Jensen; J. Dahm; B. Dalmagne; M. Dam; G. Damgaard; G. Darbo; E. Daubie; A. Daum; P. D. Dauncey; M. Davenport; J. Davies; J. Da Silva; C. Defoix; P. Delpierre; N. Demaria; A. De Angelis; H. De Boeck; W. De Boer; S. De Brabandere; C. De Clerq; M. D. M. De Fez Laso; C. De La Vaissiere; B. De Lotto; A. De Min; L. De Paula; H. Dijkstra; L. Di Ciaccio; F. Djama; J. Dolbeau; M. Donszelmann; K. Doroba; M. Dracos; J. Drees; M. Dris; Y. Dufour; F. Dupont; D. Edsall; L.-O. Eek; R. Ehret; T. Ekelof; G. Ekspong; A. Elliot Peisert; M. Elsing; J.-P. Engel; N. Ershaidat; M. Espirito Santo; D. Fassouliotis; M. Feindt; A. Fenyuk; A. Ferrer; T. A. Filippas; A. Firestone; H. Foeth; E. Fokitis; F. Fontanelli; K. A. J. Forbes; F. Formenti; J.-L. Fousset; S. Francon; B. Franek; P. Frenkiel; D. C. Fries; A. G. Frodesen; R. Fruhwirth; F. Fulda-Quenzer; H. Furstenau; J. Fuster; D. Gamba; M. Gandelman; C. Garcia; J. Garcia; C. Gaspar; U. Gasparini; Ph. Gavillet; E. N. Gazis; J.-P. Gerber; P. Giacomelli; D. Gillespie; R. Gokieli; B. Golob; V. M. Golovatyuk; J. J. Gomez Y Cadenas; G. Gopal; L. Gorn; M. Gorski; V. Gracco; F. Grard; E. Graziani; G. Grosdidier; B. Grossetete; P. Gunnarsson; J. Guy; U. Haedinger; F. Hahn; M. Hahn; S. Hahn; S. Haider; Z. Hajduk; A. Hakansson; A. Hallgren; U. Hamacher; G. Hamel De Monchenault; W. Hao; F. J. Harris; V. Hedberg; R. Henriques; J. J. Hernandez; J. A. Hernando; P. Herquet; H. Herr; T. L. Hessing; C. O. Higgins; E. Higon; H. J. Hilke; T. S. Hill; S. D. Hodgson; T. Hofmokl; S.-O. Holmgren; P. J. Holt; D. Holthuizen; P. F. Honore; M. Houlden; K. Huet; K. Hultqvist; P. Ioannou; P.-S. Iversen; J. N. Jackson; R. Jacobsson; P. Jalocha; G. Jarlskog; P. Jarry; B. Jean-Marie; E. K. Johansson; M. Jonker; L. Jonsson; P. Juillot; M. Kaiser; G. Kalkanis; G. Kalmus; F. Kapusta; M. Karlsson; E. Karvelas; S. Katsanevas; E. C. Katsoufis; R. Keranen; B. A. Khomenko; N. N. Khovanski; B. King; N. J. Kjaer; H. Klein; A. Klovning; P. Kluit; A. Koch-Mehrin; J. H. Koehne; B. Koene; P. Kokkinias; M. Koratzinos; K. Korcyl; A. V. Korytov; V. Kostioukhine; C. Kourkoumelis; O. Kouznetsov; P. H. Kramer; M. Krammer; C. Kreuter; J. Krolikowski; I. Kronkvist; W. Krupinski; W. Kucewicz; K. Kulka; K. Kurvinen; C. Lacasta; C. Lambropoulos; J. W. Lamsa; L. Lanceri; P. Langefeld; V. Lapin; I. Last; J.-P. Laugier; R. Lauhakangas; G. Leder; F. Ledroit; R. Leitner; Y. Lemoigne; J. Lemonne; G. Lenzen; V. Lepeltier; J. M. Levy; E. Lieb; D. Liko; J. Lindgren; R. Lindner; A. Lipniacka; I. Lippi; B. Loerstad; M. Lokajicek; J. G. Loken; A. Lopez-Fernandez; M. A. Lopez Aguera; M. Los; D. Loukas; J. J. Lozano; P. Lutz; L. Lyons; G. Maehlum; J. Maillard; A. Maio; A. Maltezos; F. Mandl; J. Marco; B. Marechal; M. Margoni; J.-C. Marin; C. Mariotti; A. Markou; T. Maron; S. Marti; C. Martinez-Rivero; F. Martinez-Vidal; F. Matorras; C. Matteuzzi; G. Matthiae; M. Mazzucato; M. McCubbin; R. McKay; R. McNulty; J. Medbo; C. Meroni; W. T. Meyer; M. Michelotto; E. Migliore; I. Mikulec; L. Mirabito; W. A. Mitaroff; G. V. Mitselmakher; U. Mjoernmark; T. Moa; R. Moeller; K. Moenig; M. R. Monge; P. Morettini; H. Mueller; W. J. Murray; B. Muryn; G. Myatt; F. Naraghi; F. L. Navarria; P. Negri; S. Nemecek; W. Neumann; N. Neumeister; R. Nicolaidou; B. S. Nielsen; V. Nikolaenko

1994-01-01

160

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

161

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

NASA Astrophysics Data System (ADS)

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; Conte, Riccardo; Ceotto, Michele

2014-05-01

162

Radiative association processes to specific rovibrational levels in low-energy Na++Rb87 collisions  

NASA Astrophysics Data System (ADS)

The radiative association processes for Na+ colliding with Rb87(5s ) atoms have been investigated by using the quantum-mechanical method. The total and partial cross sections that associate to the specific rovibrational states are calculated rigorously in the energy range of 10-13-1.2×10-2eV. The association cross sections display rich resonance structures. The ratios of rotationally resolved cross sections to total association cross sections and the ratios of vibrationally resolved cross sections to rotationally resolved cross sections are calculated and presented. For energies less than 10-9eV, association to X2?+ (J=1) dominates over all other association states. As the energy increases, each resonance of the total cross sections is associated with the given angular component of specific bound states. In the energy range of 10-13-1.2×10-3eV, the vibrational states v=27 and v=28 are the most probable final states. The probability for the formation of molecular ion NaRb+ in the rovibrational states is discussed. The existence of Cooper minima in the radiative association cross sections is found and illustrated.

Yan, L. L.; Li, X. Y.; Wu, Y.; Wang, J. G.; Qu, Y. Z.

2014-09-01

163

Extracting dwell time sequences from processive molecular motor data.  

PubMed

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

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

2006-11-01

164

Extracting Dwell Time Sequences from Processive Molecular Motor Data  

PubMed Central

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

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

2006-01-01

165

Reply to ‘Comment on “Four-body charge transfer processes in proton helium collisions”’  

NASA Astrophysics Data System (ADS)

Houamer and Popov have performed a first Born approximation calculation (FBA) for TTE (charge transfer with target excitation) for 300 keV proton-helium collisions. Their results are in reasonable agreement with the absolute measurements of Schöffler (2006 PhD thesis, University of Frankfurt am Main) whereas our FBA results yielded the shape of the experimental data reasonably well (except for small scattering angles) but with a magnitude that was a factor of 144 larger than experiment. Consequently, Houamer and Popov conclude that our results must have huge numerical errors. We have extensively tested our codes and we do not find any evidence to support this claim.

Chowdhury, U.; Harris, A. L.; Peacher, J. L.; Madison, D. H.

2013-01-01

166

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

167

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

168

A Study of molecular cooling via Sisyphus processes  

E-print Network

We present a study of Sisyphus cooling of molecules: the scattering of a single-photon remove a substantial amount of the molecular kinetic energy and an optical pumping step allow to repeat the process. A review of the produced cold molecules so far indicates that the method can be implemented for most of them, making it a promising method able to produce a large sample of molecules at sub-mK temperature. Considerations of the required experimental parameters, for instance the laser power and linewidth or the trap anisotropy and dimensionality, are given. Rate equations, as well as scattering and dipolar forces, are solved using Kinetic Monte Carlo methods for several lasers and several levels. For NH molecules, such detailed simulation predicts a 1000-fold temperature reduction and an increase of the phase space density by a factor of 10^7 . Even in the case of molecules with both low Franck-Condon coefficients and a non-closed pumping scheme, 60% of trapped molecules can be cooled from 100 mK to sub-mK tem...

Comparat, Daniel

2014-01-01

169

Probing topcolor-assisted technicolor from lepton flavor violating processes in photon-photon collision at ILC  

E-print Network

In topcolor-assisted technicolor models (TC2) the hitherto unconstrained lepton flavor mixing induced by the new gauge boson $Z'$ will lead to the lepton flavor violating productions of $\\tau\\bar \\mu$, $\\tau\\bar e$ and $\\mu\\bar e$ in photon-photon collision at the proposed International Linear Collider (ILC). Through a comparative analysis of these processes, we find that the better channels to probe the TC2 is the production of $\\tau\\bar \\mu$ or $\\tau\\bar e$ which occurs at a much higher rate than $\\mu\\bar e$ production due to the large mixing angle and the large flavor changing coupling, and may reach the detectable level of the ILC for a large part of the parameter space. Since the rates predicted by the Standard Model are far below the detectable level, these processes may serve as a sensitive probe for the TC2 model.

Guo-Li Liu

2010-02-03

170

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

171

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

SciTech Connect

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

Ayik, S.

1993-02-01

172

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

SciTech Connect

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

Ayik, S.

1993-02-01

173

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

NASA Technical Reports Server (NTRS)

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

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

1981-01-01

174

Prediction of the energy dependence of molecular fragmentation cross sections for collisions of swift protons with ethane and acetylene  

SciTech Connect

We report the energy-dependent fragmentation cross sections for several of the more likely fragmentation channels for protons with up to 10 keV impact energy colliding with acetylene and ethane. We find that the predominant channels are those which involve the dissociation of a carbon-hydrogen bond, and we find that the cross sections for these channels are maximum in the low-projectile-energy region. The cross sections for fragmentation involving dissociation of a C-C bond are an order of magnitude smaller and peak at somewhat higher projectile energy. Although there are no experimental values with which to compare, it appears that selection of projectile energy can be used to influence branching ratios in proton-hydrocarbon collisions and, by implication, in other ion-molecule and atom-molecule collisions.

Cabrera-Trujillo, Remigio; Sabin, John R.; Deumens, Erik; Oehrn, Yngve [Departments of Physics and Chemistry, University of Florida, Gainesville, Florida 32611-8435 (United States)

2005-04-01

175

The B-spline R-matrix method for atomic processes: application to atomic structure, electron collisions and photoionization  

NASA Astrophysics Data System (ADS)

The basic ideas of the B-spline R-matrix (BSR) approach are reviewed, and the use of the method is illustrated with a variety of applications to atomic structure, electron-atom collisions and photo-induced processes. Special emphasis is placed on complex, open-shell targets, for which the method has proven very successful in reproducing, for example, a wealth of near-threshold resonance structures. Recent extensions to a fully relativistic framework and intermediate energies have allowed for an accurate treatment of heavy targets as well as a fully nonperturbative scheme for electron-impact ionization. Finally, field-free BSR Hamiltonian and electric dipole matrices can be employed in the time-dependent treatment of intense short-pulse laser-atom interactions.

Zatsarinny, Oleg; Bartschat, Klaus

2013-06-01

176

ATOMIC AND MOLECULAR PHYSICS: Transfer Ionization of Helium in Collisions with Cq+ and Oq+ (q = 1 3)  

Microsoft Academic Search

Cross-section ratios sigmaTI\\/sigmaSC of transfer ionization (TI) to single capture (SC) of Cq+- and Oq+-He (q = 1 - 3) collisions in the energy range of 15-440keV\\/u (0.8-4.2 vBohr) are experimentally determined. It is shown that sigmaTI\\/sigmaSC strongly depends on the projectile velocity, and there is a maximum for E(keV\\/u)\\/q1\\/2 ≈ 150. Combining the Bohr-Lindhard model and the statistical model,

Bao-Hong Wang; Hong-Bin Fu; Bao-Wei Ding; De-Yang Yu; Guang-Zhi Sun; Zhao-Yuan Liu

2008-01-01

177

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

NASA Astrophysics Data System (ADS)

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

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

2011-08-01

178

Driving ordering processes in molecular-dynamics simulations.  

PubMed

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. PMID:24877946

Dittmar, Harro; Kusalik, Peter G

2014-05-16

179

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

180

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

181

SelfSimilarity in Random Collision Processes Daniel benAvraham 1 , Eli BenNaim 2 , Katja Lindenberg 3 , and Alexandre Rosas 3  

E-print Network

Self­Similarity in Random Collision Processes Daniel ben­Avraham 1 , Eli Ben­Naim 2 , Katja and nonlocal equation # #t F (k, t) + F (k, t) = F (pk, t)F (qk, t). (3) This closed equation is amenable

Ben-Naim, Eli

182

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

NASA Astrophysics Data System (ADS)

Understanding exhumation processes of high to ultra-high pressure (HP to UHP) terrains during plate convergence is a major challenge for the comprehension of plate convergence processes and mountain building. Contemporaneous contraction and extension coupled with erosion are frequently proposed to drive the exhumation process. In the internal alpine belt, HP and UHP metamorphism are recorded both in the Piemont oceanic unit and in the continental units such as the Internal Crystalline Massifs and the Briançonnais zone. In the western Alps, the consensus is to relate the top to NW then W directed D1 thrusting phase to nappe stacking and exhumation of the HP to UHP units within a subduction channel. Although there is an agreement on the occurrence of a top to the east D2 tectonic phase, its significance in terms of shortening or extensional deformation is controversial. On one hand, top to the east D2 shear zones and associated folds are interpreted as backthrusts or backfolds active during the Oligocene syn-collisional shortening phase, post-dating the exhumation of the HP units. On the other hand, D2 structures are interpreted as top the east normal faults that are active during the exhumation of the HP unit within a subduction channel. To decipher between these two different interpretations, we conducted a combined structural, petrological and geochronological study of the Modane-Aussois area in order to build a PTtD path of the Briançonnais zone. The current construction of a high velocity railway tunnel between the Maurienne and Susa valleys provides the opportunity to gather a large amount of geological data in the internal Western Alps and to extend surface observation at depth. We provide a structural analysis on ductile and brittle domains. New PT estimates are obtained using pseudosection and multiequilibra methods. Ar/Ar step heating on phengite provide time constraint on tectonic phases. Then, in light of our data and available literature, we focus on the significance of the D2 structures in the internal Western Alps. Results indicate that polyphased tectonic occurs during exhumation. The first deformation phase (D1) is characterized by nappe stacking in a context of top to the NW shearing, between 37 and 35 Ma deformation occurs between 1.0 and 0.5 GPa and 360-350°C. Top to the East deformation phase (D2) is associated with decompression up to 0.1 GPa and cooling down to 280°C. D2 deformations end at 31Ma. Following these phases of ductile deformation, two successive brittle deformation phases are evidenced: the first one is characterized by a N-S direction of extension and produce the overall tilting toward the south of the studied zone. The second one is characterized by E-W direction of extension. In the Internal Alps, the transition between Oceanic-continental subduction and continental collision occurred at 32Ma. In this context, D1 deformations that are dated between 37 and 35 Ma are clearly related to continental subduction. In the same way, brittle deformation phases are the expression of continental collision. The D2 tectonic phase took place at the transition between subduction and collision. Its attribution to one of these two processes remains ambiguous and will be discussed at the light of these new results.

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

2009-04-01

183

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, Jesus A.

2013-01-01

184

Molecular Clouds toward the Super Star Cluster NGC 3603 Possible Evidence for a Cloud-Cloud Collision in Triggering the Cluster Formation  

NASA Astrophysics Data System (ADS)

We present new large field observations of molecular clouds with NANTEN2 toward the super star cluster NGC 3603 in the transitions 12CO(J = 2-1, J = 1-0) and 13CO(J = 2-1, J = 1-0). We suggest that two molecular clouds at 13 km s-1 and 28 km s-1 are associated with NGC 3603 as evidenced by higher temperatures toward the H II region, as well as morphological correspondence. The mass of the clouds is too small to gravitationally bind them, given their relative motion of ~20 km s-1. We suggest that the two clouds collided with each other 1 Myr ago to trigger the formation of the super star cluster. This scenario is able to explain the origin of the highest mass stellar population in the cluster, which is as young as 1 Myr and is segregated within the central sub-pc of the cluster. This is the second super star cluster along with Westerlund 2 where formation may have been triggered by a cloud-cloud collision.

Fukui, Y.; Ohama, A.; Hanaoka, N.; Furukawa, N.; Torii, K.; Dawson, J. R.; Mizuno, N.; Hasegawa, K.; Fukuda, T.; Soga, S.; Moribe, N.; Kuroda, Y.; Hayakawa, T.; Kawamura, A.; Kuwahara, T.; Yamamoto, H.; Okuda, T.; Onishi, T.; Maezawa, H.; Mizuno, A.

2014-01-01

185

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

NASA Astrophysics Data System (ADS)

The energy and angular dependence of double differential cross sections d2?/d?dE were measured for p,d,t, He3,4,6, Li6,7,8, Be7,9,10, B10,11, 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 ~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 d2?/d?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.; Fidelus, M.; Filges, D.; Goldenbaum, F.; Hodde, H.; Jarczyk, L.; Kamys, B.; Kistryn, M.; Kistryn, St.; Kliczewski, St.; Kowalczyk, A.; Kozik, E.; Kulessa, P.; Machner, H.; Magiera, A.; Piskor-Ignatowicz, B.; Pysz, K.; Rudy, Z.; Siudak, R.; Wojciechowski, M.

2010-09-01

186

Collision Energy Dependence of Defect Formation in Graphene  

NASA Astrophysics Data System (ADS)

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

Mao, Fei; Zhang, Chao; Zhang, Yan-Wen; Zhang, Feng-Shou

2012-07-01

187

Particle in cell analysis of a laser-cluster interaction including collision and ionization processes.  

PubMed

A new particle-in-cell (PIC) code which includes collisional and ionization processes has been developed to study laser-plasma interaction. Using the new code, the dynamics of a cluster plasma in a strong laser field has been analyzed and the threshold intensity of the resonant heating, which was previously predicted is accurately evaluated. The angular dependence of ion energy spectrum has also been simulated. As a result, it is found that the anisotropic energy spectrum depends strongly on the presence or absence of collisional processes. PMID:20174069

Taguchi, Toshihiro; Antonsen, Thomas M; Palastro, John; Milchberg, Howard; Mima, Kunioki

2010-02-01

188

A molecular beam study of alkali promotion of NO sticking on Si(100): Local promotion in a single collision regime  

Microsoft Academic Search

Alkali–metal (K and Cs) promotion for sticking of nitrogen oxide molecule (NO) on Si(100) has been studied using a molecular beam method combined with an Auger electron spectroscopy (AES) and a laser ionization spectroscopy [resonance enhanced multiphoton ionization (REMPI)]. The observed sticking probability S shows a good correlation with alkali coverage, indicating that the alkali promotion is local in nature.

A. Namiki; S. Suzuki; H. Kato; Y. Babasaki; M. Tanaka; T. Nakamura; T. Suzaki

1992-01-01

189

Hard Processes in Proton-Proton Collisions at the Large Hadron Collider  

E-print Network

The measurement of hard scattering processes, meaning those with energy scales of more than a few GeV, is the main method by which physics is being explored and extended by the experiments at the Large Hadron Collider. We review the principal measurements made so far, and what they have told us about physics at the energy frontier.

Jonathan M. Butterworth; Guenther Dissertori; Gavin P. Salam

2012-02-02

190

Hard Processes in Proton-Proton Collisions at the Large Hadron Collider  

E-print Network

The measurement of hard scattering processes, meaning those with energy scales of more than a few GeV, is the main method by which physics is being explored and extended by the experiments at the Large Hadron Collider. We review the principal measurements made so far, and what they have told us about physics at the energy frontier.

Butterworth, Jonathan M; Salam, Gavin P

2012-01-01

191

Interfacial process of nucleation and molecular nucleation templator  

NASA Astrophysics Data System (ADS)

Interfacial effects of nucleation inhibition and promotion were identified from the nucleation of paracetamol. Unlike the classic interfacial effects, which are caused by the change in nucleation barrier, the nonepitaxial interfacial effects are only associated with kink integration kinetics. Methylparaben inhibits nucleation by increasing the desolvation free energy barrier, which is revealed as the nonepitaxial interfacial effect of nucleation inhibition. Polysaccharide revealed its nonepitaxial interfacial effects of nucleation promotion by lowering the conformation entropic barrier via liquid molecule preordering. Polysaccharide can be regarded as an example of molecular nucleation promoter based on the nonepitaxial interfacial effects.

Liu, X. Y.

2001-07-01

192

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

193

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

E-print Network

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

Yong-Ping Fu; Yun-De Li

2011-12-09

194

Two probability distributions in the pure birth process and their applications to hadron-hadron collisions  

Microsoft Academic Search

Two different probability distributions in the pure birth process are considered. They depend on initial conditions: (A) deltan,k (k is the number of hadrons at t=0). (B) sigmakdeltan,k k exp (-)\\/k! (the number of hadrons at t=0) is distributed by the Poisson law with the average multiplicity ). Moment formulae are used in analyzing data in the energy range of

Minoru Biyajima; Tetsuji Kawabe; Naomichi Suzuki

1987-01-01

195

New insights into multielectron processes in slow collisions of highly charged ions with many-electron neutral targets  

NASA Astrophysics Data System (ADS)

Recent results from triple-coincidence measurements of Auger electrons, scattered projectiles, and atomic recoil ions are reported. The studies employed supersonically cooled targets, position imaging detectors, and time-of-flight coincidence techniques; making it possible to simultaneously perform Auger-electron and cold-target recoil-ion momentum spectroscopic (COLTRIMS) measurements. The measurements provide subpartial Auger-electron spectra corresponding to specific final projectile and recoil ion charge states, as well as information on the Q values of the collisions. The measurements provide new insights into the collision dynamics as well as the relaxation pathways of multiply excited states populated during the collisions.

Ali, Rami; Hasan, Ahmad A.; Emmons, Erik D.; Hinojosa, Guillermo

2000-11-01

196

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

197

Accurate calculations of the ground state and low-lying excited states of the (RbBa)+ molecular ion: a proposed system for ultracold reactive collisions  

NASA Astrophysics Data System (ADS)

Collisions of ultracold Ba+ ions on a Rb Bose-Einstein condensate have been suggested as a possible benchmark system for ultracold ion-neutral collision experiments. However, a priori knowledge of the possible processes is desirable. For this purpose, we here present high-level four-component coupled cluster and multi-reference configuration interaction calculations of potential energy curves, dipole moments and spectroscopic constants of the experimentally interesting low-lying electronic states of the (RbBa)+ molecule. Our results show significant avoided crossings between the ^3 \\Sigma ^+_{1,0^-} Rb + Ba+ entrance channels and low-lying charge transfer ^3 \\Pi _{1,0^-} states of the Rb+ and Ba_{6\\rm{s}^1 5\\rm{d}^1}(3D) atomic channels, indicating that a fast non-radiative charge transfer is possible. Population analysis shows that a partially covalent polar bond is formed in the ground state, which thus deviates significantly from a pure Rb+ + Ba interaction. This finding is corroborated by the electric dipole moment which is found only to be 4.5 D at the equilibrium bond distance, compared with the 14 D for a pure Rb+ + Ba interaction, thereby supporting the view of a partial charge transfer between the two atoms.

Knecht, S.; Sørensen, L. K.; Jensen, H. J. Aa; Fleig, T.; Marian, C. M.

2010-03-01

198

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

199

Enhanced capacitance textile fibres for supercapacitors via an interfacial molecular templating process  

Microsoft Academic Search

The application of poly(2-methoxyaniline-5-sulfonic acid), PMAS, as a molecular template in a bi-layered co-polymerisation process onto a microporous activated carbon fibre is presented. This process produces a bound, compact molecular layer of PMAS, onto which polyaniline (PAni) or polypyrrole (PPy) is co-polymerized as a thin permeable layer coating the surface of the carbon fibre. The physical porous structure of the

Gregory J. Wilson; Mark G. Looney; A. G. Pandolfo

2010-01-01

200

Dissociation of CO molecular ions produced in collisions with 2.5 MeV/u Xe(34+)  

NASA Astrophysics Data System (ADS)

The breakup of CO molecular ions following multiple electron removal by 2.5 MeV/u Xe(34+) ions has been re-examined by means of recoil-ion momentum spectroscopy (RIMS) using a position- sensitive 80 mm diam microchannel plate detector backed by a hexagonal delay-line anode. Fragment pairs originating from molecular ions with charge up to 8e were isolated and analyzed in order to determine the distribution of total recoil-ion kinetic energy released in the breakup (KER) and the angular distribution of the ion momenta with respect to the beam direction. The results are significantly improved compared to those reported previously in terms of accuracy, resolution and overall counting statistics. The KER distributions were determined with a resolution of 1 eV (FWHM) or better. While most of the KER distributions displayed only a single broad asymmetric peak, a few of them showed a combination of well- resolved narrow peaks and partially overlapping broader peaks. The angular distributions were found to be essentially isotropic, except for those ion pairs originating from highly charged molecular ions, which indicated a slight preference for emission in the beam direction.

Horvat, Vladimir; Watson, Rand

2010-03-01

201

In-situ growth monitoring of molecular beam epitaxy processes  

NASA Astrophysics Data System (ADS)

The strong collaboration between Arizona State University and General Electric Corp. has resulted in a comprehensive program to develop intelligent, in-situ sensors for monitoring and control of semiconductor thin film growth by Molecular Beam Epitaxy (MBE). An intimate collaboration with a commercial MBE manufacturer (DCA Instruments) has resulted in a new ultra-stable substrate manipulator which is compatible with in-situ optical measurements. Another long time collaboration with an ellipsometer manufacturer (Woollam Co.) has generated a new prototype high speed in-situ spectroscopic ellipsometer. Both the manipulator and the ellipsometer have become commercial products. Adaptation of spectroscopic ellipsometry to real time MBE growth monitoring and development of advanced computer algorithms have enabled the tracking of epitaxial layer thickness, temperature and alloy composition. Temperature dependent (from room temperature to 650 deg C) optical constants of GaAs have been measured and verified. Work is continuing on obtaining optical constants for AlGaAs compound semiconductors.

Maracas, George N.; Sohie, Guy R.

1993-09-01

202

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

Farnik, Michal; Poterya, Viktoriya

2014-01-01

203

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

204

Simultaneous process and molecular design/selection through property integration  

E-print Network

CO2-Eq. Carbon dioxide equivalent d Characteristic value in Eq. (3.30) DEG Diethylene glycol DGA Diglycolamine E Emission F Process source flowrate f fresh source index fi,j flowrate of source i entering... gas treatment facility, two process sources diethylene glycol (DEG) (S1) and monoethanolamine (MEA) (S2) are used with a fresh stream of methyldiethanolamine (MDEA) (F1) to make up the solvent loss (Kohl and Nielsen, 1997). Operating experience...

Qin, Xiaoyun

2007-04-25

205

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

206

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

207

Molecular beam studies of reaction dynamics  

Microsoft Academic Search

The major thrust of this research project is to elucidate detailed dynamics of simple reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free

1990-01-01

208

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

209

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

PubMed

We have studied the effect of chain topology on the structural properties and diffusion of polymers in a dilute solution in a good solvent. Specifically, we have used three different simulation techniques to compare the chain size and diffusion coefficient of linear and ring polymers in solution. The polymer chain is modeled using a bead-spring representation. The solvent is modeled using three different techniques: molecular dynamics (MD) simulations with a particulate solvent in which hydrodynamic interactions are accounted through the intermolecular interactions, multiparticle collision dynamics (MPCD) with a point particle solvent which has stochastic interactions with the polymer, and the lattice Boltzmann method in which the polymer chains are coupled to the lattice fluid through friction. Our results show that the three methods give quantitatively similar results for the effect of chain topology on the conformation and diffusion behavior of the polymer chain in a good solvent. The ratio of diffusivities of ring and linear polymers is observed to be close to that predicted by perturbation calculations based on the Kirkwood hydrodynamic theory. PMID:22088075

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

2011-11-14

210

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

NASA Astrophysics Data System (ADS)

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

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

2011-11-01

211

Reducing Si population in the ISM by charge exchange collisions with He+: a quantum modelling of the process  

NASA Astrophysics Data System (ADS)

The possible losses of silicon atom population during star-forming evolution and in the (photon-dominated region) PDR environments of the interstellar medium (ISM) can have different origins, one being the charge exchange (CE) encounter with the helium cations (Si + He+) one of the most abundant species in those environments. This work investigates the different features of the likely interaction potentials leading to asymptotic partners like Si, Si+, Si++ and He or He+, in order to determine the influence of more accurate cross-sections on the chemical evolution of the ISM. We analyse the behaviour of interacting Si and He atoms by using ab initio quantum molecular methods. To obtain the corresponding transition probabilities, we employ a simple sequential grouping of single-crossing Landau-Zener events, and the time-dependent rate coefficients for the CE processes involved are obtained over a broad range of the gas temperatures. The results are seen to differ substantially from an earlier Langevin-type modelling of such process and further suggest a much more complex variety of possible molecular evolution mechanisms. We find, in fact, the unexpected presence of electron shake-off effects leading to Si++ generation yielding to emission of an electron, which has never been considered before and that, although with markedly smaller cross-sections, can indeed contribute to Si losses after the primary CE event. The consequences of these novel findings are tested on evolutionary model calculations and the results discussed in detail.

Satta, M.; Grassi, T.; Gianturco, F. A.; Yakovleva, S. A.; Belyaev, A. K.

2013-12-01

212

Simple model study of reactive collisions in an intense nonresonant laser field  

SciTech Connect

A simple model study of laser induced transitions between electronic surfaces in reactive molecular collisions has been undertaken. The investigation is characterized by laser and nonadiabatic couplings which are turned on during the course of a collision. Transition probabilities are determined within an exact quantum-mechanical framework, for switching between the model one-dimensional potential curves as a function of various system parameters. Such parameters include the photon energy, the reactant collision energy, and the coordinate separation between the positions of potential barrier maxima. The processes studied involve not only laser switching but, also, cooperative laser and nonadiabatic effects. A number of features of the results are emphasized.

Peploski, J.C.; Eno, L.

1985-09-15

213

Reconstructing the free-energy landscape associated to molecular motors processivity  

E-print Network

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

J. Lopez Alamilla; I. Santamaria-Holek

2012-05-16

214

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

Microsoft Academic Search

Phosphorylation of nucleic acids is an indispensable process to repair strand interruption of nucleic acids. We have studied the process of phosphoryla- tion using molecular beacon (MB) DNA probes in real-time and with high selectivity. The MB employed in this method is devised to sense the product of a 'phosphorylation-ligation' coupled enzyme reaction. Compared with the current assays, this novel

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

2005-01-01

215

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

216

Optical chemosensor for Ag+, Fe3+, and cysteine: information processing at molecular level.  

PubMed

A thiacalix[4]arene based chemosensor 3 bearing two pyrene groups has been synthesized which demonstrates ratiometric sensing with Ag(+) and fluorescence quenching with Fe(3+) ions in mixed aqueous media. The 'in situ' prepared Ag(+) and Fe(3+) complexes showed high selectivity toward cysteine. The molecular switching between three chemical inputs (Ag(+), Fe(3+), cysteine) results in various molecular logic gates which have been integrated sequentially to generate a sequential information processing device. PMID:21175135

Kumar, Manoj; Kumar, Rajesh; Bhalla, Vandana

2011-02-01

217

3D momentum imaging of molecular dissociation induced by fast, heavy-ion collisions in the strong interaction regime  

NASA Astrophysics Data System (ADS)

A system for recoil-ion momentum spectroscopy (RIMS) of molecular dissociation was constructed and its detailed description is provided. The system was tested by measuring the spectra of kinetic energy release (KER) in the dissociations of doubly and triply charged ions of CO, N 2, and O 2 molecules produced by bombardment of neutral molecules with 2.5 MeV/u Xe 34+ projectiles. Employed calibration procedures and methods of data analysis are described. The KER spectra are characterized by high counting statistics and their associated energy resolution is evaluated in detail. Each spectrum displays a multiple peak structure. A comparison is made with previously published KER spectra for the dissociation of doubly charged ions of CO and N 2 molecules and triply charged ions of N 2 molecules obtained under similar conditions (i.e., in the strong interaction regime using fast heavy-ion projectiles and measured by means of RIMS), as well as with those for the dissociation of doubly charged ions of CO, N 2, and O 2 molecules obtained by means of Doppler-free time-of-flight spectrometry using a beam of electrons.

Horvat, V.; Watson, R. L.

2011-11-01

218

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

219

Close-coupling calculations of low-energy inelastic and elastic processes in $^4$He collisions with H$_2$: A comparative study of two potential energy surfaces  

E-print Network

The two most recently published potential energy surfaces (PESs) for the HeH$_2$ complex, the so-called MR (Muchnick and Russek) and BMP (Boothroyd, Martin, and Peterson) surfaces, are quantitatively evaluated and compared through the investigation of atom-diatom collision processes. The BMP surface is expected to be an improvement, approaching chemical accuracy, over all conformations of the PES compared to that of the MR surface. We found significant differences in inelastic rovibrational cross sections computed on the two surfaces for processes dominated by large changes in target rotational angular momentum. In particular, the H$_2$($\

T. G. Lee; C. Rochow; R. Martin; T. K. Clark; R. C. Forrey; N. Balakrishnan; P. C. Stancil; D. R. Schultz; A. Dalgarno; G. J. Ferland

2004-12-09

220

Seabeam survey at the southern end of the Manila trench. Transition between subduction and collision processes, offshore Mindoro Island, Philippines  

NASA Astrophysics Data System (ADS)

The morphological and structural study conducted at the southern tip of the Manila trench, reveals that convergence between the South China Sea basin and Luzon is accommodated differently depending on the nature of the subducted slab. When the oceanic crust is subducted, a simple accretionary prism-fore arc basin pattern is developed. Conversely, where the continental margin of this basin is subducted, intraplate deformation is randomly distributed across the major part of the fore arc area which is fragmented into various crustal microblocks. Results of seabeam mapping and detailed geophysical surveying conducted at this subduction-collision transition zone, during the POP2 cruise, with R.V. "Jean Charcot" are presented and discussed here and allow us a new insight into the mechanism of such a subduction-collision transition zone.

Rangin, Claude; Stephan, Jean Francois; Blanchet, Rene; Baladad, David; Bouysee, Phillipe; Min Pen Chen; Chotin, Pierre; Collot, Jean Yves; Daniel, Jacques; Drouhot, Jean Marcel; Marchadier, Yves; Marsset, Bruno; Pelletier, Bernard; Richard, Mary Annick; Tardy, Marc

1988-01-01

221

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

E-print Network

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

Maruyama, Shigeo

222

Inorganic molecular sieves: Preparation, modification and industrial application in catalytic processes  

Microsoft Academic Search

The increasing environmental concern and promotion of “green processes” are forcing the substitution of traditional acid and base homogeneous catalysts by solid ones. Among these heterogeneous catalysts, zeolites and zeotypes can be considered as real “green” catalysts, due to their benign nature from an environmental point of view. The importance of these inorganic molecular sieves within the field of heterogeneous

Cristina Martínez; Avelino Corma

2011-01-01

223

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

E-print Network

, Surface Decomposition 1. (CNT) CVDACCVD () CNT CNT 3C 4H 6H Fig.1 Polytypes of SiC. SiC CNTSiC(1SiC Molecular Dynamics Study on Synthesis Process of Carbon Nanotubes from Surface Decomposition of SiC * Hiroki Yamaguchi , Shigeo Maruyama Dept. of Mech. Eng., The University of Tokyo, 7

Maruyama, Shigeo

224

2010 Atomic & Molecular Interactions Gordon Research Conference  

Microsoft Academic Search

The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical

Todd Martinez

2010-01-01

225

Force variations on particle induced by bubble-particle collision  

Microsoft Academic Search

The force variation on a particle during a bubble-particle collision is investigated in two different liquid phases: (1) distilled water and (2) 80 wt% glycerin in water solution. The force variations on a stationary particle due to the collision are experimentally measured and the collision processes are visualized. A simple analytical model of the collision process is developed to account

T. Hong; L.-S. Fan; D. J. Lee

1999-01-01

226

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.

227

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

228

Resonance behaviour of the bremsstrahlung process in collisions of the low-energy electrons with alkali-metal clusters  

NASA Astrophysics Data System (ADS)

The ordinary bremsstrahlung cross sections formed in collisions of low-energy electrons with clusters of lithium, sodium and potassium containing the 'magic' number of atoms (from 8 to 196) have been studied. Calculations are carried out through the continuum-continuum dipole matrix element in the length form, using the spherical jellium model for clusters and the density-functional approximation for the cluster potential and electronic wavefunctions. The resonance behaviour of the bremsstrahlung cross section is detected. The resonances are connected with the electron capture in quasi-bound states. Dependence of the resonance width and intensity on the projectile electron energy is studied.

Kurkina, L. I.

2004-07-01

229

Process evaluation of an open architecture real-time molecular laboratory platform.  

PubMed

The needs of molecular diagnostic laboratories that perform both Food and Drug Administration-cleared as well as laboratory-developed tests are usually not met on a single analytical platform. Furthermore, little information is available about the direct impact of molecular automation on labor costs and efficiency in clinical laboratories. We performed a process impact analysis from time and motion studies of a novel molecular diagnostic robotic system designed to automate sample preparation, extraction, and analysis. All 27 preanalytical tasks were quantified for the amount of time spent preparing 24 specimens for analysis. These steps were completed in 899 s (14 min, 59 s) followed by 7887 s (131 min, 27 s) of instrument operation independent of operator control (walk-away time). Postanalytical results evaluation required 1 min per specimen. The instrument automatically extracted the nucleic acid from the specimen, added the eluted DNA to the amplification reagents, and performed the analysis. Only 12% of the total instrument operations required relatively unskilled human labor. Thus, the availability of automated molecular diagnostic instruments will facilitate the expansion of molecular testing in the clinical laboratory because they reduce operator costs with respect to time and complexity of the tasks they are asked to perform. PMID:24811476

Felder, Robin A; Jackson, Keith D; Walter, Adam M

2014-10-01

230

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

231

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

NASA Astrophysics Data System (ADS)

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

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

2010-10-01

232

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

233

Reversible Simulations of Elastic Collisions  

SciTech Connect

Consider a system of N identical hard spherical particles moving in a d-dimensional box and undergoing elastic, possibly multi-particle, collisions. We develop a new algorithm that recovers the pre-collision state from the post-collision state of the system, across a series of consecutive collisions, \\textit{with essentially no memory overhead}. The challenge in achieving reversibility for an n-particle collision (where, in general, n<< N) arises from the presence of nd-d-1 degrees of freedom (arbitrary angles) during each collision, as well as from the complex geometrical constraints placed on the colliding particles. To reverse the collisions in a traditional simulation setting, all of the particular realizations of these degrees of freedom (angles) during the forward simulation must be tracked. This requires memory proportional to the number of collisions, which grows very fast with N and d, thereby severely limiting the \\textit{de facto} applicability of the scheme. This limitation is addressed here by first performing a pseudo-randomization of angles, which ensures determinism in the reverse path for any values of n and d. To address the more difficult problem of geometrical and dynamic constraints, a new approach is developed which correctly samples the constrained phase space. Upon combining the pseudo-randomization with correct phase space sampling, perfect reversibility of collisions is achieved, as illustrated for n<=3, d=2, and n=2, d=3. This result enables, for the first time, reversible simulations of elastic collisions with essentially zero memory accumulation. In principle, the approach presented here could be generalized to larger values of n, which would be of definite interest for molecular dynamics simulations at high densities.

Perumalla, Kalyan S [ORNL; Protopopescu, Vladimir A [ORNL

2013-01-01

234

Atomic and molecular processes generated by linearly polarized few-cycle laser pulses  

NASA Astrophysics Data System (ADS)

S-matrix theory is used to analyze different atomic and molecular processes in a linearly polarized few-cycle laser field. The energy spectra of high-order above-threshold ionization (HATI) are presented. Electron-atom potential scattering assisted by a few-cycle laser pulse is also analyzed. It is shown that the plateau structures in the energy spectra of the electron-atom potential scattering are dependent on the carrier-envelope phase (CEP) of the laser pulse, so that the cutoff positions of the plateaus can be controlled by changing the CEP. Regarding our analysis of the molecular HATI process, the angle-resolved spectra, obtained by different theoretical approaches, are also presented.

Busuladži?, M.; ?erki?, A.; Odžak, S.; Gazibegovi?-Busuladži?, A.; Hasovi?, E.; Habibovi?, D.; Miloševi?, D. B.

2014-09-01

235

An isomerization-induced cage-breaking process in a molecular glass former below Tg  

NASA Astrophysics Data System (ADS)

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

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

2011-03-01

236

Molecular dynamics simulations of mixed lubrication with smooth particle post-processing  

Microsoft Academic Search

A post-processing method for molecular dynamics (MD) simulations of friction based on the smooth particle approach is proposed, allowing---among other features---the introduction and evaluation of a solid-solid contact area arising due to direct asperity interaction. In order to illustrate the feasibility of this scheme, a large number of MD calculations of lubricated nanotribological systems with various asperity geometries and carefully

S. Eder; A. Vernes; G. Vorlaufer; G. Betz

2011-01-01

237

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

Microsoft Academic Search

The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate

Vesselin Yamakov; Dieter Wolf; Simon R. Phillpot; Amiya K. Mukherjee; Herbert Gleiter; Forschungszentrum Karlsruhe

2002-01-01

238

Merging Galaxies, Cosmic Collisions  

NASA Technical Reports Server (NTRS)

Exciting Hubble Space Telescope images of more than a dozen very distant colliding galaxies indicate that, at least in some cases, big massive galaxies form through collisions between smaller ones, in a generation after generation never-ending story. The Hubble image shows the paired galaxies very close together with streams of stars being pulled out of the galaxies. The colliding 'parent' galaxies lose their shape and smoother galaxies are formed. The whole merging process can take less than a billion years. The Hubble Space Telescope imaged 81 galaxies in the galaxy cluster 8 billion light-years away. Astronomers say the collisions have never been observed before at this frequency. Many of the collisions involve very massive galaxies, and the end result will be even more massive galaxies.

1999-01-01

239

Complementary molecular and elemental detection of speciated thioarsenicals using ESI-MS in combination with a xenon-based collision-cell ICP-MS with application to fortified NIST freeze-dried urine.  

PubMed

The simultaneous detection of arsenic and sulfur in thioarsenicals was achieved using xenon-based collision-cell inductively coupled plasma (ICP) mass spectrometry (MS) in combination with high-performance liquid chromatography. In an attempt to minimize the (16)O(16)O(+) interference at m/z 32, both sample introduction and collision-cell experimental parameters were optimized. Low flow rates (0.25 mL/min) and a high methanol concentration (8%) in the mobile phase produced a fourfold decrease in the m/z 32 background. A plasma sampling depth change from 3 to 7 mm produced a twofold decrease in background at m/z 32, with a corresponding fourfold increase in the signal associated with a high ionization surrogate for sulfur. The quadrupole bias and the octopole bias were used as a kinetic energy discriminator between background and analyte ions, but a variety of tuning conditions produced similar (less than twofold change) detection limits for sulfur ((32)S). A 34-fold improvement in the (32)S detection limit was achieved using xenon instead of helium as a collision gas. The optimized xenon-based collision cell ICP mass spectrometer was then used with electrospray ionization MS to provide elemental and molecular-based information for the analysis of a fortified sample of NIST freeze-dried urine. The 3sigma detection limits, based on peak height for dimethylthioarsinic acid (DMTA) and trimethylarsine sulfide (TMAS), were 15 and 12 ng/g, respectively. Finally, the peak area reproducibilities (percentage relative standard deviation) of a 5-ppm fortified sample of NIST freeze dried urine for DMTA and TMAS were 7.4 and 5.4%, respectively. PMID:18157667

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

2008-04-01

240

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

241

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

Microsoft Academic Search

Aerosol particle reactions with vapor molecules and molecular clusters are often collision rate limited, hence determination of particle-vapor molecule and particle-molecular cluster collision rates are of fundamental importance. These collisions typically occur in the mass transfer transition regime, wherein the collision kernel (collision rate coefficient) is dependent upon the diffusive Knudsen number, KnD. While this alone prohibits analytical determination of

Ranganathan Gopalakrishnan; Thaseem Thajudeen; Christopher J. Hogan

2011-01-01

242

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

NASA Astrophysics Data System (ADS)

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

Buchachenko, A. L.

2014-01-01

243

Gravitational waves from cosmic bubble collisions  

E-print Network

Cosmic bubbles are nucleated through the quantum tunneling process. After nucleation they would expand and undergo collisions with each other. In this paper, we focus in particular on collisions of two equal-sized bubbles and compute gravitational waves emitted from the collisions. First, we study the mechanism of the collisions by means of a real scalar field and a quartic potential of the field. Then, using this scalar field model, we compute gravitational waves from the collisions in a straightforward manner. In the quadrupole approximation, time-domain gravitational waveforms are directly obtained by integrating the energy-momentum tensors over the volume of the wave sources, where the energy-momentum tensors are expressed in terms of the scalar field, the local geometry and the potential; therefore, containing all information about the bubble collisions. We present gravitational waveforms emitted during (i) the initial-to-intermediate stage of strong collisions and (ii) the final stage of weak collisions...

Kim, Dong-Hoon; Lee, Wonwoo; Yang, Jongmann; Yeom, Dong-han

2014-01-01

244

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

E-print Network

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

Luca Ciandrini; M. Carmen Romano; A. Parmeggiani

2013-12-06

245

Charge exchange in Li2+(1s) + H(ls) collisions. A molecular approach including two-electron translation factors  

E-print Network

. Physique 46 (1985) 719-726 MAI 1985, Classification Physics Abstracts 34.70 1. Introduction. Collisions of the envisaged use of lithium blankets in fusion reactors, and offast neutral Li beams to heat the fusion plasma. In the present work, we treat the charge exchange reactions : .... in the impact energy range 0.5-25 keV amu

Boyer, Edmond

246

Initial elementary processes in tetrafluoroethylene plasma: An ab initio molecular orbital study  

NASA Astrophysics Data System (ADS)

Initial elementary processes in tetrafluoroethylene plasma are studied by using an ab initio molecular orbital method. The energy-surfaces at excited states are obtained by the Hartree-Fock method with a double zeta basis set, plus Rydberg orbitals. A ?-?* transition is low-lying both at singlet and triplet excited states. Vinyl-polymerization-type reactions are expected in the presence of some radical species via these transitions. The C=C bond cleaves via a triplet ?-?* transition to form CF2. The predicted elementary processes via these states are compatible with experimental results that C2F4* and CF2 are primary precursors. No excited states that bring about a C—F bond cleavage are obtained within 10 eV of the ground state. As a path for a C—F bond cleavage, a dissociative electron attachment process is found in a low energy region. This process is considered to be important for producing fluorine anions.

Sato, Kota; Komatsu, Toru; Iwabuchi, Susumu

1993-12-01

247

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

PubMed Central

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

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

2013-01-01

248

Invisible Collisions  

NSDL National Science Digital Library

This activity relates an elastic collision to the change in a satelliteâs or spacecraftâs speed and direction resulting from a planetary fly-by, often called a âgravity assistâ maneuver. Both hands-on and online interactive methods are used to explore these topics.

Hallau, Keri

2009-01-01

249

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

250

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

PubMed

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

2013-04-30

251

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

PubMed

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

252

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

253

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

254

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

255

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

NASA Astrophysics Data System (ADS)

Collisional growth and ionization is commonplace for gas phase nanoparticles (i.e., in aerosols). Nanoparticle collisions in atmospheric pressure environments occur in the mass transfer transition regime, and further attractive singular contact potentials (which arise when modeling nanoparticles as condensed matter and for which the potential energy approaches -? when two entities contact) often have a non-negligible influence on collision processes. For these reasons collision rate calculations for nanoparticles in the gas phase are not straightforward. We use mean first passage time calculations to develop a simple relationship to determine the collision rate in the gas phase, accounting for the influences of both the transition regime and singular contact potentials (specifically the non-retarded van der Waals and image potentials). In the presented analysis, methods to determine the degree of enhancement in collision rate due to attractive singular potentials in the continuum (diffusive) regime, ?C, and the degree of enhancement in the free molecular (ballistic) regime, ?FM, are first reviewed. Accounting for these enhancement factors, with mean first passage time calculations it is found that the collision rate for gas phase nanoparticles with other gas phase entities can be determined from a relationship between the dimensionless collision rate coefficient, H, and the diffusive Knudsen number, KnD, i.e., the ratio of the mean collision persistence distance to the collision length scale. This coincides with the H(KnD) relationship found to appropriately describe collisions between entities interacting via a hard-sphere potential, but with ?C and ?FM incorporated into the definitions of both H and KnD, respectively. The H(KnD) relationship is compared to the predictions of flux matching theory, used prevalently in prior work for collision rate calculation, and through this comparison it is found that at high potential energy to thermal energy ratios, flux matching theory predictions underestimate the true collision rate. Finally, a series of experimental measurements of nanoparticle-nanoparticle collision rates are compared to the determined H(KnD) expression, considering that nanoparticles interact via non-retarded van der Waals potentials. Very good agreement is found with collision rates inferred from experiments, with almost all measured values from four separate studies within 25% of model predictions.

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

2012-08-01

256

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

E-print Network

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 ...

Alver, Burak Han

257

Improved elastic collision modeling in DEGAS 2 for low-temperature Randall J. Kanzleiter  

E-print Network

-elastic collisions in low-temperature environments. For like species collisions, as in D D, quantum mechanical, 392­397 1994 by employing a set of quantum mechanical collision cross sections produced by Oak Ridge-molecular collisions in the form of D D2 are included for the first time. An integration technique is utilized

Karney, Charles

258

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

259

Hydrolysis and oxidation in subcritical and supercritical water: Connecting process engineering science to molecular interactions  

SciTech Connect

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

Tester, J.W.; Cline, J.A.

1999-11-01

260

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

261

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

262

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

263

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

PubMed

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

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

2002-09-01

264

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

SciTech Connect

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

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

2002-09-01

265

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

266

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

267

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

268

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

269

Mass and orientation effects in dissociative collisions between rare gas atoms and alkali halide molecules  

SciTech Connect

The collision induced dissociation of alkali halide molecules to ion pairs upon impact with hyperthermal rare gas atoms has been investigated using the crossed molecular beam method. Relative total cross sections for the dissociation of CsI, CsBr, RbI, and KI to ion pairs upon collision with xenon and krypton have been measured over a relative collision energy range from threshold to 10 and 8 eV, respectively. In addition, complete angular and energy distributions of both dissociated ions from Xe+CsI, CsBr, and RbI collisions and from Kr+CsI and CsBr collisions have been obtained at several collision energies within the above energy range. Mass, collision orientation, and energy dependence effects observed throughout this work define two limiting case dissociation mechanisms for the Xe(Kr)+MX..-->..Xe(Kr)+M/sup +/+X/sup -/ processes. The dominant dissociation configuration consists of the rare gas atom incident on the light atom end of the alkali halide molecule in a near collinear collision. The less preferred dissociation mechanism results when the rare gas atom is incident in a near collinear configuration on the heavy atom end of the alkali halide molecule. Experimental measurements of the percentage of energy transfer from the relative kinetic energy between Xe(Kr) and MX to the relative motion of M/sup +/--X/sup -/ range as high as 95%; these percentage energy transfers correlate well with the predictions of an impulsive collision model. Three-dimensional classical trajectory calculations using realistic interaction potentials have been performed and they verify the dynamical interpretation suggested by the experiments.

Tully, F.P.; Cheung, N.H.; Haberland, H.; Lee, Y.T.

1980-11-01

270

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

NASA Astrophysics Data System (ADS)

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

Tran, H.; Hartmann, J. M.

2011-06-01

271

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

272

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

273

Weak Neutral Current Effects in Double-Boson Exchange Processes in High Energy Positron-Electron Collisions  

Microsoft Academic Search

Double photon processes of the type e('+)e('-) (--->) e('+)e('-)(gamma)(gamma) (--->) e('+)e('-)(mu)('+)(mu)(' -), have been studied extensively. In this thesis, we shall study the neutral current effects due to double-boson processes of the type e('+)e('-) (--->) e('+)e('-)(gamma)Z('0) ( --->) e('+)e('-)(mu)('+)(mu)('-). Our work is based on the standard Weinberg-Salam SU(2) x U(1) model of electroweak interaction. We use the method of Monte

Wang Kong Cheung

1982-01-01

274

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

275

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

PubMed

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

2013-09-24

276

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

PubMed Central

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

2013-01-01

277

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

278

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

PubMed

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

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

2010-06-01

279

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

280

Weak neutral current effects in double-boson exchange processes in high energy e\\/sup +\\/e⁻ collisions  

Microsoft Academic Search

Double photon processes of the type e\\/sup +\\/e⁻ ..-->.. e\\/sup +\\/e⁻..gamma gamma.. ..-->.. e\\/sup +\\/e⁻..mu..\\/sup +\\/..mu..⁻, have been studied extensively. In this thesis, we shall study the neutral current effects due to double-boson processes of the type e\\/sup +\\/e⁻ ..-->.. e\\/sup +\\/e⁻..gamma..Z° ..-->.. e\\/sup +\\/e⁻..mu..\\/sup +\\/..mu..⁻. Our work is based on the standard Weinberg-Salam SU(2) x U(1) model of electroweak

1982-01-01

281

Puck collisions  

NASA Astrophysics Data System (ADS)

Collisions between two ice hockey pucks sliding on frictionless ice are studied, with both inelasticity and frictional contact between the colliding surfaces of the two pucks taken into account. The latter couples translational and rotational motion. The full solution depends on the sign and magnitude of the initial mismatch between the surface velocities at the point of contact. The initial state defines two physically distinct regimes for the friction coefficient. To illustrate the complexities, we discuss at length the typical situation (well known from curling) when puck number 1 is initially at rest, and is hit by puck number 2 with an arbitrary impact parameter, velocity and angular velocity. We find that the total outgoing angle between the pucks exceeds \\frac{1}{2}\\pi if and only if the collision leads to a net increase in the translational part of the kinetic energy. The conditions for this to happen are scrutinized, and the results are presented both analytically and numerically by a set of representative curves. This paper is written with an ambitious undergraduate, and her teacher, in mind.

Hauge, E. H.

2012-09-01

282

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

NASA Astrophysics Data System (ADS)

The Electron spin resonance studies on the reduction process of nitroxyl spin probes were carried out for 1mM 14N 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 14N 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; Jawahar, A.; Benial, A. Milton Franklin

2014-04-01

283

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

284

Molecular dynamics simulations of mixed lubrication with smooth particle post-processing  

NASA Astrophysics Data System (ADS)

A post-processing method for molecular dynamics (MD) simulations of friction based on the smooth particle approach is proposed, allowing—among other features—the introduction and evaluation of a solid-solid contact area arising due to direct asperity interaction. In order to illustrate the feasibility of this scheme, a large number of MD calculations of lubricated nanotribological systems with various asperity geometries and carefully selected numbers of lubricant molecules were carried out and analysed. In this manner, it is shown that the friction force as a function of load agrees very well with a three-parameter friction law which, in addition to the adhesion- and the load-controlled terms, contains a load-independent offset.

Eder, S.; Vernes, A.; Vorlaufer, G.; Betz, G.

2011-05-01

285

Molecular dynamics simulations of mixed lubrication with smooth particle post-processing.  

PubMed

A post-processing method for molecular dynamics (MD) simulations of friction based on the smooth particle approach is proposed, allowing--among other features--the introduction and evaluation of a solid-solid contact area arising due to direct asperity interaction. In order to illustrate the feasibility of this scheme, a large number of MD calculations of lubricated nanotribological systems with various asperity geometries and carefully selected numbers of lubricant molecules were carried out and analysed. In this manner, it is shown that the friction force as a function of load agrees very well with a three-parameter friction law which, in addition to the adhesion- and the load-controlled terms, contains a load-independent offset. PMID:21493976

Eder, S; Vernes, A; Vorlaufer, G; Betz, G

2011-05-01

286

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

287

An Improved Process for Fabricating High-Mobility Organic Molecular Crystal Field-Effect Transistors  

E-print Network

In this paper we present an improved process for producing elastomer transistor stamps and high-mobility organic field-effect transistors (FETs) based on semiconducting acene molecular crystals. In particular, we have removed the need to use a silanized Si wafer for curing the stamps and to handle a fragile micron-thickness polydimethylsiloxane (PDMS) insulating film and laminate it, bubble free, against the PDMS transistor stamp. We find that despite the altered design, rougher PDMS surface, and lamination and measurement of the device in air, we still achieve electrical mobilities of order 10 cm^2/Vs, comparable to the current state of the art in organic FETs. Our device shows hole conduction with a threshold voltage of order -9V, which corresponds to a trap density of 1.4 x 10^10 cm^-2.

A. P. Micolich; L. L. Bell; A. R. Hamilton

2007-06-21

288

Direct Photons in Heavy-Ion Collisions  

Microsoft Academic Search

A brief overview of direct-photon measurements in ultra-relativistic nucleus-nucleus collisions is given. The results for Pb+Pb collisions at sNN = 17.3 GeV and for Au+Au collisions at sNN = 200 GeV are compared to estimates of the direct-photon yield from hard scattering. Both results leave room for a significant thermal photon component. A description purely based on hard scattering processes,

Klaus Reygers; Klaus

2007-01-01

289

Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems  

PubMed Central

Background Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants such as crops and trees. Uncovering shared mechanisms underlying vascular development by transcriptome analysis of different vascular systems may help to transfer knowledge acquired from Arabidopsis to other economically important species. Results Conserved vascular genes and biological processes fundamental to vascular development were explored across various plants. Through comparative transcriptome analysis, 226 genes from Arabidopsis, 217 genes from poplar and 281 genes from rice were identified as constituting 107 conserved vascular gene groups. These gene groups are expressed mainly in vascular tissues and form a complex coexpression network with multiple functional connections. To date, only half of the groups have been experimentally investigated. The conserved vascular gene groups were classified into 9 essential processes for vascular development. 18 groups (17%) lack of annotations were classified as having unknown functions. Conclusion The study provides a map of fundamental biological processes conserved across different vascular systems. It identifies gaps in the experimental investigation of pathways active in vascular formation, which if explored, could lead to a more complete understanding of vascular development. PMID:23548001

2013-01-01

290

Protonated Urea Collision-Induced Dissociation. Comparison of Experiments and Chemical Dynamics Simulations  

NASA Astrophysics Data System (ADS)

Quantum mechanical plus molecular mechanical direct chemical dynamics were used, with electrospray tandem mass spectrometry experiments, potential energy surface calculations, and RRKM analyses, to study the gas-phase collision-induced dissociation (CID) of protonated urea. The direct dynamics were able to reproduce some of the experimental observations, in particular the presence of two fragmentation pathways, and, thus, to explain the dynamical origin of the two fragmentation ions observed in the CID spectra. A shattering dissociation mechanism takes place during the collision, and it becomes more important as the collision energy increases, thus explaining the linear increase of the high-energy reaction path (loss of ammonia) versus collision energy. By combining the different theoretical and experimental findings, a complete dynamical picture leading to the fragmentation was identified: (i) Oxygen-protonated urea, the most stable structure in the gas phase, must first isomerize to the nitrogen-protonated form. This can happen by multiple CID collisions or in the electrospray ionization process. (ii) Once the nitrogen-protonated isomer is formed, it can dissociate via two mechanisms: i.e, a slow, almost statistical, process forming a NH4+--NHCO intermediate that rapidly dissociates or a fast nonstatistical process which may lead to the high-energy products.

Spezia, Riccardo; Salpin, Jean-Yves; Gaigeot, Marie-Pierre; Hase, William L.; Song, Kihyung

2009-11-01

291

Pedestrian Vision and Collision Avoidance Behavior: Investigation of the Information Process Space of Pedestrians Using an Eye Tracker  

Microsoft Academic Search

\\u000a This study investigates the Information Process Space (IPS) of pedestrians, which has been widely used in microscopic pedestrian\\u000a movement simulation models. IPS is a conceptual framework to define the spatial extent within which all objects are considered\\u000a as potential obstacles for each pedestrian when computing where to move next. Particular foci of our study were on identifying\\u000a the size and

Kay Kitazawa; Taku Fujiyama

292

Electron Collisions with Atoms and Molecules Relevant to Industrial, Planetary and Astrophysical Plasmas.  

NASA Astrophysics Data System (ADS)

Collision processes involving electrons with neutral atoms and molecules are among the principal mechanisms for energy exchange in industrial and naturally occurring plasmas. In many of these plasmas, large populations of low energy, secondary electrons are generated. Such secondary electrons are very effective in many of the relevant collision processes because both the cross sections and the electron energy distributions peak at low energies. In this talk, a series of experiments involving electron collisions with atomic oxygen, vibrationally excited molecular hydrogen and molecular nitrogen will be presented. Electron collisions with these species are of particular importance in planetary plasmas as demonstrated by, for example, the auroral phenomena at Earth and Jupiter, the electroglow of Jupiter, Saturn and Uranus, and UV emission from Earth, Titan and Triton, respectively. Further, such interactions are important in plasma processing of textile materials, nitrogen gas lasers, and fusion plasmas. The experiments to be presented involve two main experimental techniques (1) electron energy loss spectroscopy and (2) electron impact induced emission spectroscopy.

Johnson, Paul

2006-10-01

293

Time-dependent many-electron approach to slow ion-atom collisions for systems with several active electrons  

NASA Astrophysics Data System (ADS)

We develop a first-principles molecular dynamics for slow ion-atom collisions, where a many-electron system is described over time allowing for its self-consistent coupling to evolving nuclear motions. Our treatment combines an eikonal description of nuclear motions and time-dependent Hartree-Fock states and introduces molecular orbitals written as linear combinations of traveling atomic functions to derive general matrix equations for state-to-state cross sections and to calculate properties. A ``relax-and-drive'' procedure is employed to propagate solutions to the coupled equations with different time scales for electronic transitions and nuclear displacements. Reduced differential cross sections have been calculated for elastic, electron transfer, and excitation processes in He++D collisions, and they compare very well to experimental values and other calculations. In addition, we present results for the evolution of atomic populations during collisions.

Runge, Keith; Micha, David A.

2000-08-01

294

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

2009-09-16

295

Enhancement of the neutral-beam stopping cross section in fusion plasmas due to multistep collision processes  

SciTech Connect

Multistep processes involving excited atomic states are found to produce a substantial increase in the stopping cross section for a neutral hydrogen beam injected into a plasma, and thus to reduce the beam penetration. For typical plasma and beam parameters of current large tokamak experiments, the stopping cross-sectional enhancement is found to vary from 25% to 50% depending on the beam energy, plasma density, and impurity level. For neutral hydrogen beams with energies greater than or equal to 500 keV, envisioned in tokamak amd mirror reactor designs, the enhancement can be as large as 80 to 90%.

Boley, C.D.; Janev, R.K.; Post, D.E.

1983-10-01

296

Double-boson-exchange processes in high-energy numue- collisions in the standard Weinberg-Salam model  

Microsoft Academic Search

In this paper, we shall study double-boson-exchange processes in the reactions numue--->mu- e+e-nue, numue--->mu+mu- e-numu, and numue--->mu+mu- mu-nue, using the standard Weinberg-Salam SU(2)×U(1) model of electroweak interactions. At neutrino laboratory energy ~ 100 GeV, the cross section for the first reaction is ~3×10-44 cm2. This reaction may be observable with experimental facilities in the near future. It could serve as

Wang Kong Cheung

1983-01-01

297

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

PubMed Central

Memory persistence is critically influenced by retrieval. In rats, a single presentation of a conditioned fear stimulus induces memory reconsolidation and fear memory persistence, while repeated fear cue presentations result in loss of fear through extinction. These two opposite behavioral outcomes are operationally linked by the number of cue presentations at memory retrieval. However, the behavioral properties and mechanistic determinants of the transition have not yet been explored; in particular, whether reconsolidation and extinction processes coexist or are mutually exclusive, depending on the exposure to non-reinforced retrieval events. We characterized both behaviorally and molecularly the transition from reconsolidation to extinction of conditioned fear and showed that an increase in calcineurin (CaN) in the basolateral amygdala (BLA) supports the shift from fear maintenance to fear inhibition. Gradually increasing the extent of retrieval induces a gradual decrease in freezing responses to the conditioned stimulus and a gradual increase in amygdala CaN level. This newly synthesized CaN is required for the extinction, but not the reconsolidation, of conditioned fear. During the transition from reconsolidation to extinction, we have revealed an insensitive state of the fear memory where NMDA-type glutamate receptor agonist and antagonist drugs are unable either to modulate CaN levels in the BLA or alter the reconsolidation or extinction processes. Together, our data indicate both that reconsolidation and extinction are mutually exclusive processes and also reveal the presence of a transitional, or “limbo,” state of the original memory between these two alternative outcomes of fear memory retrieval, when neither process is engaged. PMID:24523532

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

2014-01-01

298

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

PubMed

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

299

Molecular dynamics simulation of the deposition process of cold Ag-clusters under different landing conditions  

NASA Astrophysics Data System (ADS)

We present a series of molecular dynamics simulations on the surface deposition process of initially free silver clusters (Agn) with different sizes (n = 100-2000) and morphologies. During the whole deposition process the morphology of the clusters was studied as a function of the landing conditions. These conditions include variations of the depth and range of the substrate potential as well as the thermal coupling to the surface and a variation of the impact velocity of the free clusters. Depending on the applied conditions the clusters' final form ranges from spread out fragments via deformed and restructured heaps to quasi unchanged spherical clusters sitting at the surface. Under certain landing conditions larger clusters retain their initial multiply twinned morphology upon deposition, while smaller ones undergo structural transitions to form single domain particles. Furthermore, the occurrence of a structural transition depends on the initial structure—initially decahedral clusters tend to conserve their morphology better than icosahedral ones. The same behavior can also be observed in our experiments, where silver clusters were grown in helium nanodroplets and subsequently deposited on amorphous carbon substrates.

Thaler, Philipp; Volk, Alexander; Ratschek, Martin; Koch, Markus; Ernst, Wolfgang E.

2014-01-01

300

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

PubMed

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

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

2004-01-01

301

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

302

Experimental and ab initio studies of the reactive processes in gas phase i-C3H7Br and i-C3H7OH collisions with potassium ions  

NASA Astrophysics Data System (ADS)

Collisions between potassium ions and neutral i-C3H7Br and i-C3H7OH, all in their electronic ground state, have been studied in the 0.10-10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K+ + i-C3H7Br collisions KHBr+ formation was observed and quantified, while the analogous KH2O+ formation in K+ + i-C3H7OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C3H7+ and either KBr or KOH, respectively, have been observed. For all these processes, absolute cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr+ formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.

López, E.; Lucas, J. M.; de Andrés, J.; Albertí, M.; Bofill, J. M.; Bassi, D.; Aguilar, A.

2014-10-01

303

Simulating Collisions in the Solar System  

E-print Network

.2.5. Other physical processes in the Solar System in which collisions play a key role include the production the dust population. Roughly 15% of nearby stars surveyed by IRAS show infrared excess that could be replenished by collisions between larger parent bodies, possibly the functional equivalent of our own Kuiper

Richardson, Derek Charles

304

Molecular characterization of activated sludge from a seawater-processing wastewater treatment plant  

PubMed Central

Summary The prokaryotic community composition of activated sludge from a seawater?processing wastewater treatment plant (Almeria, Spain) was investigated by using the rRNA approach, combining different molecular techniques such as denaturing gradient gel electrophoresis (DGGE), clone libraries and in situ hybridization (FISH and CARD?FISH). Most of the sequences retrieved in the DGGE and the clone libraries were similar to uncultured members of different phyla. The most abundant sequence recovered from Bacteria in the clone library corresponded to a bacterium from the Deinococcus–Thermus cluster (almost 77% of the clones), and the library included members from other groups such as the Alpha, Gamma and Delta subclasses of Proteobacteria, the Bacteroidetes and Firmicutes. Concerning the archaeal clone library, we basically found sequences related to different orders of methanogenic Archaea, in correspondence with the recovered DGGE bands. Enumeration of DAPI (4?,6?diamidino?2?phenylindole) stained cells from two different activated sludge samples after a mechanical flocculation disruption revealed a mean cell count of 1.6?×?109?ml?1. Around 94% of DAPI counts (mean value from both samples) hybridized with a Bacteria specific probe. Alphaproteobacteria were the dominant bacterial group (36% of DAPI counts), while Beta?, Delta? and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes contributed to lower proportions (between 0.5–5.7% of DAPI counts). Archaea accounted only for 6% of DAPI counts. In addition, specific primers for amplification of the amoA (ammonia monooxygenase) gene were used to detect the presence of Beta, Gamma and archaeal nitrifiers, yielding positive amplifications only for Betaproteobacteria. This, together with negative in situ hybridizations with probes for well?known nitrifiying bacteria, suggests that nitrification is performed by still undetected microorganisms. In summary, the combination of the three approaches provided different and complementary pictures of the real assemblage composition and allowed to get closer to the main microorganisms involved in key processes of seawater?processing activated sludge. PMID:21414181

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

2011-01-01

305

Chronic alcohol exposure negatively impacts the physiological and molecular parameters of the renal biotin reabsorption process.  

PubMed

Normal body homeostasis of biotin is critically dependent on its renal recovery by kidney proximal tubular epithelial cells, a process that is mediated by the sodium-dependent multivitamin transporter (SMVT; a product of the SLC5A6 gene). Chronic ethanol consumption interferes with the renal reabsorption process of a variety of nutrients, including water-soluble vitamins. To date, however, there is nothing known about the effect of chronic alcohol feeding on physiological and molecular parameters of the renal biotin reabsorption process. We addressed these issues using rats and transgenic mice carrying the human SLC5A6 (P1P2) 5'-regulatory region as an in vivo model systems of alcohol exposure, and cultured human renal proximal tubular epithelial HK-2 cells chronically exposed to alcohol as an in vitro model of alcohol exposure. The [(3)H]biotin uptake results showed that chronic ethanol feeding in rats leads to a significant inhibition in carrier-mediated biotin transport across both renal brush border and basolateral membrane domains. This inhibition was associated with a marked reduction in the level of expression of SMVT protein, mRNA, and heterogenous nuclear RNA (hnRNA). Furthermore, studies with transgenic mice carrying the SLC5A6 5'-regulatory region showed that chronic alcohol feeding leads to a significant decrease in promoter activity. Studies with HK-2 cells chronically exposed to alcohol again showed a marked reduction in carrier-mediated biotin uptake, which was associated with a significant reduction in promoter activity of the human SLC5A6 5'-regulatory region. These findings demonstrate for the first time that chronic ethanol feeding inhibits renal biotin transport and that this effect is, at least in part, being exerted at the transcriptional level. PMID:21209005

Subramanian, Veedamali S; Subramanya, Sandeep B; Said, Hamid M

2011-03-01

306

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

E-print Network

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) hard-disk collision model. The numerical algorithm developed is suitable for simulating particle-laden flow of $N$ disk-shaped floes with arbitrary size distribution. 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 $\\bar{A}$ on the formation and characteristics of clusters is analyzed in detail. The...

Herman, Agnieszka

2011-01-01

307

Communication: Mapping water collisions for interstellar space conditions  

Microsoft Academic Search

We report a joint experimental and theoretical study that directly tests the quality of the potential energy surfaces used to calculate energy changing cross sections of water in collision with helium and molecular hydrogen, at conditions relevant for astrophysics. Fully state-to-state differential cross sections are measured for H2O-He and H2O-H2 collisions at 429 and 575 cm-1 collision energy, respectively. We

C.-H. Yang; G. Sarma; J. J. Ter Meulen; D. H. Parker; G. C. McBane; L. Wiesenfeld; A. Faure; Y. Scribano; N. Feautrier

2010-01-01

308

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

309

Molecular and physiological characterization of natural microbial communities isolated from a traditional Southern Italian processed sausage.  

PubMed

The development of the natural microbial populations during traditional processing of the "Salame di Senise", a typical little known sausage produced in the South of Italy, was investigated by using molecular and physiological techniques for taxonomic identification and technological characterization of strains. The application of RAPD-PCR over more than 90 colonies made it possible to isolate 18 bacterial and two yeast biotypes identified by partial rDNA sequencing as belonging mainly to three species of Bacillus, three species of Lactobacillus, three species of Staphylococcus and Debaryomyces hansenii. The physiological analyses revealed that the isolates belonging to Lactobacillus genus were the most acidifying, whereas Staphylococcus strains did not develop significant proteolytic and lipolytic activities. Interestingly, some Bacillus strains produced the highest values of proteolytic and lipolytic activities. The results for the technological properties of Bacillus strains isolated from this Southern Italian sausage, made without a selected starter, suggest that Bacillus strains, always present in meat curing, could play a role in the development of texture and organoleptic characteristics of the sausages. PMID:22061553

Baruzzi, Federico; Matarante, Alessandra; Caputo, Leonardo; Morea, Maria

2006-02-01

310

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

311

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

PubMed Central

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

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

2013-01-01

312

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

313

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

314

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

315

Application of Molecular Knowledge of Microbes to Studies of Ecological Processes: Why the Integration Is So Challenging  

E-print Network

Reports Application of Molecular Knowledge of Microbes to Studies of Ecological Processes: Why diversity decrease along an increasing natural nitrogen gradient?" Introduction Microbes are the drivers of decomposition and nutrient cycling both in aquatic and terrestrial environments. Microbes may also be dominant

Horton, Tom

316

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

Microsoft Academic Search

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),

Susan Deratzou

2006-01-01

317

The influence of flight experience on midair collision risk perception.  

PubMed

Although successful collision avoidance is presumed a learned skill, midair collision accidents typically involve highly experienced pilots. It is hypothesized that pilot complacency, arising from a history of incident-free flights, plays a role in the midair collision process. Pilot risk perception is explored using Laplace's Law of Succession, and the resulting perceived collision probability compared to reality. The two converge at around 5,000 hours of flight experience. PMID:1388583

Shuch, H P

1992-12-01

318

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

319

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

320

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

321

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

322

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

E-print Network

Ultra-cold Atom CollisionsUltra-cold Atom Collisions and Quantum Dynamics atand Quantum Dynamics are available at Ben-Gurion University to carry out research in ultra-cold atomic and molecular physics groups working on similar problems, including groups headed by Ami Vardi, Bilha Segev, Doron Cohen, Yshai

Band, Yehuda B.

323

Vibrational energy transfer in shocked molecular crystals.  

PubMed

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

Hooper, Joe

2010-01-01

324

The thermal model of a nonuniform molecular cloud with an IR source at the center  

Microsoft Academic Search

The energy equilibrium of molecular clouds with an IR source at the center is studied allowing the nonuniformity in density distribution. The thermal model of this kind of clouds is set up, in which several cooling and heating processes are considered, such as radiative cooling (or heating) by CO and H2O molecules, heating by dust-gas collisions, heating due to gravitational

Yuan Tang

1989-01-01

325

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

326

Self-interaction-free TDDFT for nonperturbative treatment of multiphoton processes of heteronuclear diatomic molecular systems in intense laser fields  

NASA Astrophysics Data System (ADS)

We present a self-interaction-free time-dependent density-functional theory (TDDFT) with proper asymptotic long-range potential for nonperturbative treatment of multiphoton processes of many-electron heteronuclear molecular systems in intense laser fields. A time-dependent generalized pseudospectral method is developed with the use of a new mass-weighted prolate spheroidal coordinate system for accurate solution of the electronic structure and TDDFT equations for two-center heteronuclear diatomic systems. The procedure allows nonuniform and optimal spatial grid discretization of the Hamiltonian in the adapted prolate spheroidal coordinates and a split operator scheme in energy representation is used for the time propagation of individual molecular spin orbital's in space and time. The theory is applied to a detailed all-electron study of high-order harmonic generation (HHG) and multiphoton ionization processes of CO in intense laser fields. Both even and odd-order harmonics are predicted for the CO molecule.

Heslar, John; Chu, Shih-I.

2007-06-01

327

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

SciTech Connect

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

Teboul, V.; Saiddine, M.; Accary, J.-B. [Institut des sciences et technologies moleculaires d' Angers, UMR CNRS 6200, Universite d' Angers, 2 Bd Lavoisier, F-49045 Angers (France); Nunzi, J.-M. [Departments of Chemistry and Physics, Queen's University, Kingston K7L 3N6, Ontario (Canada)

2011-03-21

328

An isomerization-induced cage-breaking process in a molecular glass former below T(g).  

PubMed

A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials. PMID:21428642

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

2011-03-21

329

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

NASA Astrophysics Data System (ADS)

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

Shuai, Zhigang; Peng, Qian

2014-04-01

330

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

331

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

EPA Science Inventory

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

332

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

333

Control of the atomic layer-by-layer growth process in laser molecular beam epitaxy with the emission monitoring method  

Microsoft Academic Search

In order to control the atomic layer-by-layer growth process in laser molecular beam epitaxy more strictly, the emission intensity accompanying the laser ablation of the target materials is monitored, and the thickness of each layer is estimated from the intensity. In some metal and oxide targets, such as Sr and CuO, the amount of the species generated by the ablation,

M. Kanai; T Kawai

1998-01-01

334

Will Spin-Relaxation Times in Molecular Magnets Permit Quantum Information Processing?  

NASA Astrophysics Data System (ADS)

Using X-band pulsed electron-spin resonance, we report the intrinsic spin-lattice (T1) and phase-coherence (T2) relaxation times in molecular nanomagnets for the first time. In Cr7M heterometallic wheels, with M=Ni and Mn, phase-coherence relaxation is dominated by the coupling of the electron spin to protons within the molecule. In deuterated samples T2 reaches 3?s at low temperatures, which is several orders of magnitude longer than the duration of spin manipulations, satisfying a prerequisite for the deployment of molecular nanomagnets in quantum information applications.

Ardavan, Arzhang; Rival, Olivier; Morton, John J. L.; Blundell, Stephen J.; Tyryshkin, Alexei M.; Timco, Grigore A.; Winpenny, Richard E. P.

2007-02-01

335

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

336

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

337

Chemical dynamics by molecular beam methods  

Microsoft Academic Search

The described research is classified in three separate categories: (a) theoretical analysis of glory scattering experiments; (b) measurements of kinetic energy thresholds (at very high energy resolution) for ion-pair production from molecular collisions, with subsequent derivation of molecular binding energies and electron affinities; and (c) formation of negative ions from high energy collisions of molecules with Cs. References to comprehensive

E. W. Rothe

1974-01-01

338

Cytochemical and molecular characteristics of the process of cornification during feather morphogenesis  

Microsoft Academic Search

Feathers are the most complex epidermal derivatives among vertebrates. The present review deals with the origin of feathers from archosaurian reptiles, the cellular and molecular aspects of feather morphogenesis, and focus on the synthesis of keratins and associated proteins. Feathers consist of different proteins among which exists a specialized group of small proteins called beta-keratins. Genes encoding these proteins in

Lorenzo Alibardi; Mattia Toni

2008-01-01

339

Surface Nano-Processes Induced by High-Speed Atomic and Molecular Beams  

Microsoft Academic Search

Surface temperature and gas pressure are major parameters for control of chemical reactions between gas molecules and solid surfaces, followed by ultra-thin layers formation or etching reactions. Molecular adsorption at surfaces are occasionally induced by translational kinetic energy of incident molecules even if the incident energy is only several eV. The chemical reaction field is extended into a bulk region

Yuden Teraoka

2007-01-01

340

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

PubMed

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

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

2010-01-01

341

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

342

Structure and relaxation processes of an anisotropic molecular fluid confined into 1D nanochannels  

E-print Network

Structural order parameters of a smectic liquid crystal confined into the columnar form of porous silicon are studied using neutron scattering and optical spectroscopic techniques. It is shown that both the translational and orientational anisotropic properties of the confined phase strongly couple to the one-dimensional character of the porous silicon matrix. The influence of this confinement induced anisotropic local structure on the molecular reorientations occuring in the picosecond timescale is discussed.

Ronan Lefort; Denis Morineau; Régis Guégan; Moréac Alain; Claude Ecolivet; Mohammed Guendouz

2006-05-04

343

The simulation of transport processes using the method of molecular dynamics. Self-diffusion coefficient  

Microsoft Academic Search

The possibility is investigated of using the method of molecular dynamics for calculating the self-diffusion coefficient of\\u000a liquids and gases. The exactness of calculation of the autocorrelation function of the velocity of molecules and of the self-diffusion\\u000a coefficient is systematically estimated. The characteristic errors of the method are analyzed. Correlations are constructed\\u000a which enable one to reduce the effect made

V. Ya. Rudyak; A. A. Belkin; D. A. Ivanov; V. V. Egorov

2008-01-01

344

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

345

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

346

MLL Becomes Functional through Intra-Molecular Interaction Not by Proteolytic Processing  

PubMed Central

The mixed lineage leukemia (MLL) protein is an epigenetic transcriptional regulator that controls proliferative expansion of immature hematopoietic progenitors, whose aberrant activation triggers leukemogenesis. A mature MLL protein is produced by formation of an intra-molecular complex and proteolytic cleavage. However the biological significance of these two post-transcriptional events remains unclear. To address their in vivo roles, mouse mutant alleles were created that exclusively express either a variant protein incapable of intra-molecular interaction (designated de) or an uncleavable mutant protein (designated uc). The de homozygous mice died during midgestation and manifested devastating failure in embryonic development and reduced numbers of hematopoietic progenitors, whereas uc homozygous mice displayed no apparent defects. Expression of MLL target genes was severely impaired in de homozygous fibroblasts but unaffected in uc homozygous fibroblasts. These results unequivocally demonstrate that intra-molecular complex formation is a crucial maturation step whereas proteolytic cleavage is dispensable for MLL-dependent gene activation and proliferation in vivo. PMID:24040009

Yokoyama, Akihiko; Ficara, Francesca; Murphy, Mark J.; Meisel, Christian; Hatanaka, Chikako; Kitabayashi, Issay; Cleary, Michael L.

2013-01-01

347

Electron collisions in gas switches  

SciTech Connect

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

Christophorou, L.G.

1989-01-01

348

Ultrarelativistic particle collisions.  

PubMed

We present results from numerical solution of the Einstein field equations describing the head-on collision of two solitons boosted to ultrarelativistic energies. We show, for the first time, that at sufficiently high energies the collision leads to black hole formation, consistent with hoop-conjecture arguments. This implies that the nonlinear gravitational interaction between the kinetic energy of the solitons causes gravitational collapse, and that arguments for black hole formation in super-Planck scale particle collisions are robust. PMID:20366461

Choptuik, Matthew W; Pretorius, Frans

2010-03-19

349

Molecular dynamics study on Ar ion bombardment effects in amorphous SiO{sub 2} deposition processes  

SciTech Connect

Argon ion bombardment effects on growing amorphous SiO{sub 2} films during reactive sputtering deposition processes were examined based on molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. The system we have considered here is a film that is subject to energetic Ar bombardment while it is formed by surface reactions of Si and O atoms separately supplied at low kinetic energies. It has been found that (1) Ar injections preferentially sputter O atoms from the surface over Si and (2) also have a compressing effect on the growing film during the deposition process. In other words, our MD/MC simulations have demonstrated at the atomic level that, with higher energy Ar injections, an amorphous SiO{sub 2} film grown in a reactive sputtering deposition process is denser and more Si rich.

Taguchi, Masafumi; Hamaguchi, Satoshi [Center for Atomic and Molecular Technologies, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 464-8603, Japan and Nippon Sheet Glass Co., 1 Kaidoshita, Konoike, Itami Hyogo 664-8520 (Japan); Center for Atomic and Molecular Technologies, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 464-8603 (Japan)

2006-12-15

350

Disequilibration by Planetary Collision  

NASA Astrophysics Data System (ADS)

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

Asphaug, E. I.; Jutzi, M.

2010-12-01

351

Ultrarelativistic oscillon collisions  

NASA Astrophysics Data System (ADS)

In this short paper we investigate the ultrarelativistic collisions of small amplitude oscillons in 1 +1 dimensions. Using the amplitude of the oscillons and the inverse relativistic boost factor ?-1 as the perturbation variables, we analytically calculate the leading order spatial and temporal phase shifts, and the change in the amplitude of the oscillons after the collisions. At leading order, we find that only the temporal phase shift receives a nonzero contribution, and that the collision is elastic. This work is also the first application of the general kinematic framework for understanding ultrarelativistic collisions [1] to intrinsically time-dependent solitons.

Amin, Mustafa A.; Banik, Indranil; Negreanu, Carina; Yang, I.-Sheng

2014-10-01

352

The effect of molecular aggregates over the interfacial charge transfer processes on dye sensitized solar cells  

NASA Astrophysics Data System (ADS)

The electron transfer reaction between the photoinjected electrons in the nanocrystalline TiO2 mesoporous sensitized films and the oxidized electrolyte in dye sensitized solar cells (DSSC) plays a major role on the device efficiency. In this communication we show that, although the presence of molecular aggregates on the free base porphyrin DSSC limits the device photocurrent response under illumination, they form an effective hydrophobic barrier against the oxidized electrolyte impeding fast back-electron transfer kinetics. Therefore, their drawback can be overcome by designing dyes with peripheral moieties that prevent the formation of the aggregates and are able to achieve efficiencies as high as 3.2% under full sun.

Planells, Miquel; Forneli, Amparo; Martínez-Ferrero, Eugenia; Sánchez-Díaz, Antonio; Sarmentero, Maria Angeles; Ballester, Pablo; Palomares, Emilio; O'Regan, Brian C.

2008-04-01

353

Robust treatment of collisions, contact and friction for cloth animation  

Microsoft Academic Search

We present an algorithm to efficiently and robustly process collisions, contact and friction in cloth simulation. It works with any technique for simulating the internal dynamics of the cloth, and allows true modeling of cloth thickness. We also show how our simulation data can be post-processed with a collision-aware subdivision scheme to produce smooth and interference free data for rendering.

Robert Bridson; Ronald Fedkiw; John Anderson

2002-01-01

354

Experimental study of the reactive processes in the gas phase K+ + i-C3H7Cl collisions: A comparison with Li and Na ions  

NASA Astrophysics Data System (ADS)

Reactive collisions between alkali ions (Li+, Na+, and K+) and halogenated hydrocarbon molecules have been studied recently in our research group. In this paper, we have reported on the K+ + i-C3H7Cl system in the 0.20-14.00 eV center-of-mass energy range using a radio frequency guided-ion beam apparatus developed in our laboratory. Aiming at increasing our knowledge about this kind of reactions, we compare our latest results for K+ with those obtained previously for Li+ and Na+. While the reaction channels are the same in all three cases, their energy profiles, reactivity, measured reactive cross-section energy dependences, and even their reaction mechanisms, differ widely. By comparing experimentally measured reactive cross-sections as a function of the collision energy with the ab initio calculations for the different potential energy surfaces, a qualitative interpretation of the dynamics of the three reactive systems is presented in the present work.

Aguilar, J.; Lucas, J. M.; de Andrés, J.; Albertí, M.; Bassi, D.; Aguilar, A.

2013-05-01

355

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, Miroslaw Marek; Laerke, Helle Nygaard; Knudsen, Knud Erik Bach

2012-01-01

356

Re-accretion Efficiencies in Small Impactor - Large Target Collisions  

NASA Astrophysics Data System (ADS)

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

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

2013-10-01

357

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

358

"Modeling Heterogeneous Catalytic Reactions: From the Molecular Process to the Technical System"  

E-print Network

. Deutschmann (Ed.), Wiley-VCH, Weinberg (2009). First-Principles Kinetic Monte Carlo Simulations on the surface chemistry, first-principles kinetic Monte Carlo (kMC) simulations for heterogeneous catalysis of elementary processes obviously needs to go be- yond a separate study of each microscopic process. Tak- ing

359

Collision statistics in sheared inelastic hard spheres  

E-print Network

The dynamics of sheared inelastic-hard-sphere systems are studied using non-equilibrium molecular dynamics simulations and direct simulation Monte Carlo. In the molecular dynamics simulations Lees-Edwards boundary conditions are used to impose the shear. The dimensions of the simulation box are chosen to ensure that the systems are homogeneous and that the shear is applied uniformly. Various system properties are monitored, including the one-particle velocity distribution, granular temperature, stress tensor, collision rates, and time between collisions. The one-particle velocity distribution is found to agree reasonably well with an anisotropic Gaussian distribution, with only a slight overpopulation of the high velocity tails. The velocity distribution is strongly anisotropic, especially at lower densities and lower values of the coefficient of restitution, with the largest variance in the direction of shear. The density dependence of the compressibility factor of the sheared inelastic hard sphere system is quite similar to that of elastic hard sphere fluids. As the systems become more inelastic, the glancing collisions begin to dominate more direct, head-on collisions. Examination of the distribution of the time between collisions indicates that the collisions experienced by the particles are strongly correlated in the highly inelastic systems. A comparison of the simulation data is made with DSMC simulation of the Enskog equation. Results of the kinetic model of Montanero et al. {[}Montanero et al., J. Fluid Mech. 389, 391 (1999){]} based on the Enskog equation are also included. In general, good agreement is found for high density, weakly inelastic systems.

Marcus N. Bannerman; Thomas E. Green; Paul Grassia; Leo Lue

2009-03-24

360

Low energy cluster impact simulated by molecular dynamics; angular distribution of sputtering yield and impact under various impact angles  

Microsoft Academic Search

The collision process of low energetic gold atoms and solid targets has been simulated using our molecular dynamics simulation code CLIMPACT II. The used algorithm is a third-order predictor Verlet algorithm [L. Verlet, Phys. Rev. 159 (1967) 98; W.F. van Gusteren and H.J.C. Berendsen, in: Molecular Liquids - Dynamics and Interfaces, A.J. Barnes et al., eds. (Reidel, 1984) p. 475.].

K. Barghorn; E. R. Hilf

1994-01-01

361

Ab initio potential energy surfaces and nonadiabatic collision dynamics in H++O2 system  

NASA Astrophysics Data System (ADS)

The adiabatic potential energy surfaces for the lowest five electronic states of 3A'' symmetry for the H++O2 collision system have been obtained at the multireference configuration interaction level of accuracy using Dunning's correlation consistent polarized valence triple zeta basis set. The radial nonadiabatic coupling terms and the mixing angle between the lowest two electronic states (1 3A'' and 2 3A''), which adiabatically correlate in the asymptotic limit to H(2S)+O2+(X 2?g) and H++O2(X 3?g-), respectively, have been computed using ab initio procedures at the same level of accuracy to yield the corresponding quasidiabatic potential energy matrix. The computed strengths of the vibrational coupling matrix elements reflect the trend observed for inelastic vibrational excitations of O2 in the experiments at collision energy of 9.5 eV. The quantum dynamics has been preformed on the newly obtained coupled quasidiabatic potential energy surfaces under the vibrational close-coupling rotational infinite-order sudden framework at the experimental collision energy of 9.5 eV. The present theoretical results for vibrational elastic/inelastic excitations of O2 are in overall good agreement with the available experimental data obtained from the proton energy-loss spectra in molecular beam experiments [F. A. Gianturco et al., J. Phys. B 14, 667 (1981)]. The results for the complementary charge transfer processes are also presented at this collision energy.

Amaran, Saieswari; Kumar, Sanjay

2008-04-01

362

Elastic and Inelastic Collisions  

ERIC Educational Resources Information Center

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

Gluck, Paul

2010-01-01

363

Molecular dynamics-based virtual screening: accelerating the drug discovery process by high-performance computing.  

PubMed

High-performance computing (HPC) has become a state strategic technology in a number of countries. One hypothesis is that HPC can accelerate biopharmaceutical innovation. Our experimental data demonstrate that HPC can significantly accelerate biopharmaceutical innovation by employing molecular dynamics-based virtual screening (MDVS). Without using HPC, MDVS for a 10K compound library with tens of nanoseconds of MD simulations requires years of computer time. In contrast, a state of the art HPC can be 600 times faster than an eight-core PC server is in screening a typical drug target (which contains about 40K atoms). Also, careful design of the GPU/CPU architecture can reduce the HPC costs. However, the communication cost of parallel computing is a bottleneck that acts as the main limit of further virtual screening improvements for drug innovations. PMID:24001302

Ge, Hu; Wang, Yu; Li, Chanjuan; Chen, Nanhao; Xie, Yufang; Xu, Mengyan; He, Yingyan; Gu, Xinchun; Wu, Ruibo; Gu, Qiong; Zeng, Liang; Xu, Jun

2013-10-28

364

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

NASA Astrophysics Data System (ADS)

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

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

2008-06-01

365

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

PubMed

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

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

2008-06-01

366

Molecular Dynamics Simulations of growth Process of SWNTs in CCVD Method from alcohol  

E-print Network

Shibuta and Shigeo Maruyama Department of Mechanical Engineering, The University of Tokyo 7-3-1 Hongo Maruyama E-mail: maruyama@photon.t.u-tokyo.ac.jp Fig. 1 Snapshots of metal-catalyzed growth process

Maruyama, Shigeo

367

Third Sound Pulse Collisions  

NASA Astrophysics Data System (ADS)

We report measurements of third sound pulses in head-on collisions (K. S. Ketola, S. Wang, and R. B. Hallock, Physica B 194--196), 651 (1994). as a function of superfluid ^4He film thickness, pulse amplitude and pulse width for temperatures near 1.5 K. The substrate is a borosilicate glass slide with two Ag thermal drivers and an Al transition edge bolometer located halfway between the drivers. By generating one heating pulse from each driver separated by a selectable time delay, we can measure the profile of a collision with the bolometer, or we can cause the collision to occur between the bolometer and one of the drivers and observe the scattered third sound pulse. We explore collisions for a variety of conditions and show how the pulse interactions depend on the drive amplitudes. Measurements of single cooling pulses, cooling pulse collisions and heating pulses in an applied steady film flow will also be presented.

Hallock, R. B.; Lilly, M. P.

1996-03-01

368

Supercritical Fluid Processing of Polymer Thin Films: An X-ray Study of Molecular-Level Porosity  

SciTech Connect

This paper reviews our recent experimental results that address the effects of solvent density inhomogeneities in supercritical carbon dioxide (scCO{sub 2}) on polymer thin film processing. The key phenomenon is excess sorption of CO{sub 2} molecules into polymer thin films even when the bulk miscibility with CO{sub 2} is very poor. We have found that the amount of the excess sorption is attributed to the large density fluctuations in scCO{sub 2} near the critical point. Further, taking advantage of the vitrification process of polymer chains through quick evaporation of CO{sub 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.

Koga,T.; Rafailovich, M.; Chu, B.; Douglas, J.; Satija, S.

2006-01-01

369

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

370

Electron loss of fast projectiles in the collisions with molecules  

E-print Network

The single and multiple electron loss of fast highly charged projectiles in the collisions with neutral molecules are studied within the framework of a nonperturbative approach. The cross sections for single, double, and triple electron losses are calculated for the collision system $Fe^{q+}\\to N_2$ ($q$=24, 25, 26) at the collision energies 10, 100, and 1000 MeV/u. The effects caused by the collision multiplicity and the orientation of the axis of target molecule are treated. It is shown that collision multiplicity effect leads to considerable differences for the cases of perpendicular and parallel orientations of the molecular axes with respect to the direction of the projectile motion, while for chaotic orientation such effect is negligible.

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

2011-05-23

371

Electron loss of fast projectiles in collisions with molecules  

SciTech Connect

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

Matveev, V. I.; Makarov, D. N. [Pomor State University, 4 Lomonosov Street, 163002 Arkhangelsk (Russian Federation); Rakhimov, Kh. Yu. [Department of Physics, National University of Uzbekistan, 100174 Tashkent (Uzbekistan)

2011-07-15

372

Energy transport through rare collisions  

E-print Network

We study a one-dimensional hamiltonian chain of masses perturbed by an energy conserving noise. The dynamics is such that, according to its hamiltonian part, particles move freely in cells and interact with their neighbors through collisions, made possible by a small overlap of size $\\epsilon > 0$ between near cells. The noise only randomly flips the velocity of the particles. If $\\epsilon \\rightarrow 0$, and if time is rescaled by a factor $1/{\\epsilon}$, we show that energy evolves autonomously according to a stochastic equation, which hydrodynamic limit is known in some cases. In particular, if only two different energies are present, the limiting process coincides with the simple symmetric exclusion process.

François Huveneers

2011-06-29

373

Processive ATP-driven substrate disassembly by the N-ethylmaleimide-sensitive factor (NSF) molecular machine.  

PubMed

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

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

2013-08-01

374

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; Kruger, Beate; Dandekar, Thomas

2013-01-01

375

Classical Theory of Atomic Collisions. I. Theory of Inelastic Collisions  

Microsoft Academic Search

In this paper, a classical theory of inelastic atomic collisions is evolved on the basis of the relations for binary collisions as well as for the Coulomb collisions derived in the laboratory system of coordinates. Built up as an approximation based on the binary collisions, i.e., the independent pair interactions of the individual elements of the colliding systems, the theory,

Michal Gryzinski

1965-01-01

376

Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes  

PubMed Central

Great progress has been made in understanding the regulation of expression of genes involved in secondary metabolism. Less is known about the mechanisms that govern the spatial distribution of the enzymes, cofactors, and substrates that mediate catalysis of secondary metabolites within the cell. Filamentous fungi in the genus Aspergillus synthesize an array of secondary metabolites and provide useful systems to analyze the mechanisms that mediate the temporal and spatial regulation of secondary metabolism in eukaryotes. For example, aflatoxin biosynthesis in A. parasiticus has been studied intensively because this mycotoxin is highly toxic, mutagenic, and carcinogenic in humans and animals. Using aflatoxin synthesis to illustrate key concepts, this review focuses on the mechanisms by which sub-cellular compartmentalization and intra-cellular molecular traffic contribute to the initiation and completion of secondary metabolism within the cell. We discuss the recent discovery of aflatoxisomes, specialized trafficking vesicles that participate in the compartmentalization of aflatoxin synthesis and export of the toxin to the cell exterior; this work provides a new and clearer understanding of how cells integrate secondary metabolism into basic cellular metabolism via the intracellular trafficking machinery. PMID:20519149

Roze, Ludmila V.; Chanda, Anindya; Linz, John E.

2010-01-01

377

A Steered Molecular Dynamics Study of Binding and Translocation Processes in the GABA Transporter  

PubMed Central

The entire substrate translocation pathway in the human GABA transporter (GAT-1) was explored for the endogenous substrate GABA and the anti-convulsive drug tiagabine. Following a steered molecular dynamics (SMD) approach, in which a harmonic restraining potential is applied to the ligand, dissociation and re-association of ligands were simulated revealing events leading to substrate (GABA) translocation and inhibitor (tiagabine) mechanism of action. We succeeded in turning the transporter from the outward facing occluded to the open-to-out conformation, and also to reorient the transporter to the open-to-in conformation. The simulations are validated by literature data and provide a substrate pathway fingerprint in terms of which, how, and in which sequence specific residues are interacted with. They reveal the essential functional roles of specific residues, e.g. the role of charged residues in the extracellular vestibule including two lysines (K76 (TM1) and K448 (TM10)) and a TM6-triad (D281, E283, and D287) in attracting and relocating substrates towards the secondary/interim substrate-binding site (S2). Likewise, E101 is highlighted as essential for the relocation of the substrate from the primary substrate-binding site (S1) towards the cytoplasm. PMID:22737235

Skovstrup, S?ren; David, Laurent; Taboureau, Olivier; J?rgensen, Flemming Steen

2012-01-01

378

Dynamical quantum processes of molecular beams at surfaces: dissociative adsorption of hydrogen on metal surfaces  

NASA Astrophysics Data System (ADS)

Due to the improvement of computer power and the development of efficient algorithms it is now possible to combine high-dimensional quantum dynamical calculations of the dissociative adsorption of molecular beams with reliable ab-initio potential energy surfaces (PES). In this brief review two recent examples of such studies of the systems {H2}/{Cu(111) }, where adsorption is hindered by a noticeable energy barrier, and {H2}/{Pd(100) }, where activated as well as non-activated paths to adsorption exist, are presented. The effect of lateral surface corrugation on the sticking probability in the tunneling and the classical regime and the role of additional parallel momentum are discussed in the context of the {H2}/{Cu(111) } results. For the system {H2}/{Pd(100) } it is shown that the initial decrease of the sticking probability with increasing kinetic energy, which is usually attributed to a precursor mechanism, can be explained by dynamical steering. In addition, the influence of rotation on the adsorption and desorption dynamics is examined.

Gross, Axel

1996-08-01

379

Control of Ultracold Collisions with Frequency-Chirped Light  

SciTech Connect

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

Wright, M.J.; Gould, P.L. [Department of Physics, U-3046, University of Connecticut, Storrs, Connecticut 06269 (United States); Gensemer, S.D. [Van der Waals-Zeeman Institut, Universiteit van Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Vala, J. [Department of Chemistry and Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720 (United States); Kosloff, R. [Department of Physical Chemistry and the Fritz Haber Research Center for Molecular Dynamics, the Hebrew University, 91094 Jerusalem (Israel)

2005-08-05

380

Insights into the semiclassical Wigner treatment of bimolecular collisions  

NASA Astrophysics Data System (ADS)

The semiclassical Wigner treatment of bimolecular collisions, proposed by Lee and Scully on a partly intuitive basis [J. Chem. Phys. 73, 2238 (1980)], is derived here from first principles. The derivation combines Heller's ideas [J. Chem. Phys. 62, 1544 (1975); Heller J. Chem. Phys. 65, 1289 (1976); Heller J. Chem. Phys. 75, 186 (1981)], the backward picture of molecular collisions [L. Bonnet, J. Chem. Phys. 133, 174108 (2010)] and the microreversibility principle.

Bonnet, L.

2013-09-01

381

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

E-print Network

Yasushi Shibuta and Shigeo Maruyama Department of Mechanical Engineering, The University of Tokyo 7 potential energy surfaces and MD simulation of the clustering process. [1] Y. Shibuta, S. Maruyama, The 26th Fullerene Nanotubes General Symposium (2004), P. 97. Corresponding Author: Shigeo Maruyama Fax: +81

Maruyama, Shigeo

382

The crucial role of atomic and molecular processes in the success of controlled fusion  

NASA Astrophysics Data System (ADS)

Atomic processes have played a key role in the success of the present and the next generation of magnetically and inertially confined controlled fusion experiments. Magnetic fusion experiments are beginning to access the plasma regimes needed for fusion reactors. Recent experiments on the TFTR tokamak at Princeton and the JET tokamak at Abingdon, UK, have produced fusion powers of 10-16 MW and temperatures in the 10 to 40 keV range. These achievements were made possible by impurity control and high power auxiliary heating, which both rely upon the successful utilization of atomic processes. Based on these and other experimental successes, in 1988 the US, Europe, Japan and Russia began participation in the International Thermonuclear Experimental Reactor project (ITER), with the goal of designing, constructing and operating a long pulse, ignited tokamak. The engineering design portion of the project will be completed in July 1998, and the ITER partners are now discussing an agreement for construction. Experiments on JT-60 U, JET, DIII-D, Alcator C-Mod, ASDEX Upgrade and other tokamaks together with computational models indicate that atomic processes can be used to reduce the peak heat fluxes on the wall to acceptable levels, control the impurity level, and minimize the impact of plasma disruptions in ITER. Two large stellarators, an alternative to the tokamak, are being built in Japan and Germany and control of atomic processes will be essential for their success. Comparable progress has also been made in Inertial Confinement Fusion. Experiments on NOVA, OMEGA, GEKKO XII and other laser facilities with both direct drive and indirect drive targets produce temperatures in the multi-keV range and capsule compression levels that scale to ignition for the National Ignition Facility (NIF) now under construction at the Lawrence Livermore National Laboratory. Atomic processes play a key role in the pellet compression and heating and are essential for diagnostics.

Post, Douglass E.

1998-07-01

383

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

384

Stellar Collisions within Very Wide Binaries  

NASA Astrophysics Data System (ADS)

Although rare in the Milky Way, star-star collisions are predicted to occur within the dense cores of globular clusters, in evolving triple star systems, and possibly very near the Galactic center. It has recently been shown that very wide binary star systems can have their stellar orbits driven to very eccentric states by other passing field stars and the Galactic tide, forcing close passages between companion stars. Here we report numerical simulations demonstrating that this process is a major but unrealized source of stellar collisions. Occasionally, the eccentricities of very wide binaries become so extreme that their periastron falls below the combined radii of the companion stars, and they collide during periastron passage. Tidal interactions between the companion stars prevent some collisions by shrinking the binary orbit thereby making it less susceptible to galactic perturbations. Nonetheless, this mechanism produces a stellar collision every 2500 years in the Galaxy, potentially making very wide binaries the dominant source of collisions in the Milky Way. These collisions should yield a small population of single, Li-depleted, rapidly rotating massive stars.

Kaib, Nathan A.; Raymond, S. N.

2014-01-01

385

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

386

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

Microsoft Academic Search

Background  Virus-like particles (VLP) have an increasing range of applications including vaccination, drug delivery, diagnostics, gene\\u000a therapy and nanotechnology. These developments require large quantities of particles that need to be obtained in efficient\\u000a and economic processes. Production of VLP in yeast is attractive, as it is a low-cost protein producer able to assemble viral\\u000a structural proteins into VLP. However, to date

William A Rodríguez-Limas; Keith EJ Tyo; Jens Nielsen; Octavio T Ramírez; Laura A Palomares

2011-01-01

387

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

388

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

PubMed Central

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

2005-01-01

389

Squeezed States and Particle Production in High Energy Collisions  

NASA Technical Reports Server (NTRS)

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

Bambah, Bindu A.

1996-01-01

390

Onset of radial flow in p+p collisions  

E-print Network

It has been debated for decades whether hadrons emerging from p+p collisions exhibit collective expansion. The answer is hindered by low multiplicity and large fluctuation in p+p collisions. Tsallis Blast-Wave (TBW) model is a thermodynamic approach, introduced to handle the overwhelming correlation and fluctuation in the hadronic processes. We have systematically studied the identified particle spectra in p+p collisions from RHIC to LHC using TBW and found no appreciable radial flow in p+p collisions below \\sqrt{s}=900 GeV. At LHC higher energy of 7 TeV in p+p collisions, the radial flow velocity achieves an average value of = 0.337 +/- 0.006. This flow velocity is comparable to that in peripheral (40-60%) Au+Au collisions at RHIC.

Kun Jiang; Yinying Zhu; Weitao Liu; Hongfang Chen; Cheng Li; Lijuan Ruan; Ming Shao; Zebo Tang; Zhangbu Xu

2013-12-16

391

Measurement of forward-backward asymmetry A{sub FB} and of the weak mixing angle in processes of dilepton production in proton-proton collisions at {radical} s = 7 TeV in the CMS experiment at the LHC  

SciTech Connect

The results obtained by measuring the forward-backward asymmetry (A{sub FB}) of Drell-Yan lepton pairs in proton-proton collisions at {radical} s = 7 TeV at the LHC are presented. This asymmetry is measured as a function of the dilepton mass and rapidity in the dielectron and dimuon channels. The values of A{sub FB} were found for invariant masses of dileptons in the range of 40 Less-Than-Or-Slanted-Equal-To M{sub ll} Less-Than-Or-Slanted-Equal-To 600 GeV. The results for the effective weak mixing angle that were deduced from data on dimuon production in Drell-Yan processes are also presented. The respective data sample was collected by using the Compact Muon Solenoid (CMS) detector over the period spanning the years 2010 and 2011. The measured asymmetry and the effective weak mixing are consistent with the respective Standard Model predictions.

Gorbunov, I. N., E-mail: Ilya.Gorbunov@cern.ch; Shmatov, S. V., E-mail: shmatov@cern.ch [Joint Institute for Nuclear Research (Russian Federation)

2013-09-15

392

Memory effects in relativistic heavy ion collisions  

NASA Astrophysics Data System (ADS)

We consider equilibration in relativistic nuclear dynamics starting from a nonequilibrium Green's-functions approach. The widely used Boltzmann-Uehling-Uhlenbeck equation is obtained only as the Markovian limit (i.e., negligible memory time). The actual memory time in energetic nuclear collisions turns out to be ~2-3 fm/c, which interferes substantially with the time scale of the relaxation process. The memory kernels of the collision process will be presented. Because of their more involved structure, depending sensitively on the kinematical regime, both less and more stopping power is observed in the reaction compared to the Markovian description.

Greiner, Carsten; Wagner, Klaus; Reinhard, Paul-Gerhard

1994-03-01

393

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

394

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

NASA Astrophysics Data System (ADS)

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

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

2012-11-01

395

New Caledonia a classic example of an arc continent collision  

NASA Astrophysics Data System (ADS)

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

Aitchison, J.

2011-12-01

396

Measurement of the underlying event in the Drell-Yan process in proton-proton collisions at ?{s} = 7 {TeV}  

NASA Astrophysics Data System (ADS)

A measurement of the underlying event (UE) activity in proton-proton collisions at a center-of-mass energy of 7 TeV is performed using Drell-Yan events in a data sample corresponding to an integrated luminosity of 2.2 fb-1, collected by the CMS experiment at the LHC. The activity measured in the muonic final state (qoverline {q} to?+?-) is corrected to the particle level and compared with the predictions of various Monte Carlo generators and hadronization models. The dependence of the UE activity on the dimuon invariant mass is well described by pythia and herwig++ tunes derived from the leading jet/track approach, illustrating the universality of the UE activity. The UE activity is observed to be independent of the dimuon invariant mass in the region above 40 GeV/ c 2, while a slow increase is observed with increasing transverse momentum of the dimuon system. The dependence of the UE activity on the transverse momentum of the dimuon system is accurately described by madgraph, which simulates multiple hard emissions.

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.; Hoch, M.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Krammer, M.; Liko, D.; Mikulec, I.; Pernicka, M.; Rahbaran, B.; Rohringer, C.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Taurok, A.; Teischinger, F.; Wagner, P.; Waltenberger, W.; Walzel, G.; Widl, E.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Bansal, S.; Benucci, L.; Cornelis, T.; 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.; Van Spilbeeck, A.; 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.; Léonard, A.; Marage, P. E.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wickens, J.; Adler, V.; Beernaert, K.; Cimmino, A.; Costantini, S.; Garcia, G.; Grunewald, M.; Klein, B.; Lellouch, J.; Marinov, A.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Vanelderen, L.; Verwilligen, P.; Walsh, S.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Bruno, G.; Ceard, L.; De Favereau De Jeneret, J.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Grégoire, G.; Hollar, J.; Lemaitre, V.; Liao, J.; Militaru, O.; Nuttens, C.; Pagano, D.; Pin, A.; Piotrzkowski, K.; Schul, N.; Beliy, N.; Caebergs, T.; Daubie, E.; Alves, G. A.; De Jesus Damiao, D.; Martins, T.; Pol, M. E.; Souza, M. H. G.; Aldá Júnior, W. L.; Carvalho, W.; Custódio, A.; 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.; Soares Jorge, L.; 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.; 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.; 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.; Asawatangtrakuldee, C.; Ban, Y.; Guo, S.; Guo, Y.; Li, W.; Liu, S.; Mao, Y.; Qian, S. J.; Teng, H.; Wang, S.; Zhu, B.; Zou, W.; Cabrera, A.; Gomez Moreno, B.; Osorio Oliveros, A. F.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; 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.; 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.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Ungaro, D.; Wendland, L.; Banzuzi, K.; 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.; Daci, N.; 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.; 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.; Falkiewicz, A.; Fay, J.; Gascon, S.; Gouzevitch, M.; Ille, B.; Kurca, T.; Le Grand, T.; Lethuillier, M.; Mirabito, L.; Perries, S.; Sordini, V.; Tosi, S.; Tschudi, Y.; Verdier, P.; Viret, S.

2012-09-01

397

An STM study of molecular exchange processes in organic thin film growth.  

PubMed

The growth of a fullerene derivative (PCBM) on top of a layer of a tetrathiafulvalene (TTF) derivative previously deposited on Au(111) has been studied by scanning tunneling microscopy (STM). The results show that the preferential interaction with the gold substrate induces the exchange of PCBM molecules with the exTTF monolayer, expelling exTTF molecules to the outer surface. This exchange process is forbidden when the thickness of the exTTF layer increases above the monolayer, and the larger surface energy of PCBM leads to the growth of 3D islands. PMID:25035072

Gallego, José M; Ecija, David; Martín, Nazario; Otero, Roberto; Miranda, Rodolfo

2014-09-01

398

Ensemble velocity of non-processive molecular motors with multiple chemical states  

E-print Network

We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of transition rates, reverse transition rates and nonlinearities in the elasticity can show interesting functional dependencies, which deviate significantly from the frequently assumed Michaelis-Menten form. We discuss how the oder of events in the duty cycle can be inferred from the measured dependence. The model also predicts the possibility of velocity reversal at a certain ATP concentration if the duty cycle contains several conformational changes of opposite directionalities.

Andrej Vilfan

2014-09-27

399

Ensemble velocity of non-processive molecular motors with multiple chemical states  

E-print Network

We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of transition rates, reverse transition rates and nonlinearities in the elasticity can show interesting functional dependencies, which deviate significantly from the frequently assumed Michaelis-Menten form. We discuss how the oder of events in the duty cycle can be inferred from the measured dependence. The model also predicts the possibility of velocity reversal at a certain ATP concentration if the duty cycle contains several conformational changes of opposite directionalities.

Vilfan, Andrej

2014-01-01

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

Determination of the molecular states of the processive endocellulase Thermobifida fusca Cel9A during crystalline cellulose depolymerization.  

PubMed

Detailed understanding of cell wall degrading enzymes is important for their modeling and industrial applications, including in the production of biofuels. Here we used Cel9A, a processive endocellulase from Thermobifida fusca, to demonstrate that cellulases that contain a catalytic domain (CD) attached to a cellulose binding module (CBM) by a flexible linker exist in three distinct molecular states. By measuring the ability of a soluble competitor to reduce Cel9A activity on an insoluble substrate, we show that the most common state of Cel9A is bound via its CBM, but with its CD unoccupied by the insoluble substrate. These findings are relevant for kinetic modeling and microscopy studies of modular glycoside hydrolases. PMID:21837665

Kostylev, Maxim; Moran-Mirabal, Jose M; Walker, Larry P; Wilson, David B

2012-01-01

402

Error Reduction in Molecular Tagging Velocimetry (MTV) Processing Using Image Filtering  

NASA Astrophysics Data System (ADS)

Prior work has shown that the error level in MTV measurements is closely tied to the image SN level. In practice the SN ratio will depend on experimental conditions such as attenuation, Field of View, laser power, camera, etc.; however, there is a minimum SN level that can be achieved for any given experiment. Experience has shown that MTV images typically have a SN=2-8. It is therefore desirable to be able to lower image noise after the images are acquired to reduce measurement error. In this work post processing MTV images using image filtering schemes such as Gaussian Blur, FFT (band pass), median filtering etc. was investigated using synthetic MTV images with added random noise. The synthetic images were filtered and then processed using a direct correlation technique. The results showed that for very noisy images (i.e. SN<4) the all filtering techniques improved the displacement error by 10-40%. As the SN increased filtering because less effective in decreasing error and in some cases increased the measurement error. The FFT band pass filter was most effective and improved measurement error for all SN levels.

Caso, Michael; Bohl, Douglas

2011-11-01

403

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 Felipe das Chagas e. Silva; Alves, Mônica Ghislaine Oliveira; Soares, Carlos Alexandre; Almeida, Janete Dias; da Silva Martinho, Herculano

2011-07-01

404

Molecular recognition and substrate mimicry drive the electron-transfer process between MIA40 and ALR  

PubMed Central

Oxidative protein folding in the mitochondrial intermembrane space requires the transfer of a disulfide bond from MIA40 to the substrate. During this process MIA40 is reduced and regenerated to a functional state through the interaction with the flavin-dependent sulfhydryl oxidase ALR. Here we present the mechanistic basis of ALR–MIA40 interaction at atomic resolution by biochemical and structural analyses of the mitochondrial ALR isoform and its covalent mixed disulfide intermediate with MIA40. This ALR isoform contains a folded FAD-binding domain at the C-terminus and an unstructured, flexible N-terminal domain, weakly and transiently interacting one with the other. A specific region of the N-terminal domain guides the interaction with the MIA40 substrate binding cleft (mimicking the interaction of the substrate itself), without being involved in the import of ALR. The hydrophobicity-driven binding of this region ensures precise protein–protein recognition needed for an efficient electron transfer process. PMID:21383138

Banci, Lucia; Bertini, Ivano; Calderone, Vito; Cefaro, Chiara; Ciofi-Baffoni, Simone; Gallo, Angelo; Kallergi, Emmanouela; Lionaki, Eirini; Pozidis, Charalambos; Tokatlidis, Kostas

2011-01-01

405

Molecular Dynamics simulation of evaporation processes of fluid bridges confined in slit-like pore  

E-print Network

A simple fluid, described by point-like particles interacting via the Lennard-Jones potential, is considered under confinement in a slit geometry between two walls at distance Lz apart for densities inside the vapor-liquid coexistence curve. Equilibrium then requires the coexistence of a liquid "bridge" between the two walls, and vapor in the remaining pore volume. We study this equilibrium for several choices of the wall-fluid interaction (corresponding to the full range from complete wetting to complete drying, for a macroscopically thick film), and consider also the kinetics of state changes in such a system. In particular, we study how this equilibrium is established by diffusion processes, when a liquid is inserted into an initially empty capillary (partial or complete evaporation into vacuum), or when the volume available for the vapor phase increases. We compare the diffusion constants describing the rates of these processes in such inhomogeneous systems to the diffusion constants in the corresponding bulk liquid and vapor phases.

Katarzyna Bucior; Leonid Yelash; Kurt Binder

2009-01-23

406

Cosmic Collisions Book List  

NSDL National Science Digital Library

This Cosmic Collisions reference list has nearly 20 books that are recommended for learning more about these hypersonic impacts. A short description is given for each title, along with author name and publisher. The references are categorized by grade level.

407

Time rate collision matrix  

SciTech Connect

The collision integral terms in Boltzmann equation are reformulated numerically leading to the substitution of the multiple integrals with a multiplicative matrix of the two colliding species velocity distribution functions which varies with the differential collision cross section. A matrix of lower rank may be constructed when one of the distribution functions is specified, in which case the matrix elements represent kinetic transition probabilities in the velocity space and the multiplication of the time rate collision matrix with the unknown velocity distribution function expresses the time rate of change of the distribution. The collision matrix may be used to describe the time evolution of systems in nonequilibrium conditions, to evaluate the rate of momentum and energy transfer between given species, or to generate validity criteria for linearized kinetic equations.

Stoenescu, M.L.; Smith, T.M.

1980-02-01

408

Cold heteromolecular dipolar collisions.  

PubMed

Cold molecules promise to reveal a rich set of novel collision dynamics in the low-energy regime. By combining for the first time the techniques of Stark deceleration, magnetic trapping, and cryogenic buffer gas cooling, we present the first experimental observation of cold collisions between two different species of state-selected neutral polar molecules. This has enabled an absolute measurement of the total trap loss cross sections between OH and ND(3) at a mean collision energy of 3.6 cm(-1) (5 K). Due to the dipolar interaction, the total cross section increases upon application of an external polarizing electric field. Cross sections computed from ab initio potential energy surfaces are in agreement with the measured value at zero external electric field. The theory presented here represents the first such analysis of collisions between a (2)? radical and a closed-shell polyatomic molecule. PMID:21881670

Sawyer, Brian C; Stuhl, Benjamin K; Yeo, Mark; Tscherbul, Timur V; Hummon, Matthew T; Xia, Yong; K?os, Jacek; Patterson, David; Doyle, John M; Ye, Jun

2011-11-14

409

Polarizing bubble collisions  

SciTech Connect

We predict the polarization of cosmic microwave background (CMB) photons that results from a cosmic bubble collision. The polarization is purely E-mode, symmetric around the axis pointing towards the collision bubble, and has several salient features in its radial dependence that can help distinguish it from a more conventional explanation for unusually cold or hot features in the CMB sky. The anomalous ''cold spot'' detected by the Wilkinson Microwave Anisotropy Probe (WMAP) satellite is a candidate for a feature produced by such a collision, and the Planck satellite and other proposed surveys will measure the polarization on it in the near future. The detection of such a collision would provide compelling evidence for the string theory landscape.

Czech, Bart?omiej; Larjo, Klaus; Levi, Thomas S.; Sigurdson, Kris [Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z1 (Canada); Kleban, Matthew, E-mail: czech@phas.ubc.ca, E-mail: mk161@nyu.edu, E-mail: larjo@phas.ubc.ca, E-mail: tslevi@phas.ubc.ca, E-mail: krs@phas.ubc.ca [CCPP, Department of Physics, New York University, New York, NY 10003 (United States)

2010-12-01

410

"Cosmic Collisions" Planetarium Show  

E-print Network

of a broader learning experience. What you will see in the Cosmic Collisions program: · Meteors ("shooting to Align Program Material with National SoLs #12;High School see High School Alignment Table "Strong

Mathis, Wayne N.

411

Collision-induced dissociation of uracil and its derivatives.  

PubMed

The collision-induced dissociation of protonated uracil has been studied by tandem mass spectrometry using models extensively labeled with stable isotopes, and derivatives of the kinds found in nucleic acids. Following collisional activation at 30 eV translational energy, protonated uracil dissociates through two principal pathways which do not occur in electron ionization mass spectra: (1) elimination of NH3 almost entirely from N-3, followed by loss of CO from C-4, 0(4); (2) loss of H2O, equally from 0(2) and 0(4). Elimination of HNCO, also the principal dissociation process from odd-electron molecular ions, proceeds primarily by loss of N-3, C-Z, O(2) and 10% from N-l, C-Z, 0(2). Several secondary dissociation products are formed with quantitative site specificity of skeletal atoms: C,HO+ (4-C0, C-5, C-6); H2CN+ (N-l, C-6); C2H2+ (N-l, C-5, C-6). First-step dissociation reactions are interpreted in terms of pyrimidine ring opening at likely sites of protonation after collisional activation of MH+. Collision-induced dissociation mass spectra of uracils with structural themes common to nucleic acids (methylation, replacement of 0 by S, C-5 substitution) follow analogous reaction paths which permit assignment of sites of substitution, and exhibit ion abundance changes attributed to differences in substituent basicity and electron density. PMID:24222588

Nelson, C C; McCloskey, J A

1994-05-01

412

Interactive collision detection  

Microsoft Academic Search

Collision detection and response can make a virtual-reality application seem more believable. Unfortunately, existing collision-detection algorithms are too slow for interactive use. The authors present a new algorithm that is not only fast but also interruptible, allowing an application to trade quality for more speed. The algorithm uses simple four-dimensional geometry to approximate motion, and sets of spheres to approximate

Philip M. Hubbard

1993-01-01

413

Launch Collision Probability  

NASA Technical Reports Server (NTRS)

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

Bollenbacher, Gary; Guptill, James D.

1999-01-01

414

Expansion shock waves in the implosion process from a time-reversible molecular-dynamics simulation of a dual explosion process  

NASA Astrophysics Data System (ADS)

Why does not an expansion shock wave exist in a gaseous medium in nature? The reason has been widely believed to be the irreversibility in nature, while an obvious demonstration for this belief has not been accomplished yet. In order to resolve the question from a microscopic viewpoint, an implosion process dual to an explosion process was investigated by means of the molecular-dynamics method (MD). To this aim, we employed a "bit-reversible algorithm (Bit MD)" that was completely time-reversible in a microscopic viewpoint and was free from any round-off error. Here we show that, through a dual implosion simulation (i.e., a time-reversible simulation of the explosion), a kind of expansion shock wave is successfully formed in the Bit MD simulation. Furthermore, we show that when the controlled noise is intentionally added to the Bit MD, the expansion shock wave disappears dramatically and turns into an isentropic expansion wave, even if the noise is extremely small. Since the controlled noise gives rise to the irreversibility in the Bit MD simulation, it can be concluded that the irreversibility in the system prohibits the expansion shock wave from appearing in the system.

Komatsu, Nobuyoshi; Abe, Takashi

2007-05-01

415

Electromagnetic signatures of collision zones in India  

NASA Astrophysics Data System (ADS)

Indian subcontinent has experienced intense tectonic activity within the continent in the form of subduction, continent-continent collision, subduction-collision-accretion tectonics. Deep electrical signatures of intense tectonic activity are presented for three different regions: Himalayan region, Central Indian Tectonic zone and Southern Granulite terrain. Two long traverses at each region are discussed along with other geophysical data. The geoelectric sections across the Himalayan region have shown a clear northward dipping signature of the anomalous conductive features at upper to mid-crustal depths. This model gave a clear evidence for the collision and subduction processes. The profiles across the Central Indian tectonic zone constituting major east-west trending faults and mobile belts provided the evidence for the presence of mantle derived fluids at mid-crustal depths and also gave a clear evidence for the collision processes between the Bundelkhand craton and the Dharwar craton. The collision-accretion tectonic process is observed in Southern Granulite terrain of south India. Evidence for the exhumation of mantle de