These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
1

Semiclassical theory of electronically nonadiabatic transitions in molecular collision processes  

NASA Technical Reports Server (NTRS)

An introductory account of the semiclassical theory of the S-matrix for molecular collision processes is presented, with special emphasis on electronically nonadiabatic transitions. This theory is based on the incorporation of classical mechanics with quantum superposition, and in practice makes use of the analytic continuation of classical mechanics into the complex space of time domain. The relevant concepts of molecular scattering theory and related dynamical models are described and the formalism is developed and illustrated with simple examples - collinear collision of the A+BC type. The theory is then extended to include the effects of laser-induced nonadiabatic transitions. Two bound continuum processes collisional ionization and collision-induced emission also amenable to the same general semiclassical treatment are discussed.

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

1979-01-01

2

Molecular collision processes in the presence of picosecond laser pulses  

NASA Technical Reports Server (NTRS)

Radiative transitions in molecular collision processes taking place in the presence of picosecond pulses are studied within a semiclassical formalism. An expression for adiabatic potential surfaces in the electronic-field representation is obtained, which directly leads to the evaluation of transition probabilities. Calculations with a Landau-Zener-type model indicate that picosecond pulses can be much more effective in inducing transitions than a single long pulse of the same intensity and the same total energy, if the intensity is sufficiently high that the perturbation treatment is not valid.

Lee, H. W.; George, T. F.

1979-01-01

3

Is photon angular momentum important in molecular collision processes occurring in a laser field  

NASA Technical Reports Server (NTRS)

The importance of the rigorous treatment of photon angular momentum in molecular-collision processes occurring in the presence of intense radiation is investigated. An alternate approximate treatment, which essentially neglects the angular momentum coupling between the photon and the molecular degrees of freedom by averaging over the angular dependence of the interaction matrix elements, is presented and applied to a model calculation. The degeneracy-averaged results of this calculation compare remarkably well with the results of a rigorous calculation, from which we conclude (with reservation) that the explicit consideration of photoangular momentum coupling in molecular-collision problems is unnecessary.

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

1978-01-01

4

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

SciTech Connect

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

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

2011-02-15

5

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

6

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

PubMed

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

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

2014-12-21

7

Molecular collisions coming into focus.  

PubMed

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

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

2014-08-14

8

Molecular Dissociation Induced by Electron Collisions  

NASA Astrophysics Data System (ADS)

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

Wolf, Andreas

2009-05-01

9

Ab Initio Molecular Dynamics Simulations of Molecular Collisions of Nitromethane  

Microsoft Academic Search

Ab initio molecular dynamics simulations of bimolecular collisions of nitromethane, and collisions of one nitromethane molecule into a cluster of 12 nitromethane molecules have been performed. For the bimolecular simulations we have examined a variety of collision orientations and collision velocities between 6.5 and 12.0 km\\/s. The lowest dissociation threshold velocity found was 7.0 km\\/s for an anti-parallel collision orientation.

Dongqing Wei; Fan Zhang; Tom K. Woo

2002-01-01

10

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

11

The "Collisions Cube" Molecular Dynamics Simulator.  

ERIC Educational Resources Information Center

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

Nash, John J.; Smith, Paul E.

1995-01-01

12

Cold State-Selected Molecular Collisions and Reactions  

E-print Network

Cold State-Selected Molecular Collisions and Reactions Benjamin K. Stuhl,1 Matthew T. Hummon,2 of techniques for produc- ing cold and even ultracold molecules without a perturbing rare-gas cluster shell by relatively simple, long-range interactions that sidestep a great deal of short-range chemical complexity

Jin, Deborah

13

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

NASA Technical Reports Server (NTRS)

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

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

1978-01-01

14

Electron capture processes in Li2+ + H collisions  

NASA Astrophysics Data System (ADS)

The electron capture processes in Li2 + + H collisions have been investigated by using the quantum-mechanical molecular-orbital close-coupling method and the two-center atomic-orbital close-coupling method in the energy ranges of 10-8-10 keV/u and 0.1-300 keV/u, respectively. The capture to singlet and triplet systems of states of Li+(1s,nl2S + 1L) is considered separately. Total, n,S-resolved and n,l,S-resolved electron capture cross sections are calculated and compared with the results of available experimental and theoretical studies. The present calculations show that the n = 2 shell of Li+ is the main capture channel for all energies considered in both the singlet and triplet case. While for collision energies E> 5 keV/u, the cross sections for capture to the n = 2 manifold are of the same order of magnitude for both the singlet and triplet states (with the 2p capture cross section being dominant), for energies below ~5 keV/u the cross sections for capture to the n = 2 triplet manifold is significantly (more than three orders of magnitude at 0.1 keV/u) larger than that for capture to the n = 2 singlet manifold of states (with the 2s capture cross section being dominant). The capture dynamics at low collision energies is discussed in considerable detail, revealing the important role of rotational couplings in population of l> 0 capture states. The elastic scattering processes have been studied as well in the energy range of 10-8-1 keV/u. The calculated elastic scattering cross section is much larger than the electron capture cross section in both the singlet and triplet case. However, as the collision energy increases, the difference between the elastic and electron capture cross sections decreases rapidly.

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

2015-01-01

15

Laser-enhanced dynamics in molecular rate processes  

NASA Technical Reports Server (NTRS)

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

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

1978-01-01

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

Atomic Collision Processes for Astrophysical and Laboratory Plasmas  

NASA Astrophysics Data System (ADS)

An accurate knowledge of atomic collision processes is important for a better understanding of many astrophysical and laboratory plasmas. Collision databases which contain electron-impact excitation, ionization, and recombination cross sections and temperature dependent rate coefficients have been constructed using perturbative distorted-wave methods and non-perturbative R-matrix pseudo-states and time-dependent close-coupling methods. We present recent atomic collision results.

Pindzola, M. S.; Loch, S. D.; Ballance, C. P.; Abdel-Naby, Sh A.; Lee, T. G.; Colgan, J.; Fontes, C. J.; Badnell, N. R.; O'Mullane, M. G.

2014-11-01

18

Collision processes in the northern Molucca Sea  

NASA Astrophysics Data System (ADS)

The Mindanao-Molucca Sea region is a collision zone between two facing island arc systems. The West Mindanao Arc, which was active from the Cretaceous through the Quaternary, apparently collided in the mid-Tertiary with the East Mindanao Arc, which was active from the Cretaceous through the Oligocene. Following the collision in the Miocene, the Agusan-Davao Trough was filled with coarse clastic sediments. The ophiolite terrane exposed in the Pujada Peninsula was probably emplaced during this collision. In the Molucca Sea region the collision between the Halmahera Arc and the Sangihe Arc is still active. Gravity data and seismic reflection profiles indicate a crustal break between the Talaud Ridge and southern Mindanao. The deformed rocks of the Talaud Islands probably represent the northern limit of the forearc terrane of the Halmahera Arc system. The East Sangihe and West Halmahera thrusts can be followed, via seismic reflection data, northward to the latitude of Talaud. The origin of the Snellius Ridge complex remains obscure, but we interpret it to be the northern extension of the Halmahera Arc terrane. A tectonic reconstruction for this complex region proposes that the collision in the Mindanao region occurred between two intraoceanic arc terranes with very little intervening sediment. The southern end of the eastern Mindanao Arc was connected with the northern end of the Halmahera Arc by a transform fault. We suggest that the thick sediments presently being deformed in the Molucca Sea collision zone were eroded from New Guinea and Halmahera in the south and from the collision zone in Mindanao. A substantial amount of strike-slip motion has probably occurred during the collision in Mindanao. In response to the collision, two new subduction zones, at the Cotabato and Philippine trenches, are propagating southward.

Moore, Gregory F.; Silver, Eli A.

19

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

E-print Network

Prediction of Peptide Ion Collision Cross Sections from Topological Molecular Structure and Amino-property relationships (QSPRs) have been developed to predict the ion mobility spec- trometry (IMS) collision cross to accurately predict the collision cross section. The models were built using multiple linear regression (MLR

Clemmer, David E.

20

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

21

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

22

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

23

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

24

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

25

Attosecond timing the ultrafast charge-transfer process in atomic collisions  

SciTech Connect

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

Hu, S. X. [Laboratory for Laser Energetics, University of Rochester, 250 East River Road, Rochester, New York 14623 (United States)

2011-04-15

26

Effect of laser frequency on a collision-induced radiative process  

NASA Technical Reports Server (NTRS)

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.

1981-01-01

27

July 19 , 2007 I.Rubinskiy: Exclusive processes in ep Collisions at HERA, EPS07 1 Exclusive processes in ep Collisions  

E-print Network

July 19 , 2007 I.Rubinskiy: Exclusive processes in ep Collisions at HERA, EPS07 1 Exclusive processes in ep Collisions at HERA Igor Rubinskiy On behalf of H1 and ZEUS = ,/,,,0 0* JV pVp #12;July 19 , 2007 I.Rubinskiy: Exclusive processes in ep Collisions at HERA, EPS07 2 Why are we measuring IP `soft

28

Crossed molecular beams study of inelastic non-adiabatic processes in gas phase collisions between sodium ions and ZnBr2 molecules in the 0.10-3.50 keV energy range.  

PubMed

Inelastic electronically non-adiabatic reactions between Na(+) ions and neutral ZnBr(2) molecules, both in their electronic ground state, have been studied using crossed beams techniques and measuring the decaying emission radiation of the excited species produced. The fluorescent emission corresponding to Na(3 (2)P) produced by a charge transfer reaction was observed, as well as that corresponding to the decay of Zn(4s 5s (3)S), generated by dissociation of the neutral target molecule, to Zn(4s 4p (3)P). The phosphorescent decaying emission of Zn*(4s 4p (3)P) to the zinc ground state was also observed. For each emission process, the cross section energy dependences have been measured in the 0.10-3.50 keV energy range in the laboratory system. The ground electronic state of the (NaZnBr(2))(+) collision system has been characterized by ab initio chemical structure calculations at the second order Möller-Plesset perturbation level of theory using pseudo-potentials. By performing restricted open shell Hartree-Fock calculations for C(2v) geometries, four singlet and four triplet potential energy surfaces of the system have been calculated and used to interpret qualitatively the observed reactions. A simple two-state dynamical model is presented that allows an estimation of the maximum values for measured cross sections at high collision energies to be made. PMID:23083158

de Andrés, J; Lucas, J M; Albertí, M; Bofill, J M; Belyaev, A; Aguilar, A

2012-10-21

29

Crossed molecular beams study of inelastic non-adiabatic processes in gas phase collisions between sodium ions and ZnBr2 molecules in the 0.10-3.50 keV energy range  

NASA Astrophysics Data System (ADS)

Inelastic electronically non-adiabatic reactions between Na+ ions and neutral ZnBr2 molecules, both in their electronic ground state, have been studied using crossed beams techniques and measuring the decaying emission radiation of the excited species produced. The fluorescent emission corresponding to Na(3 2P) produced by a charge transfer reaction was observed, as well as that corresponding to the decay of Zn(4s 5s 3S), generated by dissociation of the neutral target molecule, to Zn(4s 4p 3P). The phosphorescent decaying emission of Zn*(4s 4p 3P) to the zinc ground state was also observed. For each emission process, the cross section energy dependences have been measured in the 0.10-3.50 keV energy range in the laboratory system. The ground electronic state of the (NaZnBr2)+ collision system has been characterized by ab initio chemical structure calculations at the second order Möller-Plesset perturbation level of theory using pseudo-potentials. By performing restricted open shell Hartree-Fock calculations for C2v geometries, four singlet and four triplet potential energy surfaces of the system have been calculated and used to interpret qualitatively the observed reactions. A simple two-state dynamical model is presented that allows an estimation of the maximum values for measured cross sections at high collision energies to be made.

de Andrés, J.; Lucas, J. M.; Albertí, M.; Bofill, J. M.; Belyaev, A.; Aguilar, A.

2012-10-01

30

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

31

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

SciTech Connect

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

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

2010-09-15

32

FEATURE ARTICLE Surface Processes Induced by Collisions  

E-print Network

) are important and may play a central role in the mechanism governing heterogeneous catalytic reactions at high pressures and elevated temperatures. A number of different CIPs are discussed in this article with a strong significantly. The potential importance of this process for inducing novel catalytic routes on surfaces

Zeiri, Yehuda

33

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

NASA Astrophysics Data System (ADS)

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

Larriba, Carlos; Hogan, Christopher J.

2013-10-01

34

Spin effects in hard collision processes  

SciTech Connect

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

Ranft, G.; Ranft, J.

1984-05-01

35

Satellite structure in the 2psigma molecular orbital transitions in slow heavy ion collisions  

SciTech Connect

The binding energy of the 2psigma molecular orbital formed transiently in a slow heavy ion collision shows a flat minimum at a large internuclear distance. Electronic transitions in this minimum provide a satellite structure in the 2psigma X-ray continuum, which was not found in the original search. New measurements show that the satellite is only evident at very small collision velocities, since the collision broadening is much larger for asymmetric collision systems than the theory predicts. The present theory of collision broadening takes into account only the linear term of the change in transition energy dE/dR which may not be appropriate in cases where the second term d/sup 2/E/dR/sup 2/ is likely to be dominant.

Stockli, P.

1983-04-01

36

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

37

The Accuracy of Molecular Processes  

NASA Astrophysics Data System (ADS)

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

Stavans, Joel

38

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

NASA Astrophysics Data System (ADS)

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

Ati?, Murat; Özdo?an, Cem; Güvenç, Ziya B.

39

Fermionic Molecular Dynamics: Multifragmentation in heavy-ion collisions and in excited nuclei  

E-print Network

Within Fermionic Molecular Dynamics we investigate fragmentation of a compound system which was created in a heavy-ion collision at a beam energy in the Fermi energy domain and the decay of excited iron nuclei. We show that in FMD many-body correlations play an important role in the formation of fragments.

H. Feldmeier; J. Schnack

1997-03-17

40

1982 bibliography of atomic and molecular processes  

SciTech Connect

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

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

1984-05-01

41

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

42

1985 bibliography of atomic and molecular processes  

SciTech Connect

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

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

1986-06-01

43

1984 Bibliography of atomic and molecular processes  

SciTech Connect

This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

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

1985-04-01

44

Classical model for laser-induced nonadiabatic collision processes  

NASA Astrophysics Data System (ADS)

By synthesizing earlier work of Orel and Miller and of Meyer, McCurdy, and Miller, a model for describing laser-induced electronically nonadiabatic collision processes is constructed which treats all degrees of freedom—heavy particle (i.e., translation, rotation, and vibration) electronic, and photon—by classical mechanics. This then makes it relatively easy to carry out calculations to simulate such processes within a dynamically consistent framework. Application is made to the test case H+LiF?Li+HF reaction considered by Light and Altenberger-Siczek. The most interesting feature revealed by these classical calculations is maxima in the reaction probability as a function of initial translational energy at energies below the laser-free threshold. It is seen that this structure can be understood as a Franck-Condon-like effect.

Orel, Ann E.; Miller, William H.

1980-07-01

45

Excitation processes in proton collisions with Li atoms  

NASA Astrophysics Data System (ADS)

Excitation processes in proton collisions with Li are studied by direct solution of the time-dependent Schrödinger equation in cylindrical coordinates. Within a straight-line trajectory approximation, a time-dependent close-coupling method based on an expansion of a one-electron 3D wavefunction in rotational functions is used to calculate excitation cross sections at incident energies ranging from 10 keV to 200 keV. A peudopotential method is used to treat the 1s^2 core. The time-evolved wavefunction which includes all the inelastic processes, including charge transfer, excitation and ionization, is projected onto the lattice states to obtain excitation cross sections for the Li(2s) to Li(2p,3l,4l) transitions. Results are compared with the existing data. This work was supported in part by grants from US DOE. Computational work was carried out at NERSC in Oakland, California.

Lee, Teck-Ghee; Pindzola, M. S.

2011-06-01

46

Molecular sieving silica membrane fabrication process  

DOEpatents

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

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

1999-08-10

47

Molecular sieving silica membrane fabrication process  

DOEpatents

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

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

1999-01-01

48

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

49

Dynamical processes of low-energy carbon ion collision with the graphene supported by diamond  

NASA Astrophysics Data System (ADS)

The dynamical processes of a low-energy carbon ion collision with the graphene sheet supported by diamond at three impact positions are studied by using empirical potential molecular dynamics simulations. The energy transformation and the structural evolution have been studied. Five types of processes are observed: adsorption, hybridization, defects formation in diamond, atom emission and transmission. We find that the irradiation damage is closely related to the incident energy and impact position. In our simulations, as the projectile collides at a graphene atom, it transfers most of its energy to the primary knock-on atom, and defects are created in graphene. When the projectile moves perpendicular towards the center of a C-C bond in the graphene sheet, the energy transferred from the projectile to the atoms associated with the bond increases firstly and then decreases with the increasing incident energy, and the graphene sheet remains two-dimensional crystal structure after collision when the incident energy is larger than 360 eV. While the impact location is the center of a hexagonal ring on the graphene sheet, the energy transferred from the projectile to the atoms of the target ring is very small regardless of how large is the incident energy, and the graphene sheet is able to keep perfect crystal structure when the incident energy is larger than 34 eV.

Dai, Jinxia; Zhang, Chao; Mao, Fei; Cheng, Wei; Zhang, Feng-Shou

2014-09-01

50

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite  

E-print Network

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

A. Ito; H. Nakamura

2006-04-24

51

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

SciTech Connect

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

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

2009-04-03

52

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

NASA Astrophysics Data System (ADS)

We investigate the formation and evolution of giant molecular clouds (GMCs) in a Milky-Way-like disk galaxy with a flat rotation curve. We perform a series of three-dimensional adaptive mesh refinement numerical simulations that follow both the global evolution on scales of ~20 kpc and resolve down to scales lsim10 pc with a multiphase atomic interstellar medium. In this first study, we omit star formation and feedback, and focus on the processes of gravitational instability and cloud collisions and interactions. We define clouds as regions with n H >= 100 cm-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 ~140 Myr a large fraction of the gas in the disk has fragmented into clouds with masses ~106 M sun and a mass spectrum similar to that of Galactic GMCs. The disk settles into a quasi-steady-state in which gravitational scattering of clouds keeps the disk near the threshold of global gravitational instability. The cloud collision time is found to be a small fraction, ~1/5, of the orbital time, and this is an efficient mechanism to inject turbulence into the clouds. This helps to keep clouds only moderately gravitationally bound, with virial parameters of order unity. Many other observed GMC properties, such as mass surface density, angular momentum, velocity dispersion, and vertical distribution, can be accounted for in this simple model with no stellar feedback.

Tasker, Elizabeth J.; Tan, Jonathan C.

2009-07-01

53

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

NASA Technical Reports Server (NTRS)

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

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

1979-01-01

54

Nuclear collision processes around the Bragg peak in proton therapy.  

PubMed

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

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

2010-01-01

55

Molecular dynamics simulation of defect production in collision cascades in zircon  

NASA Astrophysics Data System (ADS)

Defect production in collision cascades in zircon has been examined by molecular dynamics simulations using a partial charge model combined with the Ziegler-Biersack-Littmark potential. U, Zr, Si and O recoils with energies ranging from 250 eV to 5 keV were simulated in the NVE ensemble. To obtain good statistics, 5-10 cascades in randomly chosen directions were simulated for each ion and energy. The damage consists of mainly Si and O Frenkel pairs, a smaller number of Zr Frenkel pairs, and Zr on Si antisite defects. Defect production, interstitial clustering, ion beam mixing and Si-O-Si polymerization increase with PKA mass and energy.

Devanathan, R.; Corrales, L. R.; Weber, W. J.; Chartier, A.; Meis, C.

2005-01-01

56

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

57

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

NASA Astrophysics Data System (ADS)

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

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

1994-05-01

58

Post-collision interaction manifestation in molecular systems probed by photoelectron-molecular ion coincidences  

NASA Astrophysics Data System (ADS)

S1s photoionization in carbonyl sulfide (OCS), followed by multiple Auger decay is investigated both experimentally and theoretically, by means of photoelectron-ion coincidences. A strong influence of post-collision interaction is observed in the energy shift and the distortion of the photoelectron spectra. The magnitude of this effect depends on the total charge of the ionic fragments, i.e., on the number of electrons emitted during the decay of the inner vacancy. A satisfactory agreement is found between experiment and theory, which allows us to estimate the lifetimes of the various two-hole states of the intermediate OCS2 + ion.

Bomme, C.; Guillemin, R.; Sheinerman, S.; Marin, T.; Journel, L.; Marchenko, T.; Kushawaha, R. K.; Trcera, N.; Piancastelli, M. N.; Simon, M.

2013-11-01

59

Green-solvent-processed molecular solar cells.  

PubMed

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

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

2014-12-22

60

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

61

An angular momentum approximation for molecular collisions in the presence of intense laser radiation  

NASA Technical Reports Server (NTRS)

An approximation to a previously presented rigorous description of molecular (atom-atom) collisions occurring in the presence of intense radiation is investigated. This rigorous description explicitly considers the angular momentum transferred between the molecule and the radiation field in the absorption or emission of a photon, but involves a complicated system of close-coupled equations which must be solved independently for each projection M of the initial, total molecular angular momentum. (This is a direct consequence of the lack of rotational invariance in the molecule-field problem). These equations are solved for a model system which mimics the collision of a halogen with a rare gas atom. Empirical observations made in the course of performing these calculations lead to the development of an approximation which avoids the repeated calculations for each initial M. This orientational average approximation greatly reduces the effort required to describe the system, and for the model calculation, yields accurate results for field intensities as high as 10 GW/sq cm.

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

1979-01-01

62

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

NASA Astrophysics Data System (ADS)

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

Managadze, G.

2010-07-01

63

Parton energy loss in high energy hard forward processes in proton-nucleus collisions  

E-print Network

We calculate the spectrum of energy loss differences due to gluon radiation in high energy hard forward processes in proton-nucleus collisions as compared to proton-proton collisions. We find that the nuclear induced energy loss scales linearly with the beam energy. We evaluate the spectrum and "typical" energy losses in a logarithmic and large $N_{c}$ approximation. The energy losses found appear large enough to be phenomenologically important.

Tseh Liou; A. H. Mueller

2014-04-22

64

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.; Goncharov, V.

2012-05-29

65

Molecular dynamics simulations of collision cascades in FeCrHe  

NASA Astrophysics Data System (ADS)

Radiation damage due to 1 and 5 keV collision cascades in Fe 90Cr 10 in the presence of 0.1%, 0.5% and 1.0% He defects, relevant for fusion reactor steels, has been studied using molecular dynamics simulations. We show that with 0.1% interstitial He the effect on the damage production in the FeCr matrix is minor, while with 1.0% He, the number of Frenkel pairs is significantly increased in comparison to pure FeCr. The positions of the He interstitials and clusters depend on the Cr atoms and the amount of He inside the cascade region is increased by about 30% due to the cascade. With substitutional He less damage is formed in the FeCr matrix due to cascades.

Juslin, N.; Nordlund, K.

2009-10-01

66

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.

67

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

E-print Network

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

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

2015-01-01

68

Scattering processes in antiprotonic hydrogen - hydrogen atom collisions  

E-print Network

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

V. P. Popov; V. N. Pomerantsev

2006-01-11

69

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

PubMed

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

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

2012-09-14

70

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

E-print Network

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

Paris-Sud XI, Université de

71

IN VIVO OPTICAL MOLECULAR IMAGING: PRINCIPLES AND SIGNAL PROCESSING ISSUES  

E-print Network

expressions, nuclear trafficking, etc. One of the main applications of cell level molecular imag- ing is high content screening (HCS) to accelerate the drug discovery process. For the radiologist, the term "molec

72

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

73

The role of three-body collisions in ? meson production processes near threshold  

Microsoft Academic Search

The amplitude of subthreshold ? meson production is calculated using dominant tree-level diagrams for three-body collisions. It is shown that the production can overwhelmingly be described by two-step processes. The effect of the genuine three-body contribution (i.e., the contribution which cannot be factorized) is discussed. The production rate of ? mesons resulting from these processes is presented for proton induced

H. W. Barz; B. Kampfer

2001-01-01

74

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

Microsoft Academic Search

The Naval Research Laboratory's Coupled Ocean-Atmosphere Mesoscale Prediction System (COAMPS) is employed to explore the relative importance of source, sink, and transport processes in producing an accurate forecast of the aerosol-cloud-drizzle system. Cloud processing, defined to be the reduction of cloud condensation nuclei (CCN) via collision-coalescence, is not uniquely related to total particle concentration, a behavior which stems from the

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

2006-01-01

75

Renewal processes and fluctuation analysis of molecular motor stepping  

NASA Astrophysics Data System (ADS)

We present a systematic method of analysis of experiments performed with single motor proteins. The use of such a method should allow a more detailed description of the motor's chemical cycle through the precise fitting of the experimental data. We model the dynamics of a processive or rotary molecular motor using a renewal process, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation function of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase.

Santos, Jaime E.; Franosch, Thomas; Parmeggiani, Andrea; Frey, Erwin

2005-09-01

76

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

77

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

E-print Network

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

Yong-Ping Fu; Yun-De Li

2011-11-29

78

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

NASA Technical Reports Server (NTRS)

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

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

1999-01-01

79

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

Microsoft Academic Search

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

Zhihui Sun; Jiahao Deng

2008-01-01

80

Spin structure of the proton and large pT processes in polarized pp collisions  

NASA Astrophysics Data System (ADS)

QCD motivated polarized parton distributions, evolved directly in x space, are used to predict rates for prompt photon and jet production at BNL RHIC and DESY HERA-N--> center of mass energies. Various scenarios for the polarized gluon distributions are considered and compared, and the possibility of using large pT processes in polarized pp collision experiments to choose between them is analyzed.

Gordon, L. E.; Ramsey, G. P.

1999-04-01

81

A molecular dynamics simulation of hydrogen atoms collisions on an H-preadsorbed silica surface  

NASA Astrophysics Data System (ADS)

The interaction of hydrogen atoms and molecules with a silica surface is relevant for many research and technological areas. Here, the dynamics of hydrogen atoms colliding with an H-preadsorbed ?-cristobalite (0?0?1) surface has been studied using a semiclassical collisional method in conjunction with a recently developed analytical potential energy surface based on density functional theory (DFT) calculations. The atomic recombination probability via an Eley-Rideal (E-R) mechanism, as well as the probabilities for other competitive surface processes, have been determined in a broad range of collision energies (0.04-3.0 eV) for off-normal (?v = 45°) and normal (?v = 0°) incidence and for two different surface temperatures (TS = 300 and 1000 K). H2,gas molecules form in roto-vibrational excited levels while the energy transferred to the solid surface is below 10% for all simulated conditions. Finally, the global atomic recombination coefficient (?E-R) and vibrational state resolved recombination coefficients (?(v)) were calculated and compared with the available experimental values. The calculated collisional data are of interest in chemical kinetics studies and fluid dynamics simulations of silica surface processes in H-based low-temperature, low-pressure plasmas.

Rutigliano, M.; Gamallo, P.; Sayós, R.; Orlandini, S.; Cacciatore, M.

2014-08-01

82

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

83

1979 bibliography of atomic and molecular processes. [Bibliography  

SciTech Connect

This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

None

1980-08-01

84

Quantum molecular dynamics simulation of multifragment production in heavy ion collisions at E/A=600 MeV  

NASA Astrophysics Data System (ADS)

With the ALADIN forward spectrometer the fragmentation of gold nuclei at 600 MeV per nucleon after interaction with carbon, aluminum, copper, and lead targets has been investigated. The results are compared to quantum-molecular-dynamics (QMD) calculations using soft and hard equations of state as well as a soft equation of state with momentum-dependent forces. Whereas the QMD has been successfully applied to heavy ion collisions at lower energies, it is not possible to reproduce the fragment distributions and the light-particle multiplicities observed in this experiment at relativistic energies. To study the reasons for the discrepancy between the experimental data and the simulations we investigated the time evolution of the nuclear system after a collision and the disintegration pattern of excited nuclei in the QMD approach.

Begemann-Blaich, M.; Müller, W. F.; Aichelin, J.; Adloff, J. C.; Bouissou, P.; Hubele, J.; Imme, G.; Iori, I.; Kreutz, P.; Kunde, G. J.; Leray, S.; Lindenstruth, V.; Liu, Z.; Lynen, U.; Meijer, R. J.; Milkau, U.; Moroni, A.; Ngô, C.; Ogilvie, C. A.; Pochodzalla, J.; Raciti, G.; Rudolf, G.; Sann, H.; Schüttauf, A.; Seidel, W.; Stuttge, L.; Trautmann, W.; Tucholski, A.

1993-08-01

85

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

E-print Network

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

2015-01-01

86

Molecular-beam studies of primary photochemical processes  

SciTech Connect

Application of the method of molecular-beam photofragmentation translational spectroscopy to the investigation of primary photochemical processes of polyatomic molecules is described. Examples will be given to illustrate how information concerning the energetics, dynamics, and mechanism of dissociation processes can be obtained from the precise measurements of angular and velocity distributions of products in an experiment in which a well-defined beam of molecules is crossed with a laser.

Lee, Y.T.

1982-12-01

87

Theoretical analysis of dynamic processes for interacting molecular motors  

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

88

Indistinguishability and interference in the coherent control of atomic and molecular processes  

SciTech Connect

The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible 'which-way' information due to quantum entanglement established in the quantum dynamics. Because quantum interference between independent pathways to the same target state occurs only when the independent pathways are indistinguishable, it is first shown that creating useful coherence between nondegenerate states of a molecule for subsequent quantum interference manipulation cannot be achieved by collisions between atoms or molecules that are prepared in momentum and energy eigenstates. Coherence can, however, be transferred from light fields to atoms or molecules. Using a particular coherent control scenario, it is shown that this coherence transfer and the subsequent coherent phase control can be readily realized by the most classical states of light, i.e., coherent states of light. It is further demonstrated that quantum states of light may suppress the extent of phase-sensitive coherent control by leaking out some which-way information while 'incoherent interference control' scenarios proposed in the literature have automatically ensured the indistinguishability of multiple excitation pathways. The possibility of quantum coherence in photodissociation product states is also understood in terms of the disentanglement between photodissociation fragments. Results offer deeper insights into quantum coherence generation in atomic and molecular processes.

Gong Jiangbin [Department of Physics and Centre for Computational Science and Engineering, National University of Singapore, Singapore 117542 (Singapore) and NUS Graduate School for Integrative Sciences and Engineering, Singapore 117597 (Singapore); Brumer, Paul [Department of Chemistry and Center for Quantum Information and Quantum Control, Chemical Physics Theory Group, University of Toronto, Toronto M5S 3H6 (Canada)

2010-02-07

89

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

NASA Astrophysics Data System (ADS)

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

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

2011-05-01

90

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

PubMed

Classical molecular dynamics simulations have been performed for gaseous CO(2) starting from an accurate anisotropic intermolecular potential. Through calculations of the evolutions of the positions and orientations of a large number of molecules, the time evolutions of the permanent and collision-induced electric dipole vector and polarizability tensor are obtained. These are computed from knowledge of static molecular parameters taking only the leading induction terms into account. The Laplace transforms of the auto-correlation functions of these tensors then directly yield the light absorption and scattering spectra. These predictions are, to our knowledge, the first in which the contributions of permanent and collision-induced tensors are simultaneously taken into account for gaseous CO(2), without any adjusted parameter. Comparisons between computations and measurements are made for absorption in the region of the ?(3) infrared band and for depolarized Rayleigh scattering in the roto-translational band. They demonstrate the quality of the model over spectral ranges from the band center to the far wings where the spectrum varies by several orders of magnitude. The contributions of the permanent and interaction-induced (dipole and polarizability) tensors are analyzed for the first time, through the purely permanent (allowed), purely induced, and cross permanent?induced components of the spectra. It is shown that, while the purely induced contribution is negligible when compared to the collision-broadened allowed component, the cross term due to interferences between permanent and induced tensors significantly participates to the wings of the bands. This successfully clarifies the long lasting, confusing situation for the mechanisms governing the wings of the CO(2) spectra considered in this work. PMID:21568511

Hartmann, J-M; Boulet, C

2011-05-14

91

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

92

Preparation and characterization of two types of separate collagen nanofibers with different widths using aqueous counter collision as a gentle top-down process  

NASA Astrophysics Data System (ADS)

Two types of single collagen nanofibers with different widths were successfully prepared from native collagen fibrils using aqueous counter collision (ACC) as a top-down process. A mild collision of an aqueous suspension at a 100 MPa ejection pressure yielded nanofibers, termed CNF100, which have an inherent axial periodicity and are ?100 nm in width and ?10 ?m in length. In contrast, ACC treatment at 200 MPa provided a non-periodic, shorter and thinner nanofiber, termed CNF10, that was ?10 nm in width and ?5 ?m in length. Both nanofibers exhibited the inherent triple helix conformation of native collagen supramolecules. Even a medial collision that exceeded the above ACC pressures provided solely a mixture of the two nanofiber products. The two nanofiber types were well characterized, and their tensile strengths were estimated based on their sonication-induced fragmentation behaviors that related to their individual fiber morphologies. As a result, CNF10, which was found to be a critical minimum nanofibril unit, and CNF10 exhibited totally different features in sizes, morphology, tensile strength and viscoelastic properties. In particular, as the mechanical strength of the molecular scaffold affects cell differentiation, the two collagen nanofibers prepared here by ACC have the potential for controlling cell differentiation in possibly different ways, as they have different mechanical properties. This encourages the consideration of the application of CNF100 and CNF10 in the fabrication of new functional materials with unique properties such as a scaffold for tissue engineering.

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

2014-12-01

93

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

94

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

95

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

96

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

SciTech Connect

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

Gianturco, F.A. [Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrae 6-10, 38173 Goettingen (Germany)] [Max-Planck-Institut fuer Stroemungsforschung, Bunsenstrae 6-10, 38173 Goettingen (Germany); Stoeckling, T. [Department of Chemistry, The University of Rome, Citta Universitaria, 00185 Rome, ItalyPhysico-chimie Theorique, 351 Cours de la Liberation, 35400, Talence (France)] [Department of Chemistry, The University of Rome, Citta Universitaria, 00185 Rome, ItalyPhysico-chimie Theorique, 351 Cours de la Liberation, 35400, Talence (France)

1997-03-01

97

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

98

Molecular beam study of the collisions of state-monitored, metastable noble gas atoms with O2(X 3Sigma g-)  

NASA Astrophysics Data System (ADS)

We describe a new molecular beam-luminescence method for measuring state-resolved cross sections for the quenching of metastable noble gas atoms, and report values for "dark" collisions of Ng*(3P2,3P0) with O2(X 3?g-), where Ng=Ar, Kr, and Xe. Cross sections for quenching ?Q and, in some cases, cross sections for excited products ?* are also given for a number of state-specific, luminescent monitor reactions. The elastic reaction of Ng* with He or Ne is employed to correct the total disappearance cross section QT for viewing losses caused by nonquenching processes. The velocity-averaged, quenching cross section QQ is obtained by subtracting the nonquenching cross section QN from QT. Values of QQ measured at average relative velocity ? (average relative kinetic energy ?) are deconvoluted to yield ?Q(?). For Ar* collisions with O2, we find ?Q[3P2] values of 35.6±1.8 Å2 for ? (?) between 690 and 2000 m/s (50 and 350 meV) that gradually decrease above 2000 m/s, and ?Q[3P0] values of 46±4 Å2 between 690 and 830 m/s (50 and 70 meV). For Kr* collisions, we report ?Q[3P2] values of 38.1±2.5 Å2 between 575 and 810 m/s (46 and 87 meV) with no apparent velocity dependence, and a ?Q[3P0] value of 56±7 Å2 at 576 m/s (46 meV). For Xe* collisions, we find ?Q[3P2] values of 48±3 Å2 at 535 m/s (44 meV) and 38±2 Å2 at 697 m/s (73 meV), and a ?Q[3P0] value of ˜125 Å2 at 535 m/s (44 meV). Comparisons with ?Q values obtained with other techniques that do not require a viewing loss correction are excellent. We also use the Ionic-Intermediate-Curve-Crossing Model (IICCM) to calculate cross sections for the Ar*(3P2)+O2?Ar+O*(1D)+O(3P) reaction. In our application of the model, the product state dissociative continuum is coupled to Ar+O2- through the predissociating O2*(E 3?u-) state that is valence Rydberg in character. Values of ?Q derived from the model are in good agreement with our experiment.

Rickey, Dawn; Krenos, John

1997-02-01

99

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

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

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

Microsoft Academic Search

B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without

C. William McCurdy; Fernando Martin

2003-01-01

102

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

Microsoft Academic Search

B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without

C. William McCurdy; Fernando Martín

2004-01-01

103

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

PubMed

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

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

2001-02-01

104

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

2009-05-31

105

Collision processes involving heavy many-electron ions interacting with neutral atoms  

NASA Astrophysics Data System (ADS)

An overview of experimental data and theoretical computational methods is given for effective cross sections of charge exchange (electron capture) and electron loss (projectile ionization) processes involving heavy many-electron ions (like Xe ^{q+}, Pb ^{q+}, W ^{q+}, U ^{q+}) colliding with neutral atoms (H, He, N, Ne, Ar, Kr, Xe) in the E \\approx 10 keV/u - 10 Gev/u energy range, i.e., from low up to relativistic energies. These charge-changing processes can occur with a high probability, reaching 10^{-14} - 10^{-16} cm ^2 cross-section values and, therefore, they play a key role in the kinetics of laboratory and astrophysical plasmas and influence the lifetimes of ion beams in accelerator facilities. Multielectron capture and loss processes are considered, as well, since their importance in the case of heavy atomic projectiles strongly increases, and a contribution to the total cross sections reaches more than 50%. An important aspect of the overview is a consideration of the influence of the inner-shell electrons of two colliding systems and a role of isotope effects in electron capture by very slow ions ( E \\approx 10 - 100 eV/u) from hydrogen isotopes H, D, and T. A short description of the corresponding computer codes is given for the calculation of cross sections of electron capture and electron loss processes for complex atoms and ions over a wide collision energy range.

Tolstikhina, Inga Yu; Shevelko, Vyacheslav P.

2013-03-01

106

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

SciTech Connect

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

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

2014-10-15

107

Molecular-dynamics-based study of the collisions of hyperthermal atomic oxygen with graphene using the ReaxFF reactive force field.  

PubMed

In this work, we have investigated the hyperthermal collisions of atomic oxygens with graphene through molecular dynamics simulations using the ReaxFF reactive force field. First, following Paci et al. (J. Phys. Chem. A 2009, 113, 4677 - 4685), 5-eV energetic collisions of atomic oxygen with a 24-atom pristine graphene sheet and a sheet with a single vacancy defect, both functionalized with oxygen atoms in the form of epoxides, were studied. We found that the removal of an O(2) molecule from the surface of the graphene sheet occurs predominantly through an Eley-Rideal-type reaction mechanism. Our results, in terms of the number of occurrences of various reactive events, compared well with those reported by Paci et al. Subsequently, energetic collisions of atomic oxygen with a 25-times-expanded pristine sheet were investigated. The steady-state oxygen coverage was found to be more than one atom per three surface carbon atoms. Under an oxygen impact, the graphene sheet was always found to buckle along its diagonal. In addition, the larger sheet exhibited trampoline-like behavior, as a result of which we observed a much larger number of inelastic scattering events than those reported by Paci et al. for the smaller system. Removal of O(2) from the larger sheet occurred strictly through an Eley-Rideal-type reaction. Investigation of the events leading to the breakup of a pristine unfunctionalized graphene sheet and the effects of the presence of a second layer beneath the graphene sheet in an AB arrangement was done through successive impacts with energetic oxygen atoms on the structures. Breakup of a graphene sheet was found to occur in two stages: epoxide formation, followed by the creation and growth of defects. Events leading to the breakup of a two-layer graphene stack included epoxide formation, transformation from an AB to an AA arrangement as a result of interlayer bonding, defect formation and expansion in the top layer, and finally erosion of the bottom layer. We observed that the breakup of the two-layer stack occurred through a sequential, layer-by-layer, erosion process. PMID:21942282

Srinivasan, Sriram Goverapet; van Duin, Adri C T

2011-11-24

108

The quasi-molecular absorption bands in UV region caused by the non-symmetric ion-atom radiative processes in the solar photosphere  

NASA Astrophysics Data System (ADS)

The aim of this research is to show that the radiative processes in strongly non- symmetric ion- atom collisions significantly influence on the opacity of the solar photosphere in UV region. Within this work only the He+H+ and H+A+ ion-atom systems, where A is the atom of one of the metal (Mg, Si and Al), are taken in to account. It is caused by the fact that the needed characteristics of the corresponding molecular ions, i.e. molecular potential curves and dipole matrix elements, have been determined by now. Here the non-symmetric radiative processes are considered under the conditions characterizing the non-LTE standard model of the solar atmosphere (Vernazza J, Avrett E and Loser R 1981 ApJS 45 635), which gives the possibility to perform all needed calculations and determined the corresponding spectral absorption coefficients. It is shown that the examined processes generate rather wide quasi-molecular absorption bands in the UV and VUV regions, whose intensity is comparable and sometimes even larger than the intensity of known one's caused by the H+H+ radiative collision processes, which are included now in the solar atmosphere models. Consequently, the presented results suggest that the non-symmetric ion-atom absorption processes have to be also included in standard models of the solar atmosphere.

Mihajlov, A. A.; Sre?kovi?, V. A.; Ignjatovi?, L. J. M.; Dimitrijevi?, M. S.; Metropoulos, A.

2012-12-01

109

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

NASA Astrophysics Data System (ADS)

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

Homan, Dean Matthew

110

Recent Advances in the Theory and Modelling of Multiple Processes in Heavy-Particle Collisions  

NASA Astrophysics Data System (ADS)

Progress in experimental methods and data analysis techniques has enabled detailed and in-depth views on the few-body dynamics which govern heavy-particle atomic collisions. Still, theoretical and computational support is needed to gain a thorough understanding of the measured spectra. This is a challenging task, in particular when multiple-electron transitions are studied in regimes in which standard perturbative methods are not applicable. This chapter explores two avenues that have been followed to meet this challenge. First, the coupled-channel basis generator method has been extended in order to calculate projectile angular differential cross sections for processes involving electron transfer. Somewhat surprisingly, it is found that the independent particle model works well, in some cases even for double capture, which is commonly believed to be a correlated process. Second, first- and higher-order perturbative models have been used in conjunction with a Monte Carlo event generator to investigate double ionization of helium. The Monte Carlo event generator provides theoretical event files which are analogous to data obtained from kinematically complete experiments. As it turns out, these event files form a seminal starting point to shed new light on the roles of different double-ionization mechanisms.

Kirchner, T.; Zapukhlyak, M.; Ciappina, M. F.; Schulz, M.

2013-09-01

111

Graphics processing units accelerated semiclassical initial value representation molecular dynamics  

SciTech Connect

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

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

2014-05-07

112

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

113

Solution processed molecular floating gate for flexible flash memories  

PubMed Central

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

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

2013-01-01

114

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

115

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

NASA Astrophysics Data System (ADS)

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

McCurdy, C. William; Martín, Fernando

2004-02-01

116

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

SciTech Connect

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

McCurdy, C. William; Martin, Fernando

2003-11-18

117

Theoretical study of charge exchange dynamics in He+ + NO collisions  

NASA Astrophysics Data System (ADS)

We investigate the charge transfer mechanism in the collisions of helium ions on nitric oxide using a molecular description framework with consideration of the orientation of the projectile toward the target. The anisotropy of the collision process has been analysed in detail in connection with the non-adiabatic interactions around avoided crossings. Potential energy curves, radial and rotational coupling matrix elements have been determined by means of ab initio quantum chemical methods. The collision dynamics is performed in the [1-25] keV collision energy range using a semiclassical approach, and the total electron transfer cross sections are analysed with regard to available experimental data.

Bene, Erika; Bacchus-Montabonel, Marie-Christine

2014-06-01

118

Molecular solution processing of metal chalcogenide thin film solar cells  

NASA Astrophysics Data System (ADS)

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

Yang, Wenbing

119

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

120

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

PubMed

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

Minaev, B F

2009-01-01

121

Molecular epidemiology biomarkers-Sample collection and processing considerations  

SciTech Connect

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

Holland, Nina T. [Environmental Health Sciences, School of Public Health, University of California, 317 Warren Hall, Berkeley 94720-7360 (United States)]. E-mail: ninah@berkeley.edu; Pfleger, Laura [Environmental Health Sciences, School of Public Health, University of California, 317 Warren Hall, Berkeley 94720-7360 (United States); Berger, Eileen [Input Automation Inc., Sonoma Mountain Road, Glen Ellen, CA 95442 (United States); Ho, Alan [Environmental Health Sciences, School of Public Health, University of California, 317 Warren Hall, Berkeley 94720-7360 (United States); Bastaki, Maria [Environmental Health Sciences, School of Public Health, University of California, 317 Warren Hall, Berkeley 94720-7360 (United States)

2005-08-07

122

Molecular epidemiology biomarkers--sample collection and processing considerations.  

PubMed

Biomarker studies require processing and storage of numerous biological samples with the goals of obtaining a large amount of information and minimizing future research costs. An efficient study design includes provisions for processing of the original samples, such as cryopreservation, DNA isolation, and preparation of specimens for exposure assessment. Use of standard, two-dimensional and nanobarcodes and customized electronic databases assure efficient management of large sample collections and tracking results of data analyses. Standard operating procedures and quality control plans help to protect sample quality and to assure validity of the biomarker data. Specific state, federal and international regulations are in place regarding research with human samples, governing areas including custody, safety of handling, and transport of human samples. Appropriate informed consent must be obtained from the study subjects prior to sample collection and confidentiality of results maintained. Finally, examples of three biorepositories of different scale (European Cancer Study, National Cancer Institute and School of Public Health Biorepository, University of California, Berkeley) are used to illustrate challenges faced by investigators and the ways to overcome them. New software and biorepository technologies are being developed by many companies that will help to bring biological banking to a new level required by molecular epidemiology of the 21st century. PMID:15967217

Holland, Nina T; Pfleger, Laura; Berger, Eileen; Ho, Alan; Bastaki, Maria

2005-08-01

123

Dynamics of molecular motors with finite processivity on heterogeneous tracks  

NASA Astrophysics Data System (ADS)

The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered.[1] Motivated by recent single-molecule experiments, we study a simple model for a motor moving along a disordered track using chemical energy while an external force opposes its motion. The motors also have finite processivity, i.e., they can leave the track with a position-dependent rate. We show that the response of the system to disorder in the hopping-off rate depends on the value of the external force. For most values of the external force, strong disorder causes the motors which survive for long times on the track to be localized at preferred positions. However, near the stall force, localization occurs for any amount of disorder. To obtain these results, we study the complex eigenvalue spectrum of the time evolution operator. Existence of localized states near the top of the band implies a stretched exponential contribution to the decay of the survival probability. A similar spectral analysis also provides a very efficient method for studying the dynamics of motors with infinite processivity. 1. Y. Kafri D. K. Lubensky and D. R. Nelson Phys. Rev. E 71, 041906 (2005).

Nelson, David

2006-03-01

124

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

125

Theory of molecular-orbital and compound-nucleus x-ray emission in heavy-ion-atom collisions with nuclear sticking  

Microsoft Academic Search

Calculations are made of x-ray emission in head-on 200-MeV (lab) Ni+Ni and 860-MeV (lab) Yb+Yb collisions for various values of the compound nucleus lifetime?. TheK x-ray emission probability is obtained by coherently summing the amplitude for a molecular-orbital x-ray transition from the 2p?, 2p?, 3p?, or 3p? to the 1s? molecular orbital with the amplitude for a compound-nucleus x-ray transition

R. Anholt

1979-01-01

126

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

NASA Astrophysics Data System (ADS)

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

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

2014-08-01

127

Molecular beam epitaxy for advanced gate stack materials and processes  

NASA Astrophysics Data System (ADS)

The material requirements for future CMOS generations - as given by the ITRS roadmap - are very challenging. This includes a high K dielectric without a low K interfacial layer, a high mobility channel and the appropriate metal gate. With the help of two projects INVEST and ET4US, we are building up a molecular beam epitaxy (MBE) infrastructure to grow this material set on large area wafers that can be further processed into small scale devices. In the INVEST project, we have developed an MBE system for the growth of complex oxides on semiconductors. The system follows the overall design of a production tool and is equipped with an RF atomic oxygen source, effusion cells, e-beam evaporators and a differential pumping stage. The oxide growth process starts with desorbing the initial surface oxide on the Si wafers in ultra-high vacuum and high temperature to create a clean reconstructed 2x1 surface. Using the atomic oxygen it is possible to oxidize the surface in a well controlled manner at low temperature and to grow very thin and dense SiOx layers, followed by the growth of 2-6 nm amorphous high K dielectrics. The process parameters permit to tune the interface layer from a SiOx rich to a silicide rich interface with a significant impact on the capacitance and the leakage. Initial focus is on developing an optimized growth recipe for high quality amorphous HfO2 and LaHfO3.5 films. This recipe was subsequently used to make wafers for a transistor batch that gave us the first N short channel MBE MOSFET's (100 nm) using an etched gate process flow. Some highlights of the first batch for 3nm HfO2 MOSFET are a high mobility (> 270 cm^2/Vs) with a corresponding low leakage current of 2 mA/cm^2). While there were some process issues for LaHfO3.5, the 3 nm MOSFET showed very low leakage currents below 10-6 A/cm^2. Interestingly all the LaHFO3.5 MOSFETs showed very low threshold voltage instabilities. In collaboration with C. Marchiori, M. Sousa, A.Guiller, H. Siegwart, D. Caimi, J. Fompeyrine, D. J Webb, C. Rossel, R. Germann of IBM Research GmbH Zurich Switzerland; L. Pantisano, M. Claes, T. Conard, M. Demand, W. Deweerd, S. DeGendt, M. Heyns, M. Houssa, M. Aoulaiche, G. Lujan, L. Ragnarsson, E. Rohr, T. Schram of IMEC Leuven Belgium; J. Hooker, Z.M Rittersma, Y. Furukawa of Philips Research Leuven Belgium and J. W. Seo of EPFL Lausanne Switzerland.

Locquet, Jean-Pierre

2005-03-01

128

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

129

Low-energy collisions with atomic and molecular ions in a photocathode electron target  

NASA Astrophysics Data System (ADS)

Dielectronic recombination of highly charged atomic ions and dissociative recombination of molecular ions have been investigated using fast ion beams merged with cold intense electron beams (down to <1meV beam temperature) from a GaAs photocathode. For beryllium-like germanium ions (Ge28+) isolated fine structure Rydberg resonances (n = 9 and 14) were observed at <0.2eV revealing configuration interaction with triply excited resonances and appearing as candidates for deriving radiative shifts of the 2s2-2s2p(3P0) excitation energy. For hydrogen fluoride ions (HF+) dissociative recombination with the cold electrons, producing n = 2 hydrogen atoms, was seen to occur for specific excited initial rotational levels. These levels were identified by their fragment energies down to about 4meV and it is envisaged to measure these energies with sub-meV accuracy.

Wolf, A.; Orlov, D. A.; Krantz, C.; Lestinsky, M.; Shornikov, A.; Novotný, O.; Stützel, J.; Buhr, H.; Mendes, M.; Petrignani, A.; Grieser, M.; Schippers, S.; Müller, A.; Ferro, F.; Lindroth, E.

2009-11-01

130

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

E-print Network

Molecular Dynamics Simulations of growth Process of SWNTs in CCVD Method from alcohol Yasushi with the classical molecular dynamics simulations. Starting from randomly distributed carbon atoms and a Ni cluster to the catalytic metal particle after around 100 ns molecular dynamics simulation, we picked up the metal particle

Maruyama, Shigeo

131

Version Date: October 23, 2001 Molecular Dynamics Simulation of Generation Process of SWNTs  

E-print Network

Version Date: October 23, 2001 Molecular Dynamics Simulation of Generation Process of SWNTs Yasushi (SWNTs) was studied with the molecular dynamics simulation. Starting from randomly distributed carbon to an elongated cage structure, which can be regarded as an imperfect SWNT. Keyword: Molecular Dynamics Simulation

Maruyama, Shigeo

132

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

133

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

134

Large Effects of Electric Fields on Atom-Molecule Collisions at Millikelvin Temperatures  

Microsoft Academic Search

Controlling interactions between cold molecules using external fields can elucidate the role of quantum mechanics in molecular collisions. We create a new experimental platform in which ultracold rubidium atoms and cold ammonia molecules are separately trapped by magnetic and electric fields and then combined to study collisions. We observe inelastic processes that are faster than expected from earlier field-free calculations.

L. P. Parazzoli; N. J. Fitch; P. S. Zuchowski; J. M. Hutson; H. J. Lewandowski

2011-01-01

135

The molecular signalling processes underlying olfactory learning and memory formation in honeybees  

E-print Network

The molecular signalling processes underlying olfactory learning and memory formation in honeybees processes underlying olfactory learning and memory formation in intact animals. Applying innovative of dynamic signalling events that contribute to different facets of olfactory learning and memory formation

136

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

137

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

PubMed

Atomic collision processes associated with surface production of negative hydrogen ions (H(-)) by particle reflection at molybdenum surface immersed in hydrogen plasma have been investigated. To calculate sputtering yields of Cs, as well as energy spectra and angular distributions of reflected hydrogen atoms from molybdenum surface by H(+) ion and Cs(+) ion bombardments, a Monte Carlo simulation code ACAT (Atomic Collision in Amorphous Target) was run with the corresponding surface conditions. A fractal surface model has been developed and adopted to ACAT for evaluating the effect due to roughness of target material. The results obtained with ACAT have indicated that the retention of hydrogen atoms leads to the reduction in sputtering yields of Cs, and the surface roughness does largely affect the sputtering yields of Cs. PMID:22380231

Kenmotsu, T; Wada, M

2012-02-01

138

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

NASA Astrophysics Data System (ADS)

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

Chapman, S.

1985-05-01

139

Molecular dynamics simulation of Li surface erosion and bubble formation  

E-print Network

Molecular dynamics simulation of Li surface erosion and bubble formation Z. Insepov *, A. Hassanein Structure and dynamical properties of liquid Li containing He atoms were studied by the Molecular Dynamics devices. Molecular dynamics (MD) method is capable of studying important collision processes and providing

Harilal, S. S.

140

Gain control in molecular information processing: lessons from neuroscience  

NASA Astrophysics Data System (ADS)

Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitates adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain control. Here, we argue that a certain simple mechanism of gain control, understood well in the context of systems neuroscience, also works for molecular signaling. The mechanism allows us to transmit more than 1 bit (on or off) of information about the signal independent of the signal variance. It does not require additional molecular circuitry beyond that already present in many molecular systems, and in particular, it does not depend on existence of feedback loops. The mechanism provides a potential explanation for abundance of ultrasensitive response curves in biological regulatory networks.

Nemenman, Ilya

2012-04-01

141

Evolutionary processes in the genus Coreocarpus: insights from molecular phylogenetics.  

PubMed

A molecular phylogenetic study of the plant genus Coreocarpus was conducted using nuclear (ITS) and plastid (rpl16 intron) DNA sequences, with phylogenies of the nuclear and plastid sequences highly congruent in defining a monophyletic group of six species (core Coreocarpus), although three other species often placed within the genus were excluded. Relationships within the genus are largely but not totally concordant with prior biosystematic studies. Despite strong molecular support, no morphological characters uniting the six species of core Coreocarpus have been identified; retention of plesiomorphic characters and the genetic lability of characters are two probable factors contributing to lack of consistent defining characters. The age of the core Coreocarpus is estimated at 1 million years because the basal species is endemic to a volcanic island that emerged in the past million years. Mapping the results of earlier breeding studies on the molecular phylogeny showed that use of cross-compatibility as a criterion for species delimitation would result in the recognition of paraphyletic species. Prior field, morphological, and biosystematic studies provided no indication of past hybridization in the evolution of Coreocarpus, and species in the genus appeared to be well defined morphologically. However, three instances of incongruence were observed. Two of these were between the nuclear and plastid partitions, and the third was between the morphological species assignment of one accession and the molecular data. If hybridization accounts for incongruence between the nuclear and plastid data, it occurred between species that now appear to be cross-incompatible and allopatric. The incongruence between morphological species assignment and the molecular data could be the result of parallel fixation of characters that have a simple genetic basis. This study suggests that the evolutionary history of Coreocarpus is much more complex than indicated from prior biosystematic investigations and that biosystematic and molecular phylogenetic studies may complement each other for elucidating the evolution and phylogeny of a group. PMID:12643567

Kimball, Rebecca T; Crawford, Daniel J; Smith, Edwin B

2003-01-01

142

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

143

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

Microsoft Academic Search

Both classical-trajectory calculations and measurements of electron capture in A+ + B(x) collisions, where the targets are Rydberg atoms, have been performed in the intermediate velocity range. Linear Stark-state targets were created inside a novel device called the Stark barrel. With this new apparatus, off-center atomic states with axial symmetry could be prepared with their axes set at angles 0-360o

Dean Matthew Homan

1997-01-01

144

Long Timestep Molecular Dynamics on the Graphical Processing Unit  

PubMed Central

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

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

2013-01-01

145

Calculations of diffusion and diffusion-limited processes in Ni3Al using accelerated molecular dynamics  

E-print Network

Calculations of diffusion and diffusion-limited processes in Ni3Al using accelerated molecular a systematic microscopic approach to diffusion and diffusion-limited processes in Ni3Al. These processes have by Rong et al. [2] in Ni3Al. They found that, during creep, edge dislocations commonly dissociated

Daw, Murray S.

146

Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes  

E-print Network

Molecular Dynamics Simulation of Nucleation Process of Single-Walled Carbon Nanotubes YASUSHI SHIBUTA, SHIGEO MARUYAMA Nucleation process of single-walled carbon nanotubes by the catalytic chemical on these potentials, interactions between catalytic metals and carbon atoms on formation process of single-walled

Maruyama, Shigeo

147

Hydrogen Atom Collision Processes in Cool Stellar Atmospheres: Effects on Spectral Line Strengths and Measured Chemical Abundances in Old Stars  

NASA Astrophysics Data System (ADS)

The precise measurement of the chemical composition of stars is a fundamental problem relevant to many areas of astrophysics. State-of-the-art approaches attempt to unite accurate descriptions of microphysics, non-local thermodynamic equilibrium (non-LTE) line formation and 3D hydrodynamical model atmospheres. In this paper I review progress in understanding inelastic collisions of hydrogen atoms with other species and their influence on spectral line formation and derived abundances in stellar atmospheres. These collisions are a major source of uncertainty in non-LTE modelling of spectral lines and abundance determinations, especially for old, metal-poor stars, which are unique tracers of the early evolution of our galaxy. Full quantum scattering calculations of direct excitation processes X(nl) + H leftrightarrow X(n'l') + H and charge transfer processes X(nl) + H leftrightarrow X+ + H- have been done for Li, Na and Mg [1,2,3] based on detailed quantum chemical data, e.g. [4]. Rate coefficients have been calculated and applied to non-LTE modelling of spectral lines in stellar atmospheres [5,6,7,8,9]. In all cases we find that charge transfer processes from the first excited S-state are very important, and the processes affect measured abundances for Li, Na and Mg in some stars by as much as 60%. Effects vary with stellar parameters (e.g. temperature, luminosity, metal content) and so these processes are important not only for accurate absolute abundances, but also for relative abundances among dissimilar stars.

Barklem, Paul S.

2012-12-01

148

Two-photon process and anomalous electron-pair production in /pi/p collisions  

SciTech Connect

The two-photon mechanism for lepton-pair production is calculated in a nonconventional way by treating the relative pion-nucleon motion in the classical limit. The results are compared with existing data for anomalous e/sup +/e/sup /minus// pairs produced in the collision of 16 GeV/c pions with protons. The results for differential cross sections as a function of the invariant pair mass, Feynman x, and transverse momentum are found to be in reasonable agreement with the data. The dominant piece of the cross section arises from the magnetic, spin-flip part of the nucleon current. 14 refs., 4 figs.

Ernst, D.J.; Albert, C.J.; Bottcher, C.; Strayer, M.R.

1989-01-01

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

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

151

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

152

Simultaneous process and molecular design/selection through property integration  

E-print Network

/selection. In particular, we focus on the problem of designing/selecting materials that are used in the context of a recycle/reuse system of process streams and for energy applications. Fresh and recycled resources (e.g., process streams, biomass, solvents, etc...

Qin, Xiaoyun

2007-04-25

153

Accelerating molecular docking calculations using graphics processing units.  

PubMed

The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein-ligand or protein-protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein-protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein-ligand interaction potentials. Additionally, we introduce a parallel version of our protein-ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein-protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60. PMID:21434638

Korb, Oliver; Stützle, Thomas; Exner, Thomas E

2011-04-25

154

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

155

Photonic, Electronic and Atomic Collisions  

NASA Astrophysics Data System (ADS)

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

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

2006-11-01

156

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

SciTech Connect

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

Yu,P.

2007-01-01

157

Atmospheric processes on ice nanoparticles in molecular beams  

NASA Astrophysics Data System (ADS)

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 molecule in clusters is also mentioned. Possible atmospheric consequences of all these results are briefly discussed.

Fárník, Michal; Poterya, Viktoriya

2014-02-01

158

Atmospheric processes on ice nanoparticles in molecular beams.  

PubMed

THIS REVIEW SUMMARIZES SOME RECENT EXPERIMENTS WITH ICE NANOPARTICLES (LARGE WATER CLUSTERS) IN MOLECULAR BEAMS AND OUTLINES THEIR ATMOSPHERIC RELEVANCE: (1) Investigation of mixed water-nitric acid particles by means of the electron ionization and sodium doping combined with photoionization revealed the prominent role of HNO3 molecule as the condensation nuclei. (2) The uptake of atmospheric molecules by water ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. (3) Photodissociation of hydrogen halides on water ice particles has been shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecules in clusters is also mentioned. Possible atmospheric consequences of all these results are briefly discussed. PMID:24790973

Fárník, Michal; Poterya, Viktoriya

2014-01-01

159

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

NASA Astrophysics Data System (ADS)

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

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

2011-01-01

160

Cellular and molecular processes leading to embryo formation in sponges: evidences for high conservation of processes throughout animal evolution.  

PubMed

The emergence of multicellularity is regarded as one of the major evolutionary events of life. This transition unicellularity/pluricellularity was acquired independently several times (King 2004). The acquisition of multicellularity implies the emergence of cellular cohesion and means of communication, as well as molecular mechanisms enabling the control of morphogenesis and body plan patterning. Some of these molecular tools seem to have predated the acquisition of multicellularity while others are regarded as the acquisition of specific lineages. Morphogenesis consists in the spatial migration of cells or cell layers during embryonic development, metamorphosis, asexual reproduction, growth, and regeneration, resulting in the formation and patterning of a body. In this paper, our aim is to review what is currently known concerning basal metazoans--sponges' morphogenesis from the tissular, cellular, and molecular points of view--and what remains to elucidate. Our review attempts to show that morphogenetic processes found in sponges are as diverse and complex as those found in other animals. In true epithelial sponges (Homoscleromorpha), as well as in others, we find similar cell/layer movements, cellular shape changes involved in major morphogenetic processes such as embryogenesis or larval metamorphosis. Thus, sponges can provide information enabling us to better understand early animal evolution at the molecular level but also at the cell/cell layer level. Indeed, comparison of molecular tools will only be of value if accompanied by functional data and expression studies during morphogenetic processes. PMID:22543423

Ereskovsky, Alexander V; Renard, Emmanuelle; Borchiellini, Carole

2013-03-01

161

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

162

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

163

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

164

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

165

Molecular processes in a high temperature shock layer  

NASA Technical Reports Server (NTRS)

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

Guberman, S. L.

1985-01-01

166

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

167

Inelastic processes in K+-He collisions in energy range 0.7-10 keV  

NASA Astrophysics Data System (ADS)

Absolute cross sections for charge exchange, ionization, stripping, and excitation in K+-He collisions were measured in the ion energy range 0.7-10 keV. The experimental data and the schematic correlation diagrams are used to analyze and determine the mechanisms for these processes. The increase of the excitation probability of inelastic channels with the angle of scattering is revealed. An exceptionally highly excited state of He is observed and a peculiarity for the excitation function of the resonance line is explained. The intensity ratio for the excitation of the K II ?=60.1 nm and ?=61.2 nm lines is 5:1, which indicates the high probability for excitation of the singlet resonance level 1P1 compared to the triplet level 3P1. The similarity of the population of the 4p state of the potassium ion and atom as well as the anomalously small values of the excitation cross sections are explained.

Lomsadze, R. A.; Gochitashvili, M. R.; Kezerashvili, R. Ya.; Mosulishvili, N. O.; Phaneuf, R.

2013-04-01

168

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

NASA Astrophysics Data System (ADS)

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

Kelley, Matthew Thomas

169

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

PubMed

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

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

2014-12-01

170

Quantum correlation dynamics in photosynthetic processes assisted by molecular vibrations  

E-print Network

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

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

2015-01-30

171

Spatially Resolved Atomic and Molecular Spectroscopy in Microelectronics Processing Plasmas  

SciTech Connect

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

Hebner, G.A.

1998-10-14

172

Bsoft: image and molecular processing in electron microscopy.  

PubMed

Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages. PMID:11472087

Heymann, J B

2001-01-01

173

An ab initio study of one-and two-electron transfer processes in collisions of Ne 2+ with He at low to intermediate energies  

E-print Network

in collisions with H and He atoms may play a role in the ionization balance [1]. In heavy-ion radiation therapy ) as well as from the metastable ions Ne 2+ ( 1 D) and Ne 2+ ( 1 S). Two-electron processes are considered cross sections show weak energy-dependence, while the present theoretical results for ground-state ion

Stancil, Phillip C.

174

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

SciTech Connect

This annotated bibliography lists 10,676 works on atomic and molecular processes reported in publications dated 1978-1981. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the county of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

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

1982-10-01

175

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

176

Molecular photoionization processes of astrophysical and aeronomical interest  

NASA Technical Reports Server (NTRS)

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

Langhoff, P. W.

1985-01-01

177

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

178

Correlating molecular spectroscopy and molecular chemometrics to explore carbohydrate functional groups and utilization of coproducts from biofuel and biobrewing processing.  

PubMed

Dried distillers grains with solubles (DDGS) was coproducts from bioethanol and biobrewing industry. It was an excellent resource of protein and energy feedstuff in China. Conventional studies often focus on traditional nutritional profiles. To data, there is little research on molecular structure-nutrition interaction of carbohydrate in coproducts. In this study, five kinds of corn-grain based DDGS and two kinds of barley-grain based DDGS were collected from different manufactures in the north of China. They were coded as "1, 2, 3, 4, 5, 6, and 7", respectively. The primary purposes of this project were to investigate the molecular structure-nutrition interaction of carbohydrate in coproducts, in terms of (1) carbohydrate-related chemical composition and nutrient profiles, (2) predicted values for energy in coproducts for animal, and (3) in situ digestion of dry matter. The result showed that acid detergent fiber content in corn DDGS and barley DDGS had negative correlation with structural carbohydrate peak area, cellulose compounds, and carbohydrate component peaks (first, second, and total peak area), which were measured with molecular spectroscopy. The correlation between carbohydrate peak area (second and total) and digestible fiber (tdNDF) were negative. There were no correlation between carbohydrate spectral intensities and energy values, carbohydrate subfractions partitioned by CNCPS system, and in situ rumen degradation. The results indicate that carbohydrate spectral profiles (functional groups) are associated with the carbohydrate nutritive values in coproducts from biofuel and biobrewing processing. PMID:24738876

Chen, Limei; Zhang, Xuewei; Yu, Peiqiang

2014-06-01

179

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

180

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

USGS Publications Warehouse

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

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

2004-01-01

181

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

NASA Astrophysics Data System (ADS)

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

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

2005-09-01

182

Onland signatures of the Palawan microcontinental block and Philippine mobile belt collision and crustal growth process: A review  

Microsoft Academic Search

The collision of the Palawan microcontinental block with the Philippine mobile belt had significantly influenced the geological evolution of the Philippines. Multiple collisions involving several fragments, through space and time, resulted into the collage of terranes of varying origin exposed in this part of central Philippines. Cusping of the overriding plate, volcanic arc gap, ophiolite emplacement, incipient back-arc rifting, island

Graciano P. Yumul; Carla B. Dimalanta; Edanjarlo J. Marquez; Karlo L. Queaño

2009-01-01

183

Modeling droplet collision and coalescence in an icing wind tunnel and the influence of these processes on droplet  

E-print Network

Modeling droplet collision and coalescence in an icing wind tunnel and the influence in an icing wind tunnel is presented here. The mutual interactions taking place within the dispersed phase content (LWC) in the bottom half of the wind tunnel. Droplet collision tends to influence the size

Frey, Pascal

184

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

SciTech Connect

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

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

2014-02-21

185

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

NASA Astrophysics Data System (ADS)

In the present research project a systematic study of the collision-induced infrared absorption (CIA) spectra of the binary mixtures of H_2 - D_2 in the region of the double fundamental vibrations of H_2 and D_2, and H_2 - Ar in the fundamental band of H_2, and of pure HD in its fundamental and first overtone regions was undertaken. The experiments were carried out with a 2.0 m high-pressure low-temperature transmission-type absorption cell at 77, 201 and 296 K at total gas densities up to 550 amagat. Infrared prism and grating spectrometers equipped with a microprocessor -controlled stepping motor were used to record the spectra. All the experimental results obtained represent first-time observations in collision-induced absorption. Collision-induced infrared absorption spectra of the double transitions of H_2(v=1>=ts 0) and D_2(v=1>=ts 0) have been observed at 77 and 201 K in the spectral region 7000-8000 cm^{-1} for total gas densities up to 550 amagat with a partial gas density ratio of 1:1 of H_2 and D_2. The observed spectra are interpreted in terms of the transitions, Q_1(J) of H_2+Q_1(J) of D _2, Q_1(J) of H_2+S _1(J) of D_2, S_1(J) of H_2 + Q_1(J) of D_2, and S_1(J) of H_2 + S_1(J) of D_2 for J = 0 and 1 for H _2 and J = 0, 1, and 2 for D_2. Analysis of the experimental absorption profiles was carried out using appropriate lineshape functions. The absorption coefficients, lineshape parameters, etc., are obtained from the analysis. Collision-induced enhancement absorption spectra of the fundamental band of H_2 in H_2 - Ar mixtures were recorded at room temperature for a base density of 72 amagat of H_2 for several partial densities of Ar up to 440 amagat. Hexadecapole-induced U transitions, U_1(1), U_1(2), Q_1(0)+U _0(1), and Q_1(1) + U_0(1) have been identified in the spectral region 5400 -6200 cm^{-1}. A "cage" model has been proposed to account for the double transitions of H_2 - H_2 in the H _2 - Ar enhancement spectra. From the analysis of the absorption profiles, the lineshape parameters and the absorption coefficients have been determined. The collision-induced absorption spectrum of the first overtone band of HD in the pure gas was observed at 77 K for gas densities up to 320 amagat. In addition to the allowed transitions P_2(1), R_2(0), and R_2(1), the CIA transitions Q_2(J)+Q_0(J), Q_1(J)+Q_1(J), Q_2(J)+S _0(J), S_2(J)+Q_0(J), Q _1(J)+S_1(J), S_2(J)+S_0(J), and S_1(J)+S_1(J) have been observed. An analysis of the observed absorption profiles has been completed. It is found that the isotropic overlap induction mechanism does not contribute to the intensity of the band and that negative contribution to the intensity of the band comes from the mixed term (2 sqrt{3}lambda_{32}exp [-(R - sigma)/rho_{32 }]times < vJmid Qmid v^' J^'>(R/a _0)^{-4}. The fundamental band of HD has been investigated at 77 K for gas densities in the range 40-310 amagat. For the first time the collision -induced transitions of the type T_1(1) + Q_0(J), Q_1(J) + T_0(1), U_1(0) + Q_0(J), Q_1(J) + U_0(0), V_1(0) + Q_0(J), and Q _1(J) + V_0(0) for HD have been identified. Here T, U, and V transitions correspond to DeltaJ = 3, 4, and 5, respectively.

Hsieh, Chang-Tsang William

186

A Molecular Dynamics Simulation of Interaction between Catalytic Metals and Carbon Atoms on Formation Process of an SWNT  

E-print Network

A Molecular Dynamics Simulation of Interaction between Catalytic Metals and Carbon Atoms) are calculated by molecular dynamics method. The simulation technique and initial condition are same as our of the Co and Fe clusters after 100 ns molecular dynamics simulation of the clustering process. #12;

Maruyama, Shigeo

187

AMS-1B crystalline borosilicate molecular sieve-based catalyst compositions and process for xylene methylation  

SciTech Connect

A process is described for making pseudocumene comprising methylating a xylene in the presence of a catalyst composition comprising a HAMS-1B crystalline borosilicate molecular sieve incorporated into an inorganic matrix. The composition is impregnated by a magnesium compound and subsequently heated to substantially convert the compound to the oxide form.

De Simone, R.E.

1987-05-12

188

AMS-1B crystalline borosilicate molecular sieve-based catalyst compositions and process for xylene isomerization  

SciTech Connect

A process is described for isomerizing a xylene feed containing a minor amount of ethylbenzene comprising contacting the xylene with a catalyst composition comprising a HAMS-1B crystalline borosilicate molecular sieve incorporated into an inorganic matrix. The composition is impregnated with a suitable phosphorus compound and is subsequently heated to substantially convert the compound to the oxide form.

Nimry, T.S.

1987-03-31

189

AMS-1B crystalline borosilicate molecular sieve-based catalyst compositions and process for toluene alkylation  

SciTech Connect

A process is described for making ethyltoluene by reacting ethylene with toluene in the presence of a catalyst composition comprising: HAMS-1B crystalline borosilicate molecular sieve incorporated into an inorganic matrix; composition impregnated by a magnesium compound and subsequently heated to substantially convert to the oxide form; and containing composition between about 4 and about 25% by weight magnesium.

Nimry, T.S.; Ellyn, G.; De Simone, R.E.

1987-06-16

190

MOLECULAR PROCESSING OF REPLICATION INTERMEDIATES IN ESCHERICHIA COLI AFTER DNA DAMAGE  

E-print Network

, such as dnaB266. We measured the amount of nascent DNA degradation, allowing us to determine how the newlyMOLECULAR PROCESSING OF REPLICATION INTERMEDIATES IN ESCHERICHIA COLI AFTER DNA DAMAGE By Jerilyn OF REPLICATION INTERMEDIATES IN ESCHERICHIA COLI AFTER DNA DAMAGE By Jerilyn Jalana Belle Approved

Courcelle, Justin

191

One Dimensional Collision Model  

NSDL National Science Digital Library

The One Dimensional Collision model allows the user to collide two objects and investigate whether momentum and/or kinetic energy are conserved in the collision process. To keep things simple, we'll confine ourselves to collisions along a single line. Special cases include the completely inelastic case, in which the objects stick together after the collision, as well as the completely elastic case, in which kinetic energy is conserved. The One Dimensional Collision was created using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_bu_Collisions1D.jar file will run the program if Java is installed.

Duffy, Andrew

2010-04-28

192

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

PubMed

RGO flakes are homogeneously dispersed in a Cu matrix through a molecular-level mixing process. This novel fabrication process prevents the agglomeration of the RGO and enhances adhesion between the RGO and the Cu. The yield strength of the 2.5 vol% RGO/Cu nanocomposite is 1.8 times higher than that of pure Cu. The strengthening mechanism of the RGO is investigated by a double cantilever beam test using the graphene/Cu model structure. PMID:23983045

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

2013-12-10

193

Measurement of the minimum binding energy of the 2p sigma molecular orbital formed in heavy ion collisions  

SciTech Connect

In order to study the minimum 2p sigma binding energy and its collision broadening, a copper ion beam was extracted from the Cs-sputter source and accelerated by the EN-tandem at Western Michigan University. Copper beams of ten different energies between 3 and 56 MeV were directed onto a pure thin (approx. 50..mu..g) and a pure thick (approx. 5 mg) copper target. The x-rays emitted under 90/sup 0/ were reduced in intensity with an 11 mil thick pure aluminum absorber and observed with an 80mm/sup 2/ Si(Li) detector. We were able to obtain quite intense 2p sigma MO-spectra with Cu-beams as slow as 3, 4, 5 and 7 MeV for thick as well as the thin targets.

Stockli, M.P.; Ferguson, S.; Tanis, J.A.

1983-01-01

194

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

NASA Astrophysics Data System (ADS)

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

Willis, Keeney; Orme, Melissa

1997-11-01

195

Large Effects of Electric Fields on Atom-Molecule Collisions at Millikelvin Temperatures  

Microsoft Academic Search

Controlling interactions between cold molecules using external fields can\\u000aelucidate the role of quantum mechanics in molecular collisions. We create a\\u000anew experimental platform in which ultracold rubidium atoms and cold ammonia\\u000amolecules are separately trapped by magnetic and electric fields and then\\u000acombined to study collisions. We observe inelastic processes that are faster\\u000athan expected from earlier field-free calculations.

L. P. Parazzoli; N. J. Fitch; P. S. Zuchowski; J. M. Hutson; H. J. Lewandowski

2011-01-01

196

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

PubMed Central

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

2013-01-01

197

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

198

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

E-print Network

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

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

2008-01-29

199

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

200

Onland signatures of the Palawan microcontinental block and Philippine mobile belt collision and crustal growth process: A review  

NASA Astrophysics Data System (ADS)

The collision of the Palawan microcontinental block with the Philippine mobile belt had significantly influenced the geological evolution of the Philippines. Multiple collisions involving several fragments, through space and time, resulted into the collage of terranes of varying origin exposed in this part of central Philippines. Cusping of the overriding plate, volcanic arc gap, ophiolite emplacement, incipient back-arc rifting, island rotation and tilting, raised coastal terraces, metamorphism, intrusion of igneous rocks and steepened subducted slab as seen in focal mechanism solutions are some of the manifestations of this collision. A late Early Miocene to early Middle Miocene age (20-16 Ma) is proposed for the major collision between the Palawan indenter and the Philippine mobile belt. The collision boundary is located from the northern part of Mindoro through the central mountain range swinging east of Sibuyan Island in the Romblon Island Group and finally threading along the Buruanga Peninsula and eastern side of the Antique Ophiolite Complex before exiting and connecting with the Negros Trench. The collision, through accretion and crustal thickening, has contributed to the crustal growth of the Philippine archipelago.

Yumul, Graciano P., Jr.; Dimalanta, Carla B.; Marquez, Edanjarlo J.; Queaño, Karlo L.

2009-05-01

201

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

202

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

SciTech Connect

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

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

2011-12-31

203

AMS-1B crystalline borosilicate molecular sieve-based catalyst compositions and process for toluene methylation  

SciTech Connect

A process is described for making paraxylene by methylating toluene in the presence of a catalyst composition comprising a HAMS-1B crystalline borosilicate molecular sieve. The majority of the crystallites are between about 1 micron and about 15 microns in largest dimension, incorporated into an inorganic matrix. The composition is impregnated by a magnesium compound and subsequently heated to substantially convert the compound to the oxide form.

De Simone, R.E.; Haddad, M.S.

1987-06-02

204

Time-Dependent Density Functional Theory for Molecular Multiphoton Processes in Intense Laser Fields  

Microsoft Academic Search

We present a new time-dependent density functional theory (TDDFT) with optimized effective potential (OEP) and self-interaction-correction (SIC) for the first nonperturbative treatment of multiphoton and nonlinear optical processes of many-electron molecular systems in intense laser fields(X. Chu and S. I. Chu, Phys. Rev. A (submitted).). The theory allows the elimination of the spurious self-interaction energy in the conventional DFT and

Xi Chu; Shih-I. Chu

2000-01-01

205

Depolarisation of rotational orientation and alignment of OH (X(2)Pi) in collisions with molecular partners: N(2) and O(2).  

PubMed

The depolarisation of selected OH (X(2)Pi(3/2)v = 0, J = 1.5 and 4.5, e) levels in collisions with the molecular partners N(2) and O(2) at room temperature (nominally 298 K) has been studied using the polarisation spectroscopy (PS) technique. We obtain total depolarisation rate constants, k, which are the combination of population transfer out of the initial level and elastic depolarisation of the tensor moment of respective rank K = 1 (orientation) or K = 2 (alignment) of its angular momentum distribution. N(2) causes more rapid decay of PS signals than O(2). There are no clear dependences of k on J for either partner. The K-dependence for N(2) mirrors that determined previously for the noble gases, but is less regular for O(2), warranting further investigation. Comparison with independent line-broadening data suggests that there may be an additional, pure-elastic-dephasing contribution to collisional broadening for N(2) that is not apparent for O(2). The presence of an independently established deeper HO-OO attractive minimum at shorter range clearly does not outweigh other factors that favour k for N(2).The most obvious explanation is stronger, longer-range attractive interactions due to the larger quadrupole moment of N(2). However, this appears to be contradicted by the rigorous ab initio calculations currently available on OH-O(2). PMID:20449027

Paterson, Grant; Marinakis, Sarandis; Costen, Matthew L; McKendrick, Kenneth G

2009-10-21

206

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

PubMed

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

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

2014-12-01

207

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

E-print Network

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

Sirmas, Nick

2015-01-01

208

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

209

Collision risk assessment  

NASA Astrophysics Data System (ADS)

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

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

2001-10-01

210

Large molecular dynamics simulations of collision cascades in single-crystal, bi-crystal, and poly-crystal UO 2  

NASA Astrophysics Data System (ADS)

Classical molecular dynamics simulations have been carried out to study the primary damage due to ?-decay self-irradiations in single-, bi-, and poly-crystal UO 2 matrices. In all the cases no amorphization has been found, only the creation of few point defects is observed. However, in all grain boundary systems numerous point defects are created along the interfaces. Furthermore, cascade morphologies depend strongly on the grain boundary structure. For symmetrical tilt grain boundaries with small misorientation angles (lower than 20°) the structure at the grain boundaries is composed of edge dislocations, whereas for higher misorientation angles is formed by Schottky defects. The grain boundary structure in the poly-crystal is found to be highly disordered. For the last two systems, cascades seem stopped by the interfaces unlike those with edge dislocation grain boundaries. These types of interface act like sink which traps moving atoms.

Van Brutzel, L.; Vincent-Aublant, E.; Delaye, J.-M.

2009-09-01

211

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

2014-05-26

212

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

PubMed

Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These macromolecules, nowadays investigated with advanced experimental techniques to unveil their molecular mechanisms and the properties of their kinetic cycles, are implicated in many biological processes, ranging from biopolymerization (e.g., RNA polymerases and ribosomes) to intracellular transport (motor proteins such as kinesins or dyneins). Although the kinetics of individual motors is well studied on both theoretical and experimental grounds, the repercussions of their stepping cycle on the collective dynamics still remains unclear. Advances in this direction will improve our comprehension of transport process in the natural intracellular medium, where processive motor enzymes might operate in crowded conditions. In this work, we therefore extend contemporary statistical kinetic analysis to study collective transport phenomena of motors in terms of lattice gas models belonging to the exclusion process class. Via numerical simulations, we show how to interpret and use the randomness calculated from single particle trajectories in crowded conditions. Importantly, we also show that time fluctuations and non-Poissonian behavior are intrinsically related to spatial correlations and the emergence of large, but finite, clusters of comoving motors. The properties unveiled by our analysis have important biological implications on the collective transport characteristics of processive motor enzymes in crowded conditions. PMID:25185553

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

2014-09-01

213

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

SciTech Connect

Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H{sub 2}O){sub 6}{sup 2+/3+} and Ru(H{sub 2}O){sub 6}{sup 2+/3+}. The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.

Zeng Xiancheng; Hu Hao; Hu Xiangqian; Cohen, Aron J.; Yang Weitao [Department of Chemistry, Duke University, Durham, North Carolina 27708 (United States)

2008-03-28

214

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

NASA Technical Reports Server (NTRS)

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

Kang, Jongmin; Pierce, Allan D.

1990-01-01

215

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

216

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

NASA Astrophysics Data System (ADS)

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

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

2004-06-01

217

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

NASA Astrophysics Data System (ADS)

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

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

2004-11-01

218

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

NASA Astrophysics Data System (ADS)

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

Odaka, Shigeru; Kurihara, Yoshimasa

2012-04-01

219

Profibrillin-1 Maturation by Human Dermal Fibroblasts: Proteolytic Processing and Molecular Chaperones  

PubMed Central

Fibrillin-1 is synthesized as a proprotein that undergoes proteolytic processing in the unique C-terminal domain by a member of the PACE/furin family of endoproteases. This family of endoproteases is active in the trans-Golgi network (TGN), but metabolic labeling studies have been controversial as to whether profibrillin-1 is processed intracellularly or after secretion. This report provides evidence that profibrillin-1 processing is not an intracellular event. Bafilomycin A1 and incubation of dermal fibroblasts at 22°C were used to block secretion in the TGN to confirm that profibrillin-1 processing did not occur in this compartment. Profibrillin-1 immunoprecipitation studies revealed that two endoplasmic reticulum-resident molecular chaperones, BiP and GRP94, interacted with profibrillin-1. To determine the proprotein convertase responsible for processing profibrillin-1, a specific inhibitor of furin, ?-1-antitrypsin, Portland variant, was both expressed in the cells and added to cells exogenously. In both cases, the inhibitor blocked the processing of profibrillin-1, providing evidence that furin is the enzyme responsible for profibrillin-1 processing. These studies delineate the secretion and proteolytic processing of profibrillin-1, and identify the proteins that interact with profibrillin-1 in the secretory pathway. PMID:14523997

Wallis, Debra D.; Putnam, Elizabeth A.; Cretoiu, Jill S.; Carmical, Sonya G.; Cao, Shi-Nian; Thomas, Gary; Milewicz, Dianna M.

2006-01-01

220

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

221

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

PubMed

Great interest in studying the molecular genetic bases of the adaptation processes is explained by their importance in understanding evolutionary changes, in the development ofintraspecific and interspecific genetic diversity, and in the creation of approaches and programs for maintaining and restoring the population. The article examines the sources and conditions for generating adaptive genetic variability and contribution of neutral and adaptive genetic variability to the population structure of the species; methods for identifying the adaptive genetic variability on the genome level are also described. Considerable attention is paid to the potential of new technologies of genome analysis, including next-generation sequencing and some accompanying methods. In conclusion, the important role of the joint use of genomics and proteomics approaches in understanding the molecular genetic bases of adaptation is emphasized. PMID:23662427

Salmenkova, E A

2013-01-01

222

Actualities on molecular pathogenesis and repairing processes of cerebral damage in perinatal hypoxic-ischemic encephalopathy  

PubMed Central

Hypoxic-ischemic encephalopathy (HIE) is the most important cause of cerebral damage and long-term neurological sequelae in the perinatal period both in term and preterm infant. Hypoxic-ischemic (H-I) injuries develop in two phases: the ischemic phase, dominated by necrotic processes, and the reperfusion phase, dominated by apoptotic processes extending beyond ischemic areas. Due to selective ischemic vulnerability, cerebral damage affects gray matter in term newborns and white matter in preterm newborns with the typical neuropathological aspects of laminar cortical necrosis in the former and periventricular leukomalacia in the latter. This article summarises the principal physiopathological and biochemical processes leading to necrosis and/or apoptosis of neuronal and glial cells and reports recent insights into some endogenous and exogenous cellular and molecular mechanisms aimed at repairing H-I cerebral damage. PMID:20846380

2010-01-01

223

What do remagnetizations tell us about regional thermo-tectonic processes in the India-Asia collision zone?  

NASA Astrophysics Data System (ADS)

Remagnetization is a common phenomenon throughout the Himalayan Range. Stable secondary remanences mostly reside in pyrrhotite formed and magnetized during last metamorphism. Many sites have samples with both normal and reverse polarities and single specimens even reveal antipodal directions during thermal demagnetization. Therefore the time span of remanence blocking was obviously sufficiently long to average on paleosecular variation. K-Ar data on illites provide a time constraint for remanence acquisition; ages ranging from Eocene/Oligocene to Oligocene/Miocene in the western and central Himalaya, respectively. The pyrrhotite remanences record net displacements since remanence acquisition. It has been demonstrated that they can contribute to decipher the regional thermo-tectonic orogenic evolution. Block rotations about vertical axes show that oroclinal bending and rotational shortening between India and Asia are the dominating processes in the western and central part of the Himalayan arc. Less data are available from the eastern part of the collision zone. First paleomagnetic results indicate that in this region large-scale material flow around the East Himalaya Syntaxis becomes significant. The transition between the western and eastern realm seems to be located in western to central Nepal. It is interesting that the general pattern of paleomagnetic block rotations match with present-day rotations derived from GPS velocities suggesting that recent crustal movements are representative also for longer-term geological processes. This is particularly important for models of the evolution of the Tibetan Plateau in which decoupling of horizontal movements of the upper crust and mantle, enabled by a soft partially molten middle crust, plays a major role. The age and nature of the secondary pyrrhotite remanences is crucial for interpretations. Their origin is either thermo-remanent related to cooling or thermo-chemical related to the pro-grade or peak metamorphic phase. Coinciding results for remanence directions of formations with peak temperatures higher and lower than the Curie temperature of pyrrhotite, respectively, suggest that remanence acquisition was close to cooling in either case. West of ca. 89°E pyrrhotite remanences clearly postdate main Himalayan folding (F1) evidencing that F1 phases stopped before metamorphic cooling. East of the Yadong Graben scatter of remanence directions may indicate that significant small-scale deformation continued after cooling in this region. In a number of areas along the Himalayan arc in situ directions show distinct small circle distributions which document large-scale tilting processes after cooling or synchronous to cooling. Application of small circle methods is essential for analysis and interpretation. Associated tilt axes predominantly show an E-W trend parallel to the main Himalayan structures; however, some are oriented closer to N-S. It is therefore likely that these late-orogenic tiltings are related to the widespread formation of the Miocene North-Himalayan gneiss domes. In the context of a partially molten middle crust beneath the Tibetan Plateau the domes could be an expression of channel flow towards frontal regions of high erosion. Paleomagnetism is a potential tool to "map" doming structures in the crust also in regions without visible indications at surface.

Appel, E.; El Bay, R.; Dunkl, I.; Ding, L.; Antolin, B.; Schill, E.; Waldhör, M.

2007-12-01

224

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

NASA Astrophysics Data System (ADS)

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

Yu, Peiqiang

2011-11-01

225

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

PubMed Central

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

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

2013-01-01

226

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

PubMed Central

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

Little, Max A.; Jones, Nick S.

2013-01-01

227

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

228

Molecular Dynamics Simulation Study of Atomic Segregation of (PdPt)147 during the Heating Process  

NASA Astrophysics Data System (ADS)

Research on the influence of alloy concentration and distribution on bimetallic cluster plays a key role in exploring new structural material. This paper studies the melting process of icosahedral bimetallic cluster (PdPt)147 with different Pt concentrations and different atomic distributions by using molecular dynamics with an embedded atom method. The results indicate that the mixed Pd-Pt cluster shows an irregular phenomenon between 580 and 630 K, i.e. the atomic energy decreases with the increase of temperature. This is because the surface energy of Pd is lower than that of Pt; the decreased energy due to Pd atomic segregation is larger than the increased energy due to heating during the segregation process. In addition, the temperature of Pd atomic segregation is strongly related to Pt concentration. This leads to that Pd atoms prefer to remain on the surface even after the cluster melted.

Xiao, X. Y.; Cheng, Z. F.; Xia, J. H.

229

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

PubMed

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. PMID:24329052

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

2013-12-14

230

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

231

Collision Dynamics of Decimeter Bodies  

NASA Astrophysics Data System (ADS)

The collision dynamics of decimeter bodies are important for the early phase of planet formation. Planets form by accretion of km-sized objects, the so called planetesimals. These planetesimals evolve from small grains, but their formation process is not yet understood entirely. Two groups of models try to explain the formation process. Decimeter bodies and their collision behavior play a vital role in both groups. The threshold between bouncing and fragmentation is especially interesting for coagulation models, as decimeter bodies are the direct precursors to meter sized bodies. But the collision dynamics are also relevant for the models, which describe planetesimal formation by gravitational collapse in dense regions of the protoplanetary disk. We will present preliminary results of our collision experiments. Previous experiments on mutual collisions of decimeter dust agglomerates showed that the threshold between bouncing and fragmentation lies at a collision velocity of 16.2 cm/s, which corresponds to a specific kinetic energy of 5 mJ/kg. We expand these experiments to investigate the conditions for “catastrophic disruption” of decimeter dust bodies. Here, “catastrophic disruption” means that the largest fragment of a collision partner has only half the mass of the original body. Furthermore, we extend the parameter range to ice aggregates. We will present first experimental results of collisions of ice aggregates in the decimeter range. In these first experiments we will analyze the threshold conditions for solid ice. We will investigate the collision dynamics for both central and non-central collisions.

Deckers, Johannes; Teiser, J.

2013-10-01

232

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

233

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

234

Immunohistochemistry of tissue prepared by a molecular-friendly fixation and processing system.  

PubMed

A recently introduced histologic fixative (Universal Molecular Fixative [UMFIX]) has been shown to preserve macromolecules in tissue at ambient temperature. When UMFIX-exposed tissues are processed by a formalin-free, microwave-assisted rapid processing system, the resulting paraffin blocks retain good histomorphology and intact nucleic acids suitable for expression microarray analysis. Because UMFIX may be used as an alternative to formalin, the authors set out to study the effect of this new fixation and processing system on immunohistochemistry (IHC) by analyzing a range of human neoplastic and non-neoplastic specimens. Parallel slices from surgically removed specimens were fixed in formalin and UMFIX and processed in a rapid microwave-assisted tissue processor. IHC was performed following routine procedures. The staining for those antibodies that normally required antigen retrieval was carried out with and without that step. The intensity and pattern of reactions were compared in 144 tissue samples fixed by the two methods using 70 monoclonal and polyclonal antibodies. The intensity of IHC reactions for most cytoplasmic antigens was generally equal or stronger in UMFIX tissues. This was particularly true with intermediate filaments and HercepTest, where the antigen retrieval step became unnecessary. Conversely, there was a decrease in the intensity of reactions for HepPar1, bcl-2, and three nuclear antigens (Ki-67, TTF-1, and estrogen receptor). Increasing their exposure times optimized the sensitivity of the latter four antibodies. The study shows that IHC staining results of tissues fixed in UMFIX and processed by the microwave-assisted system are comparable to those obtained on formalin-fixed, similarly processed specimens. There is an enhancement of the sensitivity of few antibodies in UMFIX-exposed tissue, rendering antigen retrieval unnecessary. This increased sensitivity may be due to the effect of eliminating formalin from fixation and processing or the microwave energy. PMID:16082256

Nadji, M; Nassiri, M; Vincek, V; Kanhoush, R; Morales, A R

2005-09-01

235

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

PubMed

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

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

2014-08-01

236

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

PubMed

The Long-Evans Cinnamon (LEC) rat shows age-dependent hepatic manifestations that are similar to those of Wilson's disease (WD). The pathogenic process in the brain has, however, not been evaluated in detail due to the rarity of the neurological symptoms. However, copper accumulation is noted in LEC rat brain tissue from 24 weeks of age, which results in oxidative injuries. The current study investigated the gene expression profiles of LEC rat brains at 24 weeks of age in order to identify the important early molecular changes that underlie the development of neurological symptoms in WD. Biological ontology-based analysis revealed diverse altered expressions of the genes related to copper accumulation. Of particular interest, we found altered expression of genes connected to mitochondrial respiration (Sdhaf2 and Ndufb7), calcineurin-mediated cellular processes (Ppp3ca, Ppp3cb, and Camk2a), amyloid precursor protein (Anks1b and A2m) and alpha-synuclein (Snca). In addition to copper-related changes, compensatory upregulations of Cp and Hamp reflect iron-mediated neurotoxicity. Of note, reciprocal expression of Asmt and Bhmt is an important clue that altered S-adenosylhomocysteine metabolism underlies brain injury in WD, which is directly correlated to the decreased expression of S-adenosylhomocysteine hydrolase in hepatic tissue in LEC rats. In conclusion, our study indicates that diverse molecular changes, both variable and complex, underlie the development of neurological manifestations in WD. Copper-related injuries were found to be the principal pathogenic process, but Fe- or adenosylhomocysteine-related injuries were also implicated. Investigations using other animal models or accessible human samples will be required to confirm our observations. PMID:23519153

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

2013-05-01

237

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

NASA Astrophysics Data System (ADS)

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

Gerya, Taras

2014-05-01

238

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

239

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

PubMed

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

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

2015-02-16

240

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

NASA Astrophysics Data System (ADS)

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

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

2014-12-01

241

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

PubMed

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 ?s at a temperature of 100 K, which represents a lower bound to the temperature range of earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces. Our simulations also show that eventual proton-disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects which might provide active sites for various chemical reactions in the atmosphere. PMID:25527956

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

2014-12-21

242

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

243

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

PubMed

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

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

2013-11-12

244

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

245

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

246

Himalayan Collision  

NSDL National Science Digital Library

An excellent animation of Himalayan formation, featuring captions that date events in the formation of the Himalayas. Shown as a cut-away view of the earth, it's possible to see not only the continental collision, but also the mantle and the mountain root that is created in the collision. The file is available as a QuickTime movie in two different sizes.

Center, Ucsb E.

247

One and two electron processes in 0. 9 keV/u to 60 keV/u Ar[sup 16+]+He collisions  

SciTech Connect

We have studied one- and two-electron processes in the collision of 0.9 to 60 keV/u Ar[sup 16+] on He target using the KSU CRYEBIS facility. The cross sections for single and double captures, single ionization, and transfer ionization were measured by observing the final Ar charge states in coincidence with the recoiling He ions. Single capture (SC) is dominant and relatively independent of projectile energy. Single ionization (SI) is very small but spans the measured energies. Transfer ionization (TI) dominates the two-electron processes and slowly increases with energy. Double capture (DC) is much smaller and independent of the projectile energy. The average Q-values were also determined by measuring the momentum of the recoil ions. The average Q-values for both SC and TI were found to decrease with increasing projectile energy.

Wu, W.; Giese, J.P.; Richard, P.; Stockli, M.; Ali, R.; Cocke, C.L.; Schoene, H. (J. R. Macdonald Laboratory, Kansas State University, Manhattan, Kansas 66506-2604 (United States))

1993-06-05

248

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

E-print Network

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

Naoki Tsukamoto; Masashi Kimura; Tomohiro Harada

2013-10-18

249

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

E-print Network

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

Tsukamoto, Naoki; Harada, Tomohiro

2014-01-01

250

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

SciTech Connect

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

Chu, S.I.

1981-01-01

251

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

252

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

PubMed

The synthesis process of aluminophosphate AlPO(4)-11 molecular sieve in the mixed water/1-butyl- 3-methylimidazolium bromide ([bmim]Br) ionic liquid was investigated by XRD, multinuclear solid-state NMR, scanning electron microscopy (SEM) and X-ray energy dispersive spectroscopy (EDS). It was observed that a tablet phase, named SIZ-2, was formed at the early stage of crystallization. During crystallization metastable SIZ-2 with an incompletely condensed framework phosphorus disappeared gradually, and the phosphorous species became fully condensed through hydroxyl reaction with tetrahedral aluminum to form thermodynamically stable AlPO(4)-11 in the final product. It was found that [bmim]Br, acting as the structure-directing agent, was occluded into the AlPO(4)-11 channel. PMID:22105414

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

2012-01-21

253

Charge separation process in water clusters containing HCl. Molecular dynamics study using semiempirical hamiltonians.  

PubMed

The acid dissociation of HCl in water clusters was studied using the PM3-MAIS model in a direct molecular dynamic simulations framework. Several trajectories for each cluster size were computed to improve the sampling on the potential energy surface and to increase the statistical significance of our study. We have analyzed the emergence of well-defined hydration structures around the ions and the effect they have on the charge separation process. Surface and bulk solvation situations are examined for both ions in terms of the competing circumstances for water molecules in the cluster. Our results show that the prevailing situation in all these clusters is a water mediated interaction between the ions. This situation is related to the significant interplay of several factors such as charge transfer occurring between the ions and their first hydration shells. Our results show that no significant charge redistribution occurs during the Eigen-Zundel transformation. PMID:20677821

Arillo Flores, Oscar Ivan; Bernal-Uruchurtu, Margarita I

2010-09-01

254

Quinacridone-based molecular donors for solution processed bulk-heterojunction organic solar cells.  

PubMed

New soluble quinacridone-based molecules have been developed as electron donor materials for solution-processed organic solar cells. By functionalizing the pristine pigment core of quinacridone with solubilizing alkyl chains and light absorbing/charge transporting thiophene units, i.e., bithiophene (BT) and thienylbenzo[c][1,2,5]thiadiazolethienyl (BTD), we prepared a series of multifunctional quinacridone-based molecules. These molecular donors show intense absorption in the visible spectral region, and the absorption range and intensity are well-tuned by the interaction between the quinacridone core and the incorporated thiophene units. The thin film absorption edge extends with the expansion of molecular conjugation, i.e., 552 nm for N,N'-di(2-ethylhexyl)quinacridone (QA), 592 nm for 2,9-Bis(5'-hexyl-2,2'-bithiophene)-N,N'-di(2-ethylhexyl)quinacridone (QA-BT), and 637 nm for 4-(5-hexylthiophen-2-yl)-7-(thiophen-2-yl)benzo[c][1,2,5]thiadiazole (QA-BTD). The change of molecular structure also influences the electrochemical properties. Observed from cyclic voltammetry measurements, the oxidation and reduction potentials (vs ferrocene) are 0.7 and -1.83 V for QA, 0.54 and -1.76 V for QA-BT, and 0.45 and -1.68 V for QA-BTD. Uniform thin films can be generated from both single component molecular solutions and blend solutions of these molecules with [6,6]-phenyl C70-butyric acid methyl ester (PC70BM). The blend films exhibit space-charge limited current (SCLC) hole mobilities on the order of 1×10(-4) cm(2) V(-1) S(-1). Bulk heterojunction (BHJ) solar cells using these soluble molecules as donors and PC70BM as the acceptor were fabricated. Power conversion efficiencies (PCEs) of up to 2.22% under AM 1.5 G simulated 1 sun solar illumination have been achieved and external quantum efficiencies (EQEs) reach as high as ?45%. PMID:20804141

Chen, John Jun-An; Chen, Teresa L; Kim, BongSoo; Poulsen, Daniel A; Mynar, Justin L; Fréchet, Jean M J; Ma, Biwu

2010-09-01

255

Molecular target and projectile angular scattering effects in stopping power and charge exchange at low-to-intermediate projectile energies  

Microsoft Academic Search

We analyze the implications of the molecular structure of a target and the angular scattering effects on projectile-target collisions within the Electron-Nuclear Dynamics (END) approach. We show the suitability of the END method for the analysis of molecular scattering processes such as differential cross sections, charge exchange, and energy loss as required for the study of the stopping cross section.

R. Cabrera-Trujillo; Y. Öhrn; John R. Sabin; E. Deumens

2002-01-01

256

Heavy Quark Production in ep Collisions  

E-print Network

Heavy Quark Production in ep Collisions o Introduction o Charm Production o Beauty Production o in ep collisions 23 February 2007 2/17 Heavy Flavor Production Boson-Gluon Fusion, dominant process Hard of the proton: #12;G. Leibenguth, Heavy Quarks Production in ep collisions 23 February 2007 3/17 HERA, Electron

257

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

PubMed Central

In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

de Storme, Nico; Geelen, Danny

2014-01-01

258

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

NASA Astrophysics Data System (ADS)

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

Brédas, Jean-Luc

2007-03-01

259

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

SciTech Connect

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

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

2011-01-01

260

Collisions between carbonaceous grains in the interstellar medium  

E-print Network

Semi-empirical molecular dynamics is used to simulate hydrocarbon grain sputtering and collisions which are extremely difficult to study experimentally. This microscopic and dynamic approach is particularly suited to high velocity impacts, where target destruction occurs far from equilibrium. A wide variety of processes are encountered, depending on grain size and velocity: vaporization, fragmentation, atomic implantation, sticking, elastic recoil, atomic chemisorption, H abstraction and H2 formation, etc. The impact-velocity threshold is about 10 km/s but complete grain destruction requires much higher velocities and nearly equal grain sizes. The main outcome of strong collisions is vaporization, i.e. formation of small molecules rather than solid fragments; most of the impact energy is carried away by these molecules in the form of kinetic energy. As a consequence, the energy left in the bulk is insufficient for shattering or even thermal processing. Grain size distribution is hardly affected by such collisions. These results cast doubt on the notion that collisions reduce grain lifetime so much as to require efficient growth processes in the interstellar medium.

Reanud Papoular

2003-11-11

261

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

262

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

PubMed

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 × 10(9) 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

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

2011-09-01

263

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

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

2011-01-01

264

NEWS & VIEWS collisions11  

E-print Network

NEWS & VIEWS collisions11 . More recently, applications are being found in condensed-matter physics of which made Alfred Nobel a small fortune -- was crucial to most of the large-scale construction projects the details of processes that are difficult to study in the lab, because they require no knowledge

Loss, Daniel

265

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

E-print Network

at a density of $106 cmÃ?3 and temperature of 70 mK. Collision studies between the trapped OH sample pairs [11,12]. Most of these mole- cules are in excited rovibrational states, permitting ultra- cold or Stark decel- eration, but at temperatures typically in the range of 10 mK to 1 K. For example, buffer

266

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.

267

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

268

Adaptive binary splitting for efficient RFID tag anti-collision  

Microsoft Academic Search

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

Jihoon Myung; Wonjun Lee; J. Srivastava

2006-01-01

269

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

270

Collisions between carbonaceous grains in the interstellar medium  

E-print Network

Semi-empirical molecular dynamics is used to simulate hydrocarbon grain sputtering and collisions which are extremely difficult to study experimentally. This microscopic and dynamic approach is particularly suited to high velocity impacts, where target destruction occurs far from equilibrium. A wide variety of processes are encountered, depending on grain size and velocity: vaporization, fragmentation, atomic implantation, sticking, elastic recoil, atomic chemisorption, H abstraction and H2 formation, etc. The impact-velocity threshold is about 10 km/s but complete grain destruction requires much higher velocities and nearly equal grain sizes. The main outcome of strong collisions is vaporization, i.e. formation of small molecules rather than solid fragments; most of the impact energy is carried away by these molecules in the form of kinetic energy. As a consequence, the energy left in the bulk is insufficient for shattering or even thermal processing. Grain size distribution is hardly affected by such collis...

Papoular, R J

2004-01-01

271

Theoretical Studies of Atomic and Molecular Multiphoton Processes in Intense and Superintense Laser Fields  

NASA Astrophysics Data System (ADS)

In this thesis work, several new nonperturbative theoretical formalisms and accurate and efficient computational methods are presented for ab initio comprehensive investigation of atomic and molecular multiphoton processes in intense and superintense laser fields. In the presence of strong fields, it is advantageous to treat the atoms/molecules quantum mechanically by using the time-dependent Schrodinger equation and treat the electromagnetic fields classically, leading to a set of coupled first-order time-dependent differential equations. The essence of the theoretical formalisms and computational methods developed can be summarized in the following several key elements: (1) For periodically or polychromatically time-dependent Hamiltonians, the time-dependent problems can be transformed into an equivalent time-independent infinite-dimensional Floquet Hamiltonians. (2) In the presence of external fields, all the bound states are coupled to the continuum and become quasi-bound states possessing complex quasi -energies. (3) To facilitate the calculation of the complex quasi-energies, a generalized pseudospectral technique is developed for the discretization of the non-Hermitian Floquet Hamiltonian and the construction of the Floquet matrix elements. (4) The Floquet matrices so generated are often very large scale, sparse, complex matrices. The formalisms and computational methods described above are applied to the studies of several high-intensity atomic and molecular multiphoton processes of current interests. The major accomplishments are summarized below: (1) The complex quasi-energies of excited states of atomic hydrogen in strong fields are determined for the first time. (2) Nonperturbative detailed calculations of the multiphoton detachment rates of H^- in one-color laser fields are performed for the first time. The intensity-averaged photodetachment rates calculated are in excellent agreement with those experimental data recently obtained in Los Alamos. (3) A generalized non-Hermitian two-mode Floquet theory is developed for the study of above-threshold multiphoton detachment of negative ions in intense two-color laser fields. (4) The two-color phase control of high-order harmonic generation (HHG) is investigated. It is shown that the HHG spectrum is sensitive to the relative phase of the two laser fields and a small admixture of a harmonic laser field to a fundamental laser field can lead to either increment or decrement of the HHG production rates. (5) The nature of chemical bond of D_2^+ molecules in intense one- and two-color laser fields is studied. An unexpected novel chemical bond hardening and molecular stabilization phenomenon is predicted: molecules initially prepared in highly excited vibrational states can become more stabilized and longer-lived with increasing laser intensity. Furthermore it is found that by tuning the relative phase between the fundamental and its third harmonic laser fields, the internuclear potential surface can be modified significantly, leading to a coherent control of the multiphoton dissociation dynamics. (Abstract shortened by UMI.).

Wang, Jingyan

272

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

E-print Network

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

O. B. Zaslavskii

2012-05-20

273

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

274

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

275

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

276

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

NASA Astrophysics Data System (ADS)

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

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

2009-12-01

277

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

SciTech Connect

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

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

2013-11-07

278

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

PubMed

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?m(2) on a picosecond time scale, and a low coverage might make the switching irreversible, which is in agreement with the experiments. PMID:23822319

Tian, Ziqi; Wen, Jin; Ma, Jing

2013-07-01

279

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

280

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

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

281

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

SciTech Connect

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

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

2005-01-01

282

Modeling quantum processes in classical molecular dynamics simulations of dense plasmas  

NASA Astrophysics Data System (ADS)

We present a method for treating quantum processes in a classical molecular dynamics (MD) simulation. The computational approach, called ‘Small Ball’ (SB), was originally introduced to model emission and absorption of free-free radiation. Here, we extend this approach to handle ionization/recombination reactions as well as nuclear fusion events. This method exploits the short-range nature of screened-particle interactions in a dense plasma to restrict consideration of quantum processes to a small region about a given ion, and carefully accounts for the effects of the plasma environment on two-particle interaction rates within that region. The use of a reduced set of atomic rates, corresponding to the bottleneck approximation, simplifies their implementation within an MD code. We validate the extended MD code against a collisional-radiative code for model systems under two scenarios: (i) solid-density carbon at conditions encountered in recent experiments, and (ii) high-density Xe-doped hydrogen relevant for laser fusion. We find good agreement for the time-dependent ionization evolution for both systems. We also simulate fast protons stopping in warm, dense carbon plasmas. Here, reasonable agreement with recent experimental data requires contributions from both bound electrons, as modeled by SB in the extended MD code, and free electrons; for the latter, use of the classical random phase approximation (RPA) formula instead of the MD prediction yields better agreement with the experiment, a result that can be attributed to the use of modified Coulomb potentials in MD simulations of electron-ion plasmas. Finally, we confirm that the fusion reaction rate obtained from an MD simulation agrees with analytical expressions for the reaction rate in a weakly screened plasma.

Hau-Riege, S. P.; Weisheit, J.; Castor, J. I.; London, R. A.; Scott, H.; Richards, D. F.

2013-01-01

283

Electron-capture processes of low-energy Si3+, Si4+, and Si5+ ions in collisions with helium atoms  

Microsoft Academic Search

Single- and double-electron-capture cross sections for Siq+ (q=3, 4, and 5) ions in collisions with He atoms have been measured at collision energies of a few hundred to a few thousand eV. The observed cross sections for single-electron capture are found to be of the order of 10-15 cm2, relatively independent of the collision energy, and are generally in agreement

H. Tawara; K. Okuno; C. W. Fehrenbach; C. Verzani; M. P. Stockli; B. D. Depaola; P. Richard; P. C. Stancil

2001-01-01

284

Decision Processes During Development of Molecular Biomarkers for Gonadal Phenotypic Sex  

EPA Science Inventory

Molecular biomarkers for determination of gonadal phenotypic sex in the Japanese medaka (Oryzias latipes), will serve as a case study. The medaka has unique features that aid in the development of appropriate molecular biomarkers of gonad phenotype, a) genetic sex can be determin...

285

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

286

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

PubMed

Heterogeneous catalysis and one-pot tandem reactions are key for efficient and practical organic syntheses and for green and sustainable chemistry. Heterogeneous catalysts can be recovered and reused. These catalysts can be applied to efficient systems, such as continuous-flow systems. Tandem reactions often proceed via highly reactive but unstable intermediates. Tandem reactions do not require workup or much purification of the intermediate. This Account summarizes recent developments that we have made in the field of multifunctional heterogeneous metal nanocluster catalysts for use in tandem reactions based on aerobic oxidation reactions as key processes. We constructed our heterogeneous metal nanoclusters via two important procedures--microencapsulation and cross-linking--using polystyrene-based copolymers with cross-linking moieties. These frameworks can efficiently stabilize small metal nanoclusters to maintain high catalytic activity without aggregation and leaching of nanoclusters. Aggregation and leaching are prevented by weak but multiple interactions between metal nanocluster surfaces and benzene rings in the copolymer as well as by the physical envelopment of cross-linked polymer backbones. Small nanoclusters, including multimetallic alloy clusters (nanoalloys), can be "imprisoned" into these cross-linked polymer composites. The term we use for these processes is polymer incarceration. Direct oxidative esterifications were achieved with polymer-incarcerated (PI) Au nanocluster catalysts. Amides were synthesized from alcohols and amines under aerobic oxidative conditions with PI bimetallic nanocluster catalysts composed of Au and Fe-group metals that formed separated nanoclusters rather than alloys. Oxidative lactam formation from amino alcohols was also achieved. On the other hand, imines could be prepared selectively from alcohols and amines with PI Au-Pd bimetallic nanoclusters. We also achieved the integration of the aerobic oxidation of allylic alcohols and the following Michael reaction catalyzed by trimetallic PI catalysts containing Au-Pd alloy nanoclusters and tetraalkoxyborates as cross-linkers. All of these heterogeneous catalysts could be recovered by simple operations and reused without significant loss of activity or any leaching of metals. We have demonstrated that the polymer incarceration method enables the simultaneous immobilization of several metals, with which we can achieve one-pot tandem oxidative processes using molecular oxygen as an oxidant within the multifunctional heterogeneous catalysts. Suitable choices of metals and bimetallic structures are crucial for the reactivity and the selection of reaction pathways. PMID:24661043

Miyamura, Hiroyuki; Kobayashi, Sh?

2014-04-15

287

Molecular dynamics simulation for focused ion beam processing: a comparison between computational domain and potential energy  

NASA Astrophysics Data System (ADS)

Molecular dynamics calculation was performed to simulate nano-Focused Ion Beam (FIB) processing on a Silicon surface. A combination of potential functions of impacting ion and target atoms was evaluated, and the influence of computational domain along the lateral directions was estimated. The target Silicon atoms on (100) surface of Si crystal were described by Tersoff potential. Ion-beam source was represented by Ga ions, where the optimal potential of the Ga ion was chosen by comparing Lennard-Jones, Tersoff, and ZBL (Ziegler, Biersack and Littmark) potentials. The initial velocity of ion was 3.327×105 m/sec at 40 keV. First, for the evaluation of combined potential functions of Si atoms and Ga ion, a small computation volume (2.58 nm × 2.58 nm × 51.99 nm) consisting of 19200 Si atoms was chosen with a single Ga ion impacting on Si (100) surface. On the combination of Tersoff potential for Si atom, and ZBL potential for Ga ion, the depth of the combination was found to be in good agreement with the depth of SRIM. Next, the influences of computational domain in lateral direction were evaluated by a larger region with a combination of potentials where the computational volume was (8.55 nm × 8.55 nm × 51.99 nm) constructed by 196608 Si atoms. Consequently, the energy transfer along lateral computational length was faster in larger region than in smaller region, and the entire initial energy of Ga ion was transmitted to the target material.

Satake, S.; Inoue, N.; Taniguchi, J.; Shibahara, M.

2008-03-01

288

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

PubMed

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

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

1997-05-01

289

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

290

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

NASA Astrophysics Data System (ADS)

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

Tsukamoto, Naoki; Kimura, Masashi; Harada, Tomohiro

2014-01-01

291

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

PubMed Central

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

Destro, M T; Leitão, M F; Farber, J M

1996-01-01

292

Inelastic titanium-titanium collisions  

SciTech Connect

We have measured cold inelastic collisions between neutral ground-state titanium atoms: collisions that cause transitions between the different magnetic sublevels of the [3d{sup 2}4s{sup 2}]{sup 3}F{sub 2} ground state of {sup 50}Ti, as well as collisions that cause transitions between the fine-structure levels of the [3d{sup 2}4s{sup 2}]{sup 3}F{sub J} electronic ground state. Both processes occur with large rate coefficients, as would be expected from titanium's anisotropic electronic potential.

Lu, M.-J.; Singh, Vijay; Weinstein, Jonathan D. [Department of Physics, University of Nevada, Reno, Nevada 89557 (United States)

2009-05-15

293

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

294

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

295

Continental collisions and seismic signature  

NASA Astrophysics Data System (ADS)

Reflection seismics in compressional belts has revealed the structure of crustal shortening and thickening processes, showing complex patterns of indentation and interfingering of colliding crusts and subcrustal lithospheres. Generally, in the upper crust large zones of detachments develop, often showing duplexes and 'crocodile' structures. The lower crust from zones of active collision (e.g. Alps, Pyrenees) is characterized by strongly dipping reflections. The base of the crust with the Moho must be continuously equilibrating after orogenic collapse as areas of former continental collision exhibit flat Mohos and subhorizontal reflections. The depth to the Moho increases during collision and decreases after the onset of post-orogenic extension, until finally the crustal root disappears completely together with the erosion of the mountains. Processes, active during continental collisions and orogenic collapse, create distinct structures which are imaged by reflection seismic profiling. Examples are shown and discussed.

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

1991-04-01

296

Spectroscopic studies of hydrogen collisions  

SciTech Connect

Low energy collisions involving neutral excited states of hydrogen are being studied with vacuum ultraviolet spectroscopy. Atomic hydrogen is generated by focusing an energetic pulse of ArF, KrF, or YAG laser light into a cell of molecular hydrogen, where a plasma is created near the focal point. The H{sub 2} molecules in and near this region are dissociated, and the cooling atomic hydrogen gas is examined with laser and dispersive optical spectroscopy. In related experiments, we are also investigating neutral H + O and H + metal {minus} atom collisions in these laser-generated plasmas.

Kielkopf, J.

1991-12-10

297

Self-interaction-free time-dependent density-functional theory for molecular multiphoton processes in intense laser fields  

Microsoft Academic Search

We present a new time-dependent density functional theory (TDDFT) with optimized effective potential (OEP) and self-interaction-correction (SIC) for nonperturbative treatment of multiphoton and nonlinear optical processes of many-electron molecular systems in intense laser fields. The theory allows the elimination of the spurious self-interaction energy in the conventional DFT and TDDFT, providing an accurate description of both short- and long-range potential

Xi Chu; Shih-I. Chu

2000-01-01

298

Enhancing the performance of solution-processed n-type organic field-effect transistors by blending with molecular "aligners".  

PubMed

A novel approach to enhancing the performance of solution-processed n-type organic field-effect transistors by using trace amounts of molecular "aligners" to manipulate the assembly of "matrix" molecules in thin films is demonstrated. The device performance is one order of magnitude higher in 1wt% blended thin films than that in neat films, which correlates to an induced change of preferred orientation of the in-plane ?-stacking molecules upon blending. PMID:24591009

Zhang, Yue; Hanifi, David; Lim, Eunhee; Chourou, Slim; Alvarez, Steven; Pun, Andrew; Hexemer, Alexander; Ma, Biwu; Liu, Yi

2014-02-26

299

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

NASA Astrophysics Data System (ADS)

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

Vagt, Nicole; Braun, Markus

300

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

NASA Astrophysics Data System (ADS)

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

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

2013-04-01

301

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

SciTech Connect

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

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

1993-06-01

302

Molecular scale track structure simulations in liquid water using the Geant4-DNA Monte-Carlo processes.  

PubMed

This paper presents a study of energy deposits induced by ionising particles in liquid water at the molecular scale. Particles track structures were generated using the Geant4-DNA processes of the Geant4 Monte-Carlo toolkit. These processes cover electrons (0.025 eV-1 MeV), protons (1 keV-100 MeV), hydrogen atoms (1 keV-100 MeV) and alpha particles (10 keV-40 MeV) including their different charge states. Electron ranges and lineal energies for protons were calculated in nanometric and micrometric volumes. PMID:20810287

Francis, Z; Incerti, S; Capra, R; Mascialino, B; Montarou, G; Stepan, V; Villagrasa, C

2011-01-01

303

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

E-print Network

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

David d'Enterria; Jean-Philippe Lansberg

2010-01-11

304

Notes on the Deformation Penetration Induced by Subductions and Collision Processes: Seismic Anisotropy Beneath the Adria Region (central Mediterranean)  

NASA Astrophysics Data System (ADS)

Seismic anisotropy studies help to sketch mantle deformation and related geodynamic processes. Adria is a small region in the Central Mediterranean surrounded by three mountain belts (the Alps, the Apennines and the Dinarides) generated by a long evolution of different subduction and collisional systems. We present 253 new shear wave splitting measurements obtained studying more than 100 teleseismic events for 12 seismographic stations. These data confirm that around the Adria microplate, most of the mantle has been deeply deformed by subduction processes. In its northern part, the anisotropy pattern follows the arcuate shape of the Alps, and the same occurs along the Apennines, following a NW-SE direction, but with a sudden change in the Adria foreland. This lateral variation has been analyzed to identify a distinct Adria mantle pattern, which is NE-SW along the western side of the microplate and N-S at Trieste (NE-Italy). This is interpreted as the traces left in the mantle by a drag effect due to the counterclockwise rotation of Adria, and this hypothesis is supported by GPS data. All SKS splitting measurements taken around Adria demonstrate the real 3D complexity of the upper mantle of this region. We interpret them as related to mantle flows induced by subduction processes, of which the one that generated the Alps is more efficient than its Apennine counterpart, deforming a larger volume of mantle. Moreover, the mantle flow we draw requires the existence of an escape route beneath the Alps-Apennines transition, as required by other previously suggested geodynamic models and as seen by some tomographic studies, through which the merged mantle flows of the Alps and the Apennines feed together the circulation in the Tyrrhenian mantle system.

Salimbeni, S.; Pondrelli, S.; Margheriti, L.

2013-12-01

305

Collision induced ultraviolet structure in nitrogen radar REMPI spectra  

NASA Astrophysics Data System (ADS)

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

McGuire, S.; Miles, R.

2014-12-01

306

Collision induced ultraviolet structure in nitrogen radar REMPI spectra.  

PubMed

We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a(1)?g ? X(1)?g (+) electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a(?1)?g (+) electronic state. PMID:25554145

McGuire, S; Miles, R

2014-12-28

307

Infrared absorption by molecular gases as a probe of nanoporous silica xerogel and molecule-surface collisions: Low-pressure results  

NASA Astrophysics Data System (ADS)

Transmission spectra of gases confined (but not adsorbed) within the pores of a 1.4-cm-thick silica xerogel sample have been recorded between 2.5 and 5 ?m using a high-resolution Fourier transform spectrometer. This was done for pure CO, CO2, N2O, H2O, and CH4 at room temperature and pressures of a few hectopascals. Least-squares fits of measured absorption lines provide the optical-path lengths within the confined (LC) and free (LF) gas inside the absorption cell and the half width at half maximum ?C of the lines of the confined gases. The values of LC and LF retrieved using numerous transitions of all studied species are very consistent. Furthermore, LC is in satisfactory agreement with values obtained from independent measurements, thus showing that reliable information on the open porosity volume can be retrieved from an optical experiment. The values of ?C, here resulting from collisions of the molecules with the inner surfaces of the xerogel pores, are practically independent of the line for each gas and inversely proportional to the square root of the probed-molecule molar mass. This is a strong indication that, for the studied transitions, a single collision of a molecule with a pore surface is sufficient to change its rotational state. A previously proposed simple model, used for the prediction of the line shape, leads to satisfactory agreement with the observations. It also enables a determination of the average pore size, bringing information complementary to that obtained from nitrogen adsorption porosimetry.

Vander Auwera, J.; Ngo, N. H.; El Hamzaoui, H.; Capoen, B.; Bouazaoui, M.; Ausset, P.; Boulet, C.; Hartmann, J.-M.

2013-10-01

308

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

Microsoft Academic Search

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

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

2001-01-01

309

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

310

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

E-print Network

through a typical 4 nm oxide shell in 10 ps. Mechanical properties of nanocrystalline -Fe2O3 +fcc 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

Southern California, University of

311

Hydrolysis and Oxidation in Subcritical and Supercritical Water: Connecting Process Engineering Science to Molecular Interactions  

Microsoft Academic Search

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

Jefferson Tester; Jason Cline

1999-01-01

312

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

PubMed

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. PMID:25362302

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

2014-10-28

313

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

314

Hints on the deformation penetration induced by subductions and collision processes: Seismic anisotropy beneath the Adria region (Central Mediterranean)  

NASA Astrophysics Data System (ADS)

is a small region surrounded by three mountain belts: the Alps, the Apennines, and the Dinarides, built up by long evolution of subduction and collisional systems. We present 253 shear wave splitting measurements obtained by studying more than 100 teleseismic events for 12 stations. SKS splitting measurements show 3-D complexity and quite strong upper mantle deformation. We carefully analyzed results in terms of back azimuthal coverage and interpret measurements as related to Adria rotation and to subductions evolution. In the northern part of Adria, the anisotropy pattern follows the arcuate shape of the Alps; the same pattern, parallel to the mountains, occurs along the Apennines, but fast directions show a sudden change in the Adria foreland. This lateral variation has been analyzed to isolate a distinct Adria mantle anisotropic pattern, which is identified as NE-SW fast direction along the western microplate boundary and as N-S fast direction at Trieste. This pattern might be induced by drag effect of the counterclockwise rotation of Adria lithosphere that behaves as an independent microplate as identified by GPS data. Our measurements suggest that the geodynamic process that generated the Alps is more efficient deforming a larger volume of mantle than its Apennine counterpart. Moreover, the mantle circulation we hypothesize looking at the regional-scale patterns of anisotropy requires the existence of an escape route beneath the Alps-Apennines transition, through which the mantle flows and feed circulation in the Tyrrhenian mantle system as suggested by previous geodynamic models and as seen by some tomographic studies.

Salimbeni, Simone; Pondrelli, Silvia; Margheriti, Lucia

2013-11-01

315

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

SciTech Connect

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

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

1997-06-01

316

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

NASA Technical Reports Server (NTRS)

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

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

1980-01-01

317

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

SciTech Connect

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

Cao, X. G.; Zhang, G. Q. [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Cai, X. Z.; Ma, Y. G.; Guo, W.; Chen, J. G.; Tian, W. D.; Fang, D. Q.; Wang, H. W. [Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China)

2010-06-15

318

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

PubMed

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

Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

2014-12-10

319

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

PubMed Central

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

Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

2014-01-01

320

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

NASA Technical Reports Server (NTRS)

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

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

2006-01-01

321

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

322

Collision-induced intensity of the b{sup 1}{Sigma}{sub g}{sup +}-a{sup 1}{triangle}g transition in molecular oxygen: Model calculations for the collision complex O{sub 2} + H{sub 2}  

SciTech Connect

Ab initio configuration interaction (CI) calculations have been performed for the O{sub 2} + H{sub 2} complex in a trapezoidlike collision arrangement with C{sub 2v} symmetry. The potential energy surfaces of the four lowest states of this van der Waals complex (arising from the X{sup 3}{Sigma}{sub g}{sup +} states of the oxygen moiety), as well as the collision-induced b{sup 1}{Sigma}{sub g}{sup +}-a{sup 1}{triangle}g electric dipole transition moment (M{sub b-a}), have been analyzed for different CI expansions, using as a reference determinant the restricted open-shell Hartree-Fock (ROHF) function for the ground state of the complex H{sub 2}(X{sup 1}{Sigma}{sub g}{sup +}) + O{sub 2}(X{sup 3}{Sigma}{sub g}{sup -}). The geometry optimized at the ROHF/6-311G level was refined by a partial optimization at the CI level scanning intermolecular distance. The equilibrium distances for the X, a, and b states have been found to be a slightly different in the region 3.02-2.98 A. The larger binding energy of the b{sup 1}{Sigma}{sub g}{sup +} state (2.96 kJ/mol) in comparison with the a{sup 1}{triangle}g (2.1 kJ/mol) and ground X{sup 3}{Sigma}{sub g}{sup -} states (1.35 kJ/mol) presumably could be explained as resulting from charge-transfer interactions. A good convergence of the calculated transition moment M{sub b-a} for the larger CI expansions (approximately 50,000 configuration-state functions) has been obtained. The calculated collision-induced intensity of the b{sup 1}{Sigma}{sub g}{sup +} - a{sup 1}{triangle}g and a{sup 1}{triangle}g - X{sup 3}{Sigma}{sub g}{sup -} transitions in molecular oxygen are in reasonable agreement with recent experimental data for several foreign gases.

Minaev, B.F.; Kobzev, G.I. [Uppsala Univ., Cherkassy (Ukraine); Lunell, S. [Uppsala Univ., Uppsala (Sweden)

1994-12-31

323

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

324

Coulomb excitation of highly charged projectile ions in relativistic collisions with diatomic molecules  

SciTech Connect

We investigate the Coulomb excitation of highly charged ions colliding with diatomic molecules. In this process, the coherent interaction between the projectile electron and two molecular centers may cause clear interference patterns in the (collision) energy dependencies of the total cross sections and alignment parameters. We discuss such a Young-type interference for the particular case of the K{yields}L excitation of hydrogen- and helium-like projectile ions. Calculations, performed for the scattering of these ions on nitrogen molecules, indicate that the interference effects are extremely sensitive to the collisional geometry and are pronounced only if the molecular axis is aligned almost parallel to the incident beam trajectory.

Artemyev, A. N.; McConnell, S. R.; Surzhykov, A.; Najjari, B.; Voitkiv, A. B. [Physikalisches Institut, Universitaet Heidelberg, Philosophenweg 12, D-69120 Heidelberg, Germany and GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, D-64291 Darmstadt (Germany); Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, D-69117 Heidelberg (Germany)

2011-10-15

325

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

NASA Astrophysics Data System (ADS)

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

Avakyan, Sergei

2010-05-01

326

Integrated Collision Avoidance System for Air Vehicle  

NASA Technical Reports Server (NTRS)

Collision with ground/water/terrain and midair obstacles is one of the common causes of severe aircraft accidents. The various data from the coremicro AHRS/INS/GPS Integration Unit, terrain data base, and object detection sensors are processed to produce collision warning audio/visual messages and collision detection and avoidance of terrain and obstacles through generation of guidance commands in a closed-loop system. The vision sensors provide more information for the Integrated System, such as, terrain recognition and ranging of terrain and obstacles, which plays an important role to the improvement of the Integrated Collision Avoidance System.

Lin, Ching-Fang (Inventor)

2013-01-01

327

Analyzing Collisions in Terms of Newton's Laws  

NASA Astrophysics Data System (ADS)

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

Roeder, John L.

2003-02-01

328

The preparation of B?Sb thin films by molecular flow region PVD process  

NASA Astrophysics Data System (ADS)

The present paper is the first description on the preparation of B-Sb films by molecular flow region PVD method using the reaction of decaborane gas with evaporated antimony gas on Si(1 0 0) substrate at the temperatures 200-400°C. The cracking of evaporated Sb 2 into Sb 1 produced the films with the composition of amorphous B 12Sb 2 determined by X-ray photoelectron spectroscopy and infrared spectra. Ohmic metals of the films were examined by making evaporated Ag followed by annealing at 200°C.

Kumashiro, Y.; Nakamura, K.; Doi, Y.; Hirata, K.; Yokoyama, T.; Sato, K.

2002-04-01

329

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

SciTech Connect

The electron transfer reaction between the photoinjected electrons in the nanocrystalline TiO{sub 2} 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; Martinez-Ferrero, Eugenia; Sanchez-Diaz, Antonio; Sarmentero, Maria Angeles [Institute of Chemical Research of Catalonia (ICIQ). Avda. Paiesos Catalans, 16 Tarragona 43007 (Spain); Ballester, Pablo; Palomares, Emilio [Institute of Chemical Research of Catalonia (ICIQ). Avda. Paiesos Catalans, 16 Tarragona 43007 (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluis Companys, 23 08010 Barcelona (Spain); O'Regan, Brian C. [Centre for Electronic Materials and Devices, Imperial College of London, Exhibition Road, SW7 2AZ London (United Kingdom)

2008-04-14

330

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

331

Changes in Molecular Characteristics of Cereal Carbohydrates after Processing and Digestion  

PubMed Central

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

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

2012-01-01

332

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

333

First-principles molecular dynamics simulations of (sulfuric acid)1(dimethylamine)1 cluster formation  

NASA Astrophysics Data System (ADS)

The clustering process (sulfuric acid) + (base)?(sulfuric acid)1(base)1 is of fundamental importance in the atmospheric new-particle formation. Especially interesting are the collisions where a proton transfer reaction can happen, as the reaction often leads to relatively strongly bound clusters. Here, we studied the clustering process of (sulfuric acid) + (dimethylamine) ? (sulfuric acid)1(dimethylamine)1 using first-principles molecular dynamics simulations. The collision of the two molecules was simulated starting with various spatial orientations and the evolution of the cluster was followed in the NVE ensemble. The simulations suggest that the proton transfer reaction takes place regardless of the intial collision orientation. However, due to the energy released in the process, the newly-formed cluster is not able to reach the minimun energy configuration, which might affect the following growth processes.

Loukonen, Ville; Bork, Nicolai; Vehkamäki, Hanna

2013-05-01

334

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

335

Preparation and characterization of molecularly homogeneous silica-titania film by sol-gel process with different synthetic strategies.  

PubMed

Three silica-titania thin films with various degrees of molecular homogeneity were synthesized by the sol-gel process with the same precursor formula but different reaction paths. The dried films prepared by a single spin-coating process have a thickness of 500-700 nm and displayed no cracks or pin holes. The transmittances and refractive indices of the samples are >97.8% in the range of 350-1800 nm and 1.62-1.65 at 500 nm, respectively. The in-plane and out-of-plane chemical homogeneities of the films were analyzed by X-ray photoelectron spectroscopy and Auger electron spectroscopy, respectively. For the film with the highest degree of homogeneity, the deviations of O, Si, and Ti atomic contents in both in-plane and out-of-plane directions are less than 1.5%, indicating that the film is highly molecularly homogeneous. It also possesses the highest transparency and the lowest refractive index among the three samples. PMID:22934676

Chen, Hsueh-Shih; Huang, Sheng-Hsin; Perng, Tsong-Pyng

2012-10-24

336

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

337

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

E-print Network

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

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

2014-01-01

338

Electronic and phonon processes of MnO4 - molecular impurities in alkali halide crystals  

NASA Astrophysics Data System (ADS)

We present the results of a detailed study of the near-infrared photoluminescence and the luminescence excitation spectra of iodide (KI and RbI) and bromide (KBr and RbBr) crystals doped with MnO-4, MnO42- and MnO43- molecular ions. The experimental and the theoretical study of the NIRL integral intensity temperature dependence in a wide temperature interval 4-300 K shows unusual thermoactivation behavior of the intensity for MnO4- doped crystals. The thermo-photo-induced transformation of MnO-4 into MnO42- was observed for both types of crystals doped by the MnO4- ions.

Maksimova, T. I.; Hermanovich, K.; Hanuza, J.; Happek, U.

2005-01-01

339

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

NSDL National Science Digital Library

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

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

2008-10-21

340

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

NASA Technical Reports Server (NTRS)

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

Luther, George W., III

1987-01-01

341

Absolute Cross Sections for Molecular Photoabsorption, Partial Photoionization, and Ionic Photofragmentation Processes  

NASA Astrophysics Data System (ADS)

A compilation is provided of absolute total photoabsorption and partial-channel photoionization cross sections for the valence shells of selected molecules, including diatomics (H2, N2, O2, CO, NO) and triatomics (CO2, N2O), simple hydrides (H2O, NH3, CH4), hydrogen halides (HF, HCl, HBr, HI), sulfur compounds (H2S, CS2, OCS, SO2, SF6), and chlorine compounds (Cl2, CCl4). The partial-channel cross sections presented refer to production of the individual electronic states of molecular ions and also to production of parent and specific fragment ions, as functions of incident photon energy, typically from ˜20 to 100 eV. Total photoabsorption cross sections above the first ionization threshold are reported from conventional optical measurements obtained using line and continuum sources and from ``equivalent-photon'' dipole (e,e) electron scattering experiments. Partial photoionization cross sections for production of electronic states of molecular ions are obtained from photoelectron spectroscopy and from dipole (e,2e) coincidence measurements. Photoionization mass spectrometry and dipole (e, e+ion) coincidence studies provide measurements of partial cross sections for ionic photofragmentation (i.e., dissociative photoionization). Photoelectron anisotropy factors, which together with electronic partial cross sections provide cross sections differential in photon energy and in ejection angle, are also reported. There is generally good agreement between cross sections measured by the physically distinct optical and dipole electron-impact methods. The cross sections and anisotropy factors also compare favorably with selected ab initio and model potential (X-alpha) calculations which provide a basis for interpretation of the measurements.

Gallagher, J. W.; Brion, C. E.; Samson, J. A. R.; Langhoff, P. W.

1988-01-01

342

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

SciTech Connect

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

Walsh, S.P.

1992-01-01

343

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

SciTech Connect

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

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

2008-08-06

344

Multielectron processes in 10-keV/u Ar[sup [ital q]+] (5[le][ital q][le]17) on Ar collisions  

SciTech Connect

We have used time-of-flight coincidence techniques to study multielectron reactions in 10-keV/u ([ital v]=0.632 a.u.) Ar[sup [ital q]+] (5[le][ital q][le]17) on Ar collisions. Absolute cross sections for total charge-transfer ([sigma][sub [ital q

Ali, R.; Cocke, C.L.; Raphaelian, M.L.A.; Stockli, M. (J. R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506-2604 (United States))

1994-05-01

345

Computation of the effective cross section of thallium atom collisions  

Microsoft Academic Search

Translated from Izmer. Tekh.; 16: No. 2, 60-61 (Feb 1973). The ; experimental data on the distribution of velocities in molecular beams is used ; for computing the effective cross section of collisions for thallium atoms. ; (JFP);

Yu. G. Abashev; G. F. Voronin; R. A. Valitov

1973-01-01

346

Molecular specialization of astrocyte processes at nodes of Ranvier in rat optic nerve  

PubMed Central

The HNK-1 and L2 monoclonal antibodies are thought to recognize identical or closely associated carbohydrate epitopes on a family of neural plasma membrane glycoproteins, including myelin-associated glycoprotein, the neural cell adhesion molecule, and the L1 and J1 glycoproteins, all of which have been postulated to play a part in mediating cell-cell interactions in the nervous system. We have used these two antibodies in immunofluorescence and immunogold-electron microscopic studies of semithin and ultrathin frozen sections of adult rat optic nerve, respectively, and we show that they bind mainly to astrocyte processes around nodes of Ranvier. Most other elements of the nerve, including astrocyte cell bodies and large astrocytic processes, are not labeled by the antibodies. To our knowledge, this is the first demonstration that perinodal astrocyte processes are biochemically specialized. We provide evidence that one of the HNK-1+/L2+ molecules concentrated around perinodal astrocyte processes is the J1 glycoprotein; our findings, taken together with previously reported observations, suggest that the other known HNK-1+/L2+ molecules are not concentrated on these processes. Since anti-J1 antibodies previously have been shown to inhibit neuron to astrocyte adhesion in vitro, we hypothesize that J1 may play an important part in the axon-glial interactions that presumably are involved in the assembly and/or maintenance of nodes of Ranvier. PMID:2419343

1986-01-01

347

Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic orbal processes.  

PubMed

Aerated-anoxic processes operate under the principle that small additions of oxygen to an anoxic reactor induce simultaneous nitrification and denitrification. In these systems, ammonia oxidation in the anoxic zone can easily account for 30-50% of the total nitrification in the reactor, even though the dissolve oxygen concentration is usually below detection limit. To investigate whether the nitrification efficiency in aerated-anoxic processes was due to the presence of specialized ammonia-oxidizing bacteria (AOB), an analysis of the AOB population in an aerated-anoxic Orbal process and a conventional nitrogen removal process was carried out using phylogenetic analyses based on the ammonia monooxygenase A (amoA) gene. Terminal restriction fragment length polymorphism (TRFLP) analyses revealed that Nitrosospira-like organisms were one of the major contributors to ammonia oxidation in a full-scale aerated-anoxic Orbal reactor. However, the relative populations of Nitrosospira-like and Nitrosomonas-like AOB were not constant and appeared to have seasonal variability. Cloning and sequence comparison of amoA gene fragments demonstrated that most of the AOB in the aerated-anoxic Orbal process belonged to the Nitrosospira sp. and Nitrosomonas oligotropha lineages. The abundance of Nitrosospira-like organisms in aerated-anoxic reactors is significant, since this group of AOB has not been usually associated with nitrification in wastewater treatment plants. PMID:12216636

Park, H-D; Regan, J M; Noguera, D R

2002-01-01

348

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

349

New section of the HITRAN database: Collision-induced absorption (CIA)  

E-print Network

New section of the HITRAN database: Collision-induced absorption (CIA) C. Richard a , I.E. Gordon Keywords: Collision-induced absorption HITRAN Atmospheric absorption Interacting molecular pairs a b s t r a c t This paper describes the addition of Collision-Induced Absorption (CIA) into the HITRAN

Chance, Kelly

350

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

351

Food forensics: Analysis of food, raw and processed materials with molecular biological methods  

Microsoft Academic Search

The identification of species is vital for product quality control as well as for detection of fraud and even more so for the investigation of crimes when biological trace material is found. They all have in common that the correct assignment of biological samples to species is aggravated due to highly degraded (e.g. due to heavy processing) or low amounts

R. Schubbert; W. Hell; T. Brendel; S. Rittler; S. Schneider; K. Klöpper

2008-01-01

352

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

Microsoft Academic Search

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

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

2005-01-01

353

Absolute cross sections for molecular photoabsorption, partial photoionization, and ionic photofragmentation process  

SciTech Connect

A compilation is provided of absolute total photoabsorption and partial-channel photoionization cross sections for the valence shells of selected molecules, including diatomics (H2, N2, O2, CO, NO) and triatomics (CO2, N2O), simple hydrides (H2O, NH3, CH4), hydrogen halides (HF, HCl, HBr, HI), sulfur compounds (H2S, CS2, OCS, SO2, SF6),and chlorine compounds (Cl2, CCl4). The partial-channel cross sections presented refer to production of the individual electronic states of molecular ions and also to production of parent and specific fragment ions, as functions of incident photon energy, typically from approximately 20 to 100 eV. Photoelectron anisotropy factors, which together with electronic partial cross sections provide cross sections differential in photon energy and in ejection angle, are also reported. There is generally good agreement between cross sections measured by the physically distinct optical and dipole electron-impact methods. The cross sections and anisotropy factors also compare favorably with selection ab initio and model potential (X-alpha) calculations which provide a basis for interpretation of the measurements.

Gallagher, J.W.; Brion, C.E.; Samson, J.A.R.; Langhoff, P.W.

1988-01-01

354

Molecular cloning, sequence, expression, and processing of the interleukin 16?precursor  

PubMed Central

Interleukin 16 (IL-16) has been shown to function as chemoattractant factor, as a modulator of T-cell activation, and as an inhibitor of immunodeficiency virus replication. The recent identification of inconsistencies in published IL-16 cDNA nucleotide sequences led to the proposal that IL-16 is synthesized in the form of a large precursor protein (pro-IL-16). To identify the true transcriptional start of the IL-16 mRNA rapid amplification of cDNA ends methods were applied. The complete pro-IL-16 cDNA was subsequently molecularly cloned, sequenced, and expressed in COS-7 cells. We report here that pro-IL-16 is most likely synthesized as a 67-kDa protein and is encoded from a major 2.6-kb transcript. Recombinant pro-IL-16 polypeptides are specifically cleaved in lysates of CD8(+) cells, suggesting that the naturally secreted bioactive form of IL-16 is smaller than the originally published 130 amino acids fragment. Moreover, in contrast to other interleukins such as IL-15, IL-16 mRNA expression is almost exclusively limited to lymphatic tissues underlining the potential of IL-16 as an immune regulatory molecule. PMID:9144227

Baier, Michael; Bannert, Norbert; Werner, Albrecht; Lang, Kurt; Kurth, Reinhard

1997-01-01

355

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

356

Insights into the DNA repair process by the formamidopyrimidine-DNA glycosylase investigated by molecular dynamics  

PubMed Central

Formamidopyrimidine-DNA glycosylase (Fpg) identifies and removes 8-oxoguanine from DNA. All of the X-ray structures of Fpg complexed to an abasic site containing DNA exhibit a common disordered region present in the C-terminal domain of the enzyme. However, this region is believed to be involved in the damaged base binding site when the initial protein/DNA complex is formed. The dynamic behavior of the disordered polypeptide (named Loop) in relation to the supposed scenario for the DNA repair mechanism was investigated by molecular dynamics on different models, derived from the X-ray structure of Lactococcus lactis Fpg bound to an abasic site analog-containing DNA and of Bacillus stearothermophilus Fpg bound to 8-oxoG. This study shows that the presence of the damaged base influences the dynamics of the whole enzyme and that the Loop location is dependent on the presence and on the conformation of the 8-oxoG in its binding site. In addition, from our results, the conformation of the 8-oxoG seems to be favored in syn in the L. lactis models, in agreement with the available X-ray structure from B. stearothermophilus Fpg and with a possible catalytic role of the flexibility of the Loop region. PMID:15273302

Amara, Patricia; Serre, Laurence; Castaing, Bertrand; Thomas, Aline

2004-01-01

357

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

358

Text mining and network analysis of molecular interaction in non-small cell lung cancer by using natural language processing.  

PubMed

Lung cancer including non-small cell lung cancer (NSCLC) and small cell lung cancer is one of the most aggressive tumors with high incidence and low survival rate. The typical NSCLC patients account for 80-85 % of the total lung cancer patients. To systemically explore the molecular mechanisms of NSCLC, we performed a molecular network analysis between human and mouse to identify key genes (pathways) involved in the occurrence of NSCLC. We automatically extracted the human-to-mouse orthologous interactions using the GeneWays system by natural language processing and further constructed molecular (gene and its products) networks by mapping the human-to-mouse interactions to NSCLC-related mammalian phenotypes, followed by module analysis using ClusterONE of Cytoscape and pathway enrichment analysis using the database for annotation, visualization and integrated discovery (DAVID) successively. A total of 70 genes were proven to be related to the mammalian phenotypes of NSCLC, and seven genes (ATAD5, BECN1, CDKN2A, FNTB, E2F1, KRAS and PTEN) were found to have a bearing on more than one mammalian phenotype (MP) each. Four network clusters centered by four genes thyroglobulin (TG), neurofibromatosis type-1 (NF1 ), neurofibromatosis type 2 (NF2 ) and E2F transcription factor 1 (E2F1) were generated. Genes in the four network modules were enriched in eight KEGG pathways (p value < 0.05), including pathways in cancer, small cell lung cancer, cell cycle and p53 signaling pathway. Genes p53 and E2F1 may play important roles in NSCLC occurrence, and thus can be considered as therapeutic targets for NSCLC. PMID:25205120

Li, Jun; Bi, Lintao; Sun, Yanxia; Lu, Zhenxia; Lin, Yumei; Bai, Ou; Shao, Hui

2014-12-01

359

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

SciTech Connect

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. [International Thermonuclear Experimental Reactor Garching (Germany) and San Diego (United States) Joint Work Sites (Germany)

1998-07-08

360

Metamorphism and Continental Collision  

NSDL National Science Digital Library

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

Howard, Kenneth

361

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

362

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

363

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

364

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

SciTech Connect

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

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

2005-09-01

365

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

SciTech Connect

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

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

2007-08-28

366

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

PubMed

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 order 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. PMID:25485083

Vilfan, Andrej

2014-12-01

367

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

368

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

369

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

NASA Astrophysics Data System (ADS)

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

Kohler, Felix; Rohrbach, Alexander

2015-01-01

370

Fine-sorting one-dimensional particle-in-cell algorithm with Monte-Carlo collisions on a graphics processing unit  

Microsoft Academic Search

Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a considerable amount of time for convergence. Most of the computations can be massively parallelized, since particles behave independently of each other within one

Philipp Mertmann; Denis Eremin; Thomas Mussenbrock; Ralf Peter Brinkmann; Peter Awakowicz

2011-01-01

371

Sub-laser-cycle electron pulses for probing molecular dynamics.  

PubMed

Experience shows that the ability to make measurements in any new time regime opens new areas of science. Currently, experimental probes for the attosecond time regime (10(-18) 10(-15) s) are being established. The leading approach is the generation of attosecond optical pulses by ionizing atoms with intense laser pulses. This nonlinear process leads to the production of high harmonics during collisions between electrons and the ionized atoms. The underlying mechanism implies control of energetic electrons with attosecond precision. We propose that the electrons themselves can be exploited for ultrafast measurements. We use a 'molecular clock', based on a vibrational wave packet in H(2)(+) to show that distinct bunches of electrons appear during electron ion collisions with high current densities, and durations of about 1 femtosecond (10(-15) s). Furthermore, we use the molecular clock to study the dynamics of non-sequential double ionization. PMID:12087396

Niikura, Hiromichi; Légaré, F; Hasbani, R; Bandrauk, A D; Ivanov, Misha Yu; Villeneuve, D M; Corkum, P B

2002-06-27

372

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

PubMed Central

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

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

2008-01-01

373

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

PubMed

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

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

2013-11-28

374

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

PubMed Central

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

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

2008-01-01

375

Ion and electron beam processing of condensed molecular solids to form thin films  

SciTech Connect

Electron and ion beams can be used to deposit thin films and etch surfaces using gas phase precursors. However, the generation of undesirable gas phase products and the diffusion of the reactive species beyond the region irradiated by the electron or ion beam can limit selectivity. In this paper, the feasibility of processing condensed precursors such as diborane, tri-methyl aluminum, ammonia and water at 78 K with low energy ( 100--1000 eV) electron and ion beams (Ar[sup +], N[sub 2][sup +] and H[sub 2][sup +]) ranging in current density from 50 nA to several [mu]a per cm[sup 2] is examined. It was found that boron, boron nitride and stoichiometric aluminum oxide films could be deposited from the condensed volatile; species using charged particle beams and some of the physical and chemical aspects and limitations of this new technique are discussed.

Ruckman, M.W.; Strongin, M. (Brookhaven National Lab., Upton, NY (United States)); Mowlem, J.K.; Moore, J.F.; Strongin, D.R. (State Univ. of New York, Stony Brook, NY (United States). Dept. of Chemistry)

1992-01-01

376

Ion and electron beam processing of condensed molecular solids to form thin films  

SciTech Connect

Electron and ion beams can be used to deposit thin films and etch surfaces using gas phase precursors. However, the generation of undesirable gas phase products and the diffusion of the reactive species beyond the region irradiated by the electron or ion beam can limit selectivity. In this paper, the feasibility of processing condensed precursors such as diborane, tri-methyl aluminum, ammonia and water at 78 K with low energy ( 100--1000 eV) electron and ion beams (Ar{sup +}, N{sub 2}{sup +} and H{sub 2}{sup +}) ranging in current density from 50 nA to several {mu}a per cm{sup 2} is examined. It was found that boron, boron nitride and stoichiometric aluminum oxide films could be deposited from the condensed volatile; species using charged particle beams and some of the physical and chemical aspects and limitations of this new technique are discussed.

Ruckman, M.W.; Strongin, M. [Brookhaven National Lab., Upton, NY (United States); Mowlem, J.K.; Moore, J.F.; Strongin, D.R. [State Univ. of New York, Stony Brook, NY (United States). Dept. of Chemistry

1992-12-31

377

Distinct molecular interactions mediate neuronal process outgrowth on non-neuronal cell surfaces and extracellular matrices  

PubMed Central

We have compared neurite outgrowth on extracellular matrix (ECM) constituents to outgrowth on glial and muscle cell surfaces. Embryonic chick ciliary ganglion (CG) neurons regenerate neurites rapidly on surfaces coated with laminin (LN), fibronectin (FN), conditioned media (CM) from several non-neuronal cell types that secrete LN, and on intact extracellular matrices. Neurite outgrowth on all of these substrates is blocked by two monoclonal antibodies, CSAT and JG22, that prevent the adhesion of many cells, including neurons, to the ECM constituents LN, FN, and collagen. Neurite outgrowth is inhibited even on mixed LN/poly-D-lysine substrates where neuronal attachment is independent of LN. Therefore, neuronal process outgrowth on extracellular matrices requires the function of neuronal cell surface molecules recognized by these antibodies. The surfaces of cultured astrocytes, Schwann cells, and skeletal myotubes also promote rapid process outgrowth from CG neurons. Neurite outgrowth on these surfaces, though, is not prevented by CSAT or JG22 antibodies. In addition, antibodies to a LN/proteoglycan complex that block neurite outgrowth on several LN-containing CM factors and on an ECM extract failed to inhibit cell surface-stimulated neurite outgrowth. After extraction with a nonionic detergent, Schwann cells and myotubes continue to support rapid neurite outgrowth. However, the activity associated with the detergent insoluble residue is blocked by CSAT and JG22 antibodies. Detergent extraction of astrocytes, in contrast, removes all neurite- promoting activity. These results provide evidence for at least two types of neuronal interactions with cells that promote neurite outgrowth. One involves adhesive proteins present in the ECM and ECM receptors on neurons. The second is mediated through detergent- extractable macromolecules present on non-neuronal cell surfaces and different, uncharacterized receptor(s) on neurons. Schwann cells and skeletal myotubes appear to promote neurite outgrowth by both mechanisms. PMID:3025222

1986-01-01

378

Tiny Molecular Beacons: LNA/2'-O-methyl RNA Chimeric Probes for Imaging Dynamic mRNA Processes in Living Cells  

PubMed Central

New approaches for imaging dynamic processes involving RNAs in living cells are continuously being developed and optimized. The use of molecular beacons synthesized from 2'-O-methylribonucleotides (which are resistant to cellular nucleases) is an established approach for visualizing native mRNAs in real time. In order to spatially and temporally resolve dynamic steps involving RNA in cells, molecular beacons need to efficiently hybridize to their RNA targets. To expand the repertoire of target sites accessible to molecular beacons, we decreased the length of their probe sequences and altered their backbone by the inclusion of LNA (locked nucleic acid) nucleotides. We named these new LNA/2'-O-methyl RNA chimera oligonucleotides, “tiny molecular beacons”. We analyzed these tiny molecular beacons and found that the incorporation of just a few LNA nucleotides enables these shorter probes to stably anneal to more structured regions of the RNA than is possible with conventional molecular beacons. The ease of synthesis of tiny molecular beacons, and the flexibility to couple them to a large variety of fluorophores and quenchers, renders them optimal for the detection of less abundant and/or highly structured RNAs. To determine their efficiency to detect endogenous mRNAs in live specimens, we designed tiny molecular beacons that were specific for oskar mRNA and microinjected them into living Drosophila melanogaster oocytes. We then imaged the live oocytes via spinning disc confocal microscopy. The results demonstrate that tiny molecular beacons hybridize to target mRNA at faster rates than classically designed molecular beacons, and are able to access previously inaccessible target regions. PMID:22738327

Catrina, Irina E.; Marras, Salvatore A.E.; Bratu, Diana P.

2012-01-01

379

Cellular and molecular mechanism study of declined intestinal transit function in the cholesterol gallstone formation process of the guinea pig.  

PubMed

The aim of this study was to investigate the cellular and molecular mechanisms of declined intestinal transit (IT) function in the cholesterol gallstone (CG) formation process. Forty guinea pigs were divided into an experimental group (EG) and a control group (CoG), and the reverse transcription-polymerase chain reaction (RT-PCR) was performed for the analysis of c-kit and stem cell factor (scf) mRNA expression in the small bowel. In addition, immunofluorescence staining and confocal laser microscopy were performed for the observation of the changes in the number of interstitial cells of Cajal (ICCs) in the terminal ileum of each group. RT-PCR showed that, compared with the CoG, the intestinal c-kit and scf mRNA expression levels in the EG were significantly decreased; the average positive area of ICCs in the ileum in the EG was also significantly reduced. During the diet-induced CG formation procedure, the c-kit and scf mRNA expression levels in the small intestine decreased and the number of ICCs decreased. Inhibition of the c-kit/scf pathway may be involved in the declined IT function during the CG formation process. PMID:25289052

Fan, Ying; Wu, Shuodong; Yin, Zhenhua; Fu, Bei-Bei

2014-11-01

380

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

NASA Astrophysics Data System (ADS)

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

Jorn, Ryan Paul

381

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

382

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

PubMed

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

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

2014-10-16

383

Thermal decomposition process in algaenan of Botryococcus braunii race L. Part 2: Molecular dynamics simulations using the ReaxFF reactive force field  

Microsoft Academic Search

This paper reports ReaxFF MD simulation results on pyrolysis of a molecular model of the algaenan Botryococcus braunii race L biopolymer, specifically, ReaxFF predictions on the pyrolysis of prototypical chemical structures involving aliphatic chain esters and aldehydes. These preliminary computational experiments are then used to analyze the thermal cracking process within algaenan race L biopolymers. The simulations indicate that the

Elodie Salmon; Adri C. T. van Duin; François Lorant; Paul-Marie Marquaire; William A. Goddard III

2009-01-01

384

Comparative transcripts profiling reveals new insight into molecular processes regulating lycopene accumulation in a sweet orange (Citrus sinensis) red-flesh mutant  

Microsoft Academic Search

BACKGROUND: Interest in lycopene metabolism and regulation is growing rapidly because accumulative studies have suggested an important role for lycopene in human health promotion. However, little is known about the molecular processes regulating lycopene accumulation in fruits other than tomato so far. RESULTS: On a spontaneous sweet orange bud mutant with abnormal lycopene accumulation in fruits and its wild type,

Qiang Xu; Keqin Yu; Andan Zhu; Junli Ye; Qing Liu; Jianchen Zhang; Xiuxin Deng

2009-01-01

385

Fragmentation model dependence of collision cascades  

NASA Astrophysics Data System (ADS)

Mass depletion of bodies through successive collisional disruptions (i.e., collision cascade) is one of the most important processes in the studies of the asteroids belt, the Edgeworth-Kuiper belt, debris disks, and planetary formation. The collisional disruption is divided into two types, i.e., catastrophic disruption and cratering. Although some studies of the collision cascades neglected the effect of cratering, it is unclear which type of disruption makes a dominant contribution to the collision cascades. In the present study, we construct a simple outcome model describing both catastrophic disruption and cratering, which has some parameters characterizing the total ejecta mass, the mass of the largest fragment, and the power-law exponent of the size distribution of fragments. Using this simple outcome model with parameters, we examine the model dependence of the mass depletion time in collision cascades for neglect of coalescence of colliding bodies due to high collisional velocities. We find the cratering collisions are much more effective in collision cascades than collisions with catastrophic disruption in a wide region of the model parameters. It is also found that the mass depletion time in collision cascades is mainly governed by the total ejecta mass and almost insensitive to the mass of the largest fragment and the power-law exponent of fragments for a realistic parameter region. The total ejecta mass is usually determined by the ratio of the impact energy divided by the target mass (i.e. Q-value) to its threshold value QD? for catastrophic disruption, as well as in our simple model. We derive a mass depletion time in collision cascades, which is determined by QD? of the high-mass end of collision cascades. The mass depletion time derived with our model would be applicable to debris disks and planetary formation.

Kobayashi, Hiroshi; Tanaka, Hidekazu

2010-04-01

386

Spectroscopic studies of hydrogen collisions. Progress report  

SciTech Connect

Low energy collisions involving neutral excited states of hydrogen are being studied with vacuum ultraviolet spectroscopy. Atomic hydrogen is generated by focusing an energetic pulse of ArF, KrF, or YAG laser light into a cell of molecular hydrogen, where a plasma is created near the focal point. The H{sub 2} molecules in and near this region are dissociated, and the cooling atomic hydrogen gas is examined with laser and dispersive optical spectroscopy. In related experiments, we are also investigating neutral H + O and H + metal {minus} atom collisions in these laser-generated plasmas.

Kielkopf, J.

1991-12-10

387

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

PubMed

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

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

2012-03-01

388

Influence of double-tip scratch and single-tip scratch on nano-scratching process via molecular dynamics simulation  

NASA Astrophysics Data System (ADS)

A three-dimensional molecular dynamics model was proposed to study the influences of scratch feed, depth and crystal orientation on the shape and surface quality of the scratched groove during nano-scratching process. In this paper, comparisons were made between the results of double tips simultaneously scratching the surface and those of single tip successively scratching the surface with the same scratch feed, depth and crystal orientation. EAM potential was used to model the interaction of copper atoms, and Morse potential was used to model the interaction between copper and carbon atoms. The residual profiles of scratched grooves and scratching forces were recorded during the simulations. Simulational results show that when single tip scratches the surface at an extremely small feed, the second time scratch significantly influences the previous groove. The second time scratch has a significant influence on the previous groove by increasing scratch depth. Compared with scratching along crystal orientation [1 0 0], scratching along crystal orientation [0 1 1] and [1 1 1] are easy to obtain two parallel grooves. However, when double tips simultaneously scratch the surface regardless of scratch feed, depth and crystal orientation, two parallel grooves are always obtained. Thus, in order to obtain scratched grooves of high quality, it is quite beneficial to design and machine multiple-tip tools.

Zhang, Peng; Zhao, Hongwei; Shi, Chengli; Zhang, Lin; Huang, Hu; Ren, Luquan

2013-09-01

389

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

PubMed

High-speed fluorescence molecular tomography (FMT) reconstruction for 3-D heterogeneous media is still one of the most challenging problems in diffusive optical fluorescence imaging. In this paper, we propose a fast FMT reconstruction method that is based on Monte Carlo (MC) simulation and accelerated by a cluster of graphics processing units (GPUs). Based on the Message Passing Interface standard, we modified the MC code for fast FMT reconstruction, and different Green's functions representing the flux distribution in media are calculated simultaneously by different GPUs in the cluster. A load-balancing method was also developed to increase the computational efficiency. By applying the Fre?chet derivative, a Jacobian matrix is formed to reconstruct the distribution of the fluorochromes using the calculated Green's functions. Phantom experiments have shown that only 10 min are required to get reconstruction results with a cluster of 6 GPUs, rather than 6 h with a cluster of multiple dual opteron CPU nodes. Because of the advantages of high accuracy and suitability for 3-D heterogeneity media with refractive-index-unmatched boundaries from the MC simulation, the GPU cluster-accelerated method provides a reliable approach to high-speed reconstruction for FMT imaging. PMID:21361702

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

2011-02-01

390

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

391

A LOW-COST PROCESS FOR THE SYNTHESIS OF NANOSIZE YTTRIA-STABILIZED ZIRCONIA (YSZ) BY MOLECULAR DECOMPOSITION  

SciTech Connect

This report summarizes the results of work done during the performance period on this project, between October 1, 2002 and December 31, 2003, with a three month no-cost extension. The principal objective of this work was to develop a low-cost process for the synthesis of sinterable, fine powder of YSZ. The process is based on molecular decomposition (MD) wherein very fine particles of YSZ are formed by: (1) Mixing raw materials in a powder form, (2) Synthesizing compound containing YSZ and a fugitive constituent by a conventional process, and (3) Selectively leaching (decomposing) the fugitive constituent, thus leaving behind insoluble YSZ of a very fine particle size. While there are many possible compounds, which can be used as precursors, the one selected for the present work was Y-doped Na{sub 2}ZrO{sub 3}, where the fugitive constituent is Na{sub 2}O. It can be readily demonstrated that the potential cost of the MD process for the synthesis of very fine (or nanosize) YSZ is considerably lower than the commonly used processes, namely chemical co-precipitation and combustion synthesis. Based on the materials cost alone, for a 100 kg batch, the cost of YSZ made by chemical co-precipitation is >$50/kg, while that of the MD process should be <$10/kg. Significant progress was made during the performance period on this project. The highlights of the progress are given here in a bullet form. (1) From the two selected precursors listed in Phase I proposal, namely Y-doped BaZrO{sub 3} and Y-doped Na{sub 2}ZrO{sub 3}, selection of Y-doped Na{sub 2}ZrO{sub 3} was made for the synthesis of nanosize (or fine) YSZ. This was based on the potential cost of the precursor, the need to use only water for leaching, and the short time required for the process. (2) For the synthesis of calcia-stabilized zirconia (CSZ), which has the potential for use in place of YSZ in the anode of SOFC, Ca-doped Na{sub 2}ZrO{sub 3} was demonstrated as a suitable precursor. (3) Synthesis of Y-doped Na{sub 2}ZrO{sub 3} and Ca-doped Na{sub 2}ZrO{sub 3} was achieved using a conventional calcination process. The corresponding surface area was {approx}1 to 2 m{sup 2}/g. (4) By leaching with water, nanosize (very fine) YSZ and CSZ powders were synthesized. The corresponding surface area was {approx}65 m{sup 2}/g. This demonstrates the MD concept, namely macroscopic precursor {yields} leaching {yields} very fine (nanosize) product. (5) Crystallite size was determined by TEM ({approx}5 nm). (6) Anode-supported cells, with YSZ and CSZ made by the MD process, were successfully made by a conventional pressing and sintering process. (7) Single cells were made with as-synthesized YSZ and CSZ as a constituent in anode support. (8) A single cell (LSM + YSZ cathode) was tested at 800 C with H{sub 2}/air, with maximum power density of {approx}1.2 W/cm{sup 2}. (9) Dense samples of both YSZ and CSZ made by the MD process were fabricated. (10) Preliminary cost analysis, based on materials cost only, showed that the cost of YSZ powder made by the MD process should be considerably lower than that made by either chemical co-precipitation or combustion synthesis. For an anode-supported cell design, for an assumed power density of 0.5 W/cm{sup 2}, the cost of YSZ made by the MD process is estimated to be {approx}$5/kW. By contrast, the cost per kW for chemical co-precipitation or combustion synthesis is {approx}$70/kW and {approx}$23/kW, respectively. Efforts are currently underway to fabricate 5 cm x 5 cm active anode-supported cells with YSZ made by the MD process.

Anil V. Virkar

2004-05-06

392

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

PubMed

The objectives of this experiment were to detect the sensitivity and response of protein molecular structure of whole canola seed to different heat processing [moisture (autoclaving) vs. dry (roasting) heating] and quantify heat-induced protein molecular structure changes in relation to protein utilization and availability. In this study, whole canola seeds were autoclaved (moisture heating) and dry (roasting) heated at 120 °C for 1h, respectively. The parameters assessed included changes in (1) chemical composition profile, (2) CNCPS protein subfractions (PA, PB1, PB2, PB3, PC), (3) intestinal absorbed true protein supply, (4) energy values, and (5) protein molecular structures (amide I, amide II, ratio of amide I to II, ?-helix, ?-sheet, ratio of ?-helix to ?-sheet). The results showed that autoclave heating significantly decreased (P<0.05) but dry heating increased (P<0.05) the ratio of protein ?-helix to ?-sheet (with the ratios of 1.07, 0.95, 1.10 for the control (raw), autoclave heating and dry heating, respectively). The multivariate molecular spectral analyses (PCA, CLA) showed that there were significantly molecular structural differences in the protein amide I and II fingerprint region (ca. 1714-1480 cm(-1)) among the control, autoclave and dry heating. These differences were indicated by the form of separate class (PCA) and group of separate ellipse (CLA) between the treatments. The correlation analysis with spearman method showed that there were significantly and highly positive correlation (P<0.05) between heat-induced protein molecular structure changes in terms of ?-helix to ?-sheet ratios and in situ protein degradation and significantly negative correlation between the protein ?-helix to ?-sheet ratios and intestinal digestibility of undegraded protein. The results indicated that heat-induced changes of protein molecular structure revealed by vibration molecular spectroscopy could be used as a potential predictor to protein degradation and intestinal protein digestion of whole canola seed. Future study is needed to study response and impact of heat processing to each inherent layer of canola seed from outside to inside tissues and between yellow canola and brown canola. PMID:23318774

Samadi; Theodoridou, Katerina; Yu, Peiqiang

2013-03-15

393

Chronic alcohol consumption and intestinal thiamin absorption: effects on physiological and molecular parameters of the uptake process.  

PubMed

Thiamin is essential for normal cellular functions, and its deficiency leads to a variety of clinical abnormalities. Humans and other mammals obtain the vitamin via intestinal absorption. The intestine is exposed to two sources of thiamin, a dietary and a bacterial (i.e., normal microflora of the large intestine) source. Chronic alcohol consumption is associated with thiamin deficiency, which is caused (in part) by inhibition in intestinal thiamin absorption. However, little is known about the physiological and molecular aspects of the intestinal thiamin uptake process that are affected by chronic alcohol use. To address these issues, we used rats fed an alcohol-liquid diet and human intestinal epithelial HuTu-80 cells chronically exposed to ethanol as model systems. The results showed that chronic alcohol feeding to rats led to a significant inhibition in carrier-mediated thiamin transport across both the jejunal brush-border membrane and basolateral membrane domains. This was associated with a significant reduction in level of expression of thiamin transporter-1 (THTR-1), but not THTR-2, at the protein and mRNA levels. Level of expression of the heterogenous nuclear RNA of THTR-1 in the intestine of alcohol-fed rats was also decreased compared with their pair-fed controls. Chronic alcohol feeding also caused a significant inhibition in carrier-mediated thiamin uptake in rat colon. Studies with HuTu-80 cells chronically exposed to ethanol also showed a significant inhibition in carrier-mediated thiamin uptake. This inhibition was associated with a reduction in level of expression of human THTR-1 and THTR-2 at the protein, mRNA, and transcriptional (promoter activity) levels. These studies demonstrate that chronic alcohol feeding inhibits intestinal thiamin absorption via inhibition of the individual membrane transport event across the polarized absorptive epithelial cells. Furthermore, the inhibition is, at least in part, mediated via transcriptional mechanism(s). PMID:20448146

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

2010-07-01

394

Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease.  

PubMed

Panicum mosaic virus (PMV) and its satellite virus (SPMV) together infect several small grain crops, biofuel, and forage and turf grasses. Here, we establish the emerging monocot model Brachypodium (Brachypodium distachyon) as an alternate host to study PMV- and SPMV-host interactions and viral synergism. Infection of Brachypodium with PMV+SPMV induced chlorosis and necrosis of leaves, reduced seed set, caused stunting, and lowered biomass, more than PMV alone. Toward gaining a molecular understanding of PMV- and SPMV-affected host processes, we used a custom-designed microarray and analyzed global changes in gene expression of PMV- and PMV+SPMV-infected plants. PMV infection by itself modulated expression of putative genes functioning in carbon metabolism, photosynthesis, metabolite transport, protein modification, cell wall remodeling, and cell death. Many of these genes were additively altered in a coinfection with PMV+SPMV and correlated to the exacerbated symptoms of PMV+SPMV coinfected plants. PMV+SPMV coinfection also uniquely altered expression of certain genes, including transcription and splicing factors. Among the host defenses commonly affected in PMV and PMV+SPMV coinfections, expression of an antiviral RNA silencing component, SILENCING DEFECTIVE3, was suppressed. Several salicylic acid signaling components, such as pathogenesis-related genes and WRKY transcription factors, were up-regulated. By contrast, several genes in jasmonic acid and ethylene responses were down-regulated. Strikingly, numerous protein kinases, including several classes of receptor-like kinases, were misexpressed. Taken together, our results identified distinctly altered immune responses in monocot antiviral defenses and provide insights into monocot viral synergism. PMID:22961132

Mandadi, Kranthi K; Scholthof, Karen-Beth G

2012-11-01

395

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

396

Effect of thermal processing on estimated metabolizable protein supply to dairy cattle from camelina seeds: relationship with protein molecular structural changes.  

PubMed

This study evaluated the effect of thermal processing on the estimated metabolizable protein (MP) supply to dairy cattle from camelina seeds (Camelina sativa L. Crantz) and determined the relationship between heat-induced changes in protein molecular structural characteristics and the MP supply. Seeds from two camelina varieties were sampled in two consecutive years and were either kept raw or were heated in an autoclave (moist heating) or in an air-draft oven (dry heating) at 120 °C for 1 h. The MP supply to dairy cattle was modeled by three commonly used protein evaluation systems. The protein molecular structures were analyzed by Fourier transform/infrared-attenuated total reflectance molecular spectroscopy. The results showed that both the dry and moist heating increased the contents of truly absorbable rumen-undegraded protein (ARUP) and total MP and decreased the degraded protein balance (DPB). However, the moist-heated camelina seeds had a significantly higher (P < 0.05) content of ARUP and total MP and a significantly lower (P < 0.05) content of DPB than did the dry-heated camelina seeds. The regression equations showed that intensities of the protein molecular structural bands can be used to estimate the contents of ARUP, MP, and DPB with high accuracy (R(2) > 0.70). These results show that protein molecular structural characteristics can be used to rapidly assess the MP supply to dairy cattle from raw and heat-treated camelina seeds. PMID:25046194

Peng, Quanhui; Khan, Nazir A; Wang, Zhisheng; Zhang, Xuewei; Yu, Peiqiang

2014-08-20

397

Three-body collision contributions to recombination and collision-induced dissociation. 1: Cross sections  

SciTech Connect

Atomic and molecular recombination and collision-induced dissociation (CID) reactions comprise two of the most fundamental types of chemical reactions. They are important in all gas phase chemistry; for example, about half of the 196 reactions identified as important in combustion chemistry are recombination or CID reactions. Many of the current chemical kinetics textbooks and kinetics papers treat atomic and molecular recombination and CID as occurring only via sequences of two-body collisions. Actually, there is considerable evidence from experiment and classical trajectory calculations for contributions by true three-body collisions to the recombination of atomic and diatomic radicals, and that evidence is reviewed. Then, an approximate quantum method treating both two-body and three-body collisions simultaneously and on equal footing is used to calculate cross sections for the reaction Ne{sub 2} + H {rightleftharpoons} Ne + Ne + H. The results provide clear quantum evidence that direct three-body collisions do contribute significantly to recombination and CID.

Pack, R.T.; Walker, R.B.; Kendrick, B.K.

1998-04-10

398

H2O-H2O Collision Rate Coefficients  

NASA Astrophysics Data System (ADS)

H2O-H2O collision cross sections are calculated by adapting the method developed by Anderson and Tsao and Cornette for the calculation of collision broadening of molecular spectral lines. Cross sections are computed with a cutoff limit at 20 Å2 for the rotational levels of water with J<=10 and E<2000 cm-1 in the temperature range 100-800 K. The accuracy of the calculated values is estimated to be 10%-20%.

Buffa, Giovanni; Tarrini, Ottavio; Scappini, Flavio; Cecchi-Pestellini, Cesare

2000-06-01

399

Quantum Chaos in Ultracold Collisions of Erbium  

E-print Network

Atomic and molecular samples reduced to temperatures below 1 microkelvin, yet still in the gas phase, afford unprecedented energy resolution in probing and manipulating how their constituent particles interact with one another. For simple atoms, such as alkalis, scattering resonances are extremely well-characterized. However, ultracold physics is now poised to enter a new regime, where far more complex species can be cooled and studied, including magnetic lanthanide atoms and even molecules. For molecules, it has been speculated that a dense forest of resonances in ultracold collision cross sections will likely express essentially random fluctuations, much as the observed energy spectra of nuclear scattering do. According to the Bohigas-Giannoni-Schmit conjecture, these fluctuations would imply chaotic dynamics of the underlying classical motion driving the collision. This would provide a paradigm shift in ultracold atomic and molecular physics, necessitating new ways of looking at the fundamental interaction...

Frisch, Albert; Aikawa, Kiyotaka; Ferlaino, Francesca; Bohn, John L; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana

2013-01-01

400

Reactive collisions in confined geometries  

E-print Network

We consider low energy threshold reactive collisions of particles interacting via a van der Waals potential at long range in the presence of external confinement and give analytic formulas for the confinement modified scattering in such circumstances. The reaction process is described in terms of the short range reaction probability. Quantum defect theory is used to express elastic and inelastic or reaction collision rates analytically in terms of two dimensionless parameters representing phase and reactivity. We discuss the modifications to Wigner threshold laws for quasi-one-dimensional and quasi-two-dimensional geometries. Confinement-induced resonances are suppressed due to reactions and are completely absent in the universal limit where the short-range loss probability approaches unity.

Idziaszek, Zbigniew; Julienne, Paul S

2014-01-01

401

Reactive collisions in confined geometries  

E-print Network

We consider low energy threshold reactive collisions of particles interacting via a van der Waals potential at long range in the presence of external confinement and give analytic formulas for the confinement modified scattering in such circumstances. The reaction process is described in terms of the short range reaction probability. Quantum defect theory is used to express elastic and inelastic or reaction collision rates analytically in terms of two dimensionless parameters representing phase and reactivity. We discuss the modifications to Wigner threshold laws for quasi-one-dimensional and quasi-two-dimensional geometries. Confinement-induced resonances are suppressed due to reactions and are completely absent in the universal limit where the short-range loss probability approaches unity.

Zbigniew Idziaszek; Krzysztof Jachymski; Paul S. Julienne

2015-02-06

402

Reactive collisions in confined geometries  

E-print Network

We consider low energy threshold reactive collisions of particles interacting via a van der Waals potential at long range in the presence of external confinement and give analytic formulas for the confinement modified scattering in such circumstances. The reaction process is described in terms of the short range reaction probability. Quantum defect theory is used to express elastic and inelastic or reaction collision rates analytically in terms of two dimensionless parameters representing phase and reactivity. We discuss the modifications to Wigner threshold laws for quasi-one-dimensional and quasi-two-dimensional geometries. Confinement-induced resonances are suppressed due to reactions and are completely absent in the universal limit where the short-range loss probability approaches unity.

Zbigniew Idziaszek; Krzysztof Jachymski; Paul S. Julienne

2014-12-08

403

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