WorldWideScience

Sample records for bimolecular reaction dynamics

  1. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

    KAUST Repository

    Lipková, Jana

    2011-01-01

    A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.

  2. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  3. RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics

    KAUST Repository

    Suleimanov, Yu.V.; Allen, J.W.; Green, W.H.

    2013-01-01

    We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.

  4. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    Bradforth, S.E.

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound [yields] bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN[sup [minus

  5. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    Bradforth, Stephen Edmund [Univ. of California, Berkeley, CA (United States)

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound {yields} bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN-, NCO- and NCS-. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH30H,F + C2H5OH,F + OH and F + H2. A time dependent framework for the simulation and interpretation of the bound → free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH → O(3P, 1D) + HF and F + H2. The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H2 system, comparisons with three-dimensional quantum calculations are made.

  6. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    International Nuclear Information System (INIS)

    Bradforth, S.E.

    1992-11-01

    The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound → bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN - , NCO - and NCS - . Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH 3 0H,F + C 2 H 5 OH,F + OH and F + H 2 . A time dependent framework for the simulation and interpretation of the bound → free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH → O( 3 P, 1 D) + HF and F + H 2 . The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H 2 system, comparisons with three-dimensional quantum calculations are made

  7. Bimolecular reactions of carbenes: Proton transfer mechanism

    Science.gov (United States)

    Abu-Saleh, Abd Al-Aziz A.; Almatarneh, Mansour H.; Poirier, Raymond A.

    2018-04-01

    Here we report the bimolecular reaction of trifluoromethylhydroxycarbene conformers and the water-mediated mechanism of the 1,2-proton shift for the unimolecular trans-conformer by using quantum chemical calculations. The CCSD(T)/cc-pVTZ//MP2/cc-pVDZ potential-energy profile of the bimolecular reaction of cis- and trans-trifluoromethylhydroxycarbene, shows the lowest gas-phase barrier height of 13 kJ mol-1 compared to the recently reported value of 128 kJ mol-1 for the unimolecular reaction. We expect bimolecular reactions of carbene's stereoisomers will open a valuable field for new and useful synthetic strategies.

  8. The stereodynamics of photon-initiated bimolecular reactions

    International Nuclear Information System (INIS)

    Hughes, D.W.

    1999-01-01

    This thesis concerns the stereodynamics of the product state resolved reaction: H( 2 S) + CO 2 → (HOCO) → OH(X 2 Π Ω ; v, N, f) + CO( 1 Σ + ). Translationally excited hydrogen atoms were generated from HBr and HCl precursor molecules, via polarised laser photolysis, and the Doppler lineshapes of nascent OH products were monitored using polarised laser radiation. Four different OH product channels were investigated at a collision energy of 2.5 eV, and two OH product channels were studied at a collision energy of 1.8 eV. Three main sources of product state specific information were recovered from the Doppler profiles: Differential cross-sections (DCS); Product translational energy distributions (P(f)); Product rotational angular momentum distributions. Product state specific differential cross-sections (generated through collisions at 2.5 eV) suggest that OH( 2 Π 1/2 ) products may be produced through a more 'direct' route than OH( 2 Π 3/2 ) products. Differential cross-sections recorded for OH products generated through collisions at 1.8 eV, however, imply that neither OH spin-orbit state is populated through a 'direct' mechanism. The P(f t ) distributions for all OH product channels exhibit more product translational excitation than would be expected on the basis of phase space theory. This may imply either that the lifetimes of the collision complexes are short with respect to the timescale for intramolecular internal energy randomisation, or that there are significant exit channel interactions. The polarisation of the OH rotational angular momentum distribution is seen to be highly sensitive to the rotational and spin-orbit state of the OH products, but less sensitive to the collision energy and lambda-doublet state of the OH product. This thesis outlines the scope of present day experimental stereodynamical studies of gas-phase reactions (chapter 1), the theory of vector correlations in photoninitiated bimolecular reactions (chapter 2) and the

  9. Photochemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Moore, B.C. [Lawrence Berkeley Laboratory, Livermore, CA (United States)

    1993-12-01

    The purpose of the program is to develop a fundamental understanding of unimolecular and bimolecular reaction dynamics with application in combustion and energy systems. The energy dependence in ketene isomerization, ketene dissociation dynamics, and carbonyl substitution on organometallic rhodium complexes in liquid xenon have been studied. Future studies concerning unimolecular processes in ketene as well as energy transfer and kinetic studies of methylene radicals are discussed.

  10. Single-molecule stochastic times in a reversible bimolecular reaction

    Science.gov (United States)

    Keller, Peter; Valleriani, Angelo

    2012-08-01

    In this work, we consider the reversible reaction between reactants of species A and B to form the product C. We consider this reaction as a prototype of many pseudobiomolecular reactions in biology, such as for instance molecular motors. We derive the exact probability density for the stochastic waiting time that a molecule of species A needs until the reaction with a molecule of species B takes place. We perform this computation taking fully into account the stochastic fluctuations in the number of molecules of species B. We show that at low numbers of participating molecules, the exact probability density differs from the exponential density derived by assuming the law of mass action. Finally, we discuss the condition of detailed balance in the exact stochastic and in the approximate treatment.

  11. Infrared laser induced organic reactions. 2. Laser vs. thermal inducment of unimolecular and hydrogen bromide catalyzed bimolecular dehydration of alcohols

    International Nuclear Information System (INIS)

    Danen, W.C.

    1979-01-01

    It has been demonstrated that a mixture of reactant molecules can be induced by pulsed infrared laser radiation to react via a route which is totally different from the pathway resulting from heating the mixture at 300 0 C. The high-energy unimolecular elimination of H 2 O from ethanol in the presence of 2-propanol and HBr can be selectively induced with a pulsed CO 2 laser in preference to either a lower energy bimolecular HBr-catalyzed dehydration or the more facile dehydration of 2-propanol. Heating the mixture resulted in the almost exclusive reaction of 2-propanol to produce propylene. It was demonstrated that the bimolecular ethanol + HBr reaction cannot be effectively induced by the infrared laser radiation as evidenced by the detrimental effect on the yield of ethylene as the HBr pressure was increased. The selective, nonthermal inducement of H 2 O elimination from vibrationally excited ethanol in the presence of 2-propanol required relatively low reactant pressures. At higher pressures intermolecular V--V energy transfer allowed the thermally more facile dehydration from 2-propanol to become the predominant reaction channel

  12. Efficient Homodifunctional Bimolecular Ring-Closure Method for Cyclic Polymers by Combining RAFT and Self-Accelerating Click Reaction.

    Science.gov (United States)

    Qu, Lin; Sun, Peng; Wu, Ying; Zhang, Ke; Liu, Zhengping

    2017-08-01

    An efficient metal-free homodifunctional bimolecular ring-closure method is developed for the formation of cyclic polymers by combining reversible addition-fragmentation chain transfer (RAFT) polymerization and self-accelerating click reaction. In this approach, α,ω-homodifunctional linear polymers with azide terminals are prepared by RAFT polymerization and postmodification of polymer chain end groups. By virtue of sym-dibenzo-1,5-cyclooctadiene-3,7-diyne (DBA) as small linkers, well-defined cyclic polymers are then prepared using the self-accelerating double strain-promoted azide-alkyne click (DSPAAC) reaction to ring-close the azide end-functionalized homodifunctional linear polymer precursors. Due to the self-accelerating property of DSPAAC ring-closing reaction, this novel method eliminates the requirement of equimolar amounts of telechelic polymers and small linkers in traditional bimolecular ring-closure methods. It facilitates this method to efficiently and conveniently produce varied pure cyclic polymers by employing an excess molar amount of DBA small linkers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. The influence of the “cage effect” on the mechanism of reversible bimolecular multistage chemical reactions in solutions

    International Nuclear Information System (INIS)

    Doktorov, Alexander B.

    2015-01-01

    Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants

  14. The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions.

    Science.gov (United States)

    Doktorov, Alexander B

    2015-08-21

    Manifestations of the "cage effect" at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a "cage complex." Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the "cage effect" leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

  15. The influence of the “cage effect” on the mechanism of reversible bimolecular multistage chemical reactions in solutions

    Energy Technology Data Exchange (ETDEWEB)

    Doktorov, Alexander B., E-mail: doktorov@kinetics.nsc.ru [Voevodsky Institute of Chemical Kinetics & Combustion, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia and Novosibirsk State University, Novosibirsk 630090 (Russian Federation)

    2015-08-21

    Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

  16. Theoretical study on the mechanism of the reaction of FOX-7 with OH and NO2 radicals: bimolecular reactions with low barrier during the decomposition of FOX-7

    Science.gov (United States)

    Zhang, Ji-Dong; Zhang, Li-Li

    2017-12-01

    The decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7) attracts great interests, while the studies on bimolecular reactions during the decomposition of FOX-7 are scarce. This study for the first time investigated the bimolecular reactions of OH and NO2 radicals, which are pyrolysis products of ammonium perchlorate (an efficient oxidant usually used in solid propellant), with FOX-7 by computational chemistry methods. The molecular geometries and energies were calculated using the (U)B3LYP/6-31++G(d,p) method. The rate constants of the reactions were calculated by canonical variational transition state theory. We found three mechanisms (H-abstraction, OH addition to C and N atom) for the reaction of OH + FOX-7 and two mechanisms (O abstraction and H abstraction) for the reaction of NO2 + FOX-7. OH radical can abstract H atom or add to C atom of FOX-7 with barriers near to zero, which means OH radical can effectively degrade FOX-7. The O abstraction channel of the reaction of NO2 + FOX-7 results in the formation of NO3 radical, which has never been detected experimentally during the decomposition of FOX-7.

  17. Real-time observation of intersystem crossing induced by charge recombination during bimolecular electron transfer reactions

    KAUST Repository

    Alsam, Amani Abdu

    2016-09-21

    Real-time probing of intersystem crossing (ISC) and triplet-state formation after photoinduced electron transfer (ET) is a particularly challenging task that can be achieved by time-resolved spectroscopy with broadband capability. Here, we examine the mechanism of charge separation (CS), charge recombination (CR) and ISC of bimolecular photoinduced electron transfer (PET) between poly[(9,9-di(3,3′-N,N’-trimethyl-ammonium) propyl fluorenyl-2,7-diyl)-alt-co-(9,9-dioctyl-fluorenyl-2,7-diyl)] diiodide salt (PFN) and dicyanobenzene (DCB) using time-resolved spectroscopy. PET from PFN to DCB is confirmed by monitoring the transient absorption (TA) and infrared spectroscopic signatures for the radical ion pair (DCB─•-PFN+•). In addition, our time-resolved results clearly demonstrate that CS takes place within picoseconds followed by CR within nanoseconds. The ns-TA data exhibit the clear spectroscopic signature of PFN triplet-triplet absorption, induced by the CR of the radical ion pairs (DCB─•-PFN+•). As a result, the triplet state of PFN (3PFN*) forms and subsequently, the ground singlet state is replenished within microseconds. © 2016

  18. Does increasing pressure always accelerate the condensed material decay initiated through bimolecular reactions? A case of the thermal decomposition of TKX-50 at high pressures.

    Science.gov (United States)

    Lu, Zhipeng; Zeng, Qun; Xue, Xianggui; Zhang, Zengming; Nie, Fude; Zhang, Chaoyang

    2017-08-30

    Performances and behaviors under high temperature-high pressure conditions are fundamentals for many materials. We study in the present work the pressure effect on the thermal decomposition of a new energetic ionic salt (EIS), TKX-50, by confining samples in a diamond anvil cell, using Raman spectroscopy measurements and ab initio simulations. As a result, we find a quadratic increase in decomposition temperature (T d ) of TKX-50 with increasing pressure (P) (T d = 6.28P 2 + 12.94P + 493.33, T d and P in K and GPa, respectively, and R 2 = 0.995) and the decomposition under various pressures initiated by an intermolecular H-transfer reaction (a bimolecular reaction). Surprisingly, this finding is contrary to a general observation about the pressure effect on the decomposition of common energetic materials (EMs) composed of neutral molecules: increasing pressure will impede the decomposition if it starts from a bimolecular reaction. Our results also demonstrate that increasing pressure impedes the H-transfer via the enhanced long-range electrostatic repulsion of H +δ H +δ of neighboring NH 3 OH + , with blue shifts of the intermolecular H-bonds. And the subsequent decomposition of the H-transferred intermediates is also suppressed, because the decomposition proceeds from a bimolecular reaction to a unimolecular one, which is generally prevented by compression. These two factors are the basic root for which the decomposition retarded with increasing pressure of TKX-50. Therefore, our finding breaks through the previously proposed concept that, for the condensed materials, increasing pressure will accelerate the thermal decomposition initiated by bimolecular reactions, and reveals a distinct mechanism of the pressure effect on thermal decomposition. That is to say, increasing pressure does not always promote the condensed material decay initiated through bimolecular reactions. Moreover, such a mechanism may be feasible to other EISs due to the similar intermolecular

  19. Effect of micellar environment on Marcus correlation curves for photoinduced bimolecular electron transfer reactions

    Science.gov (United States)

    Kumbhakar, Manoj; Nath, Sukhendu; Mukherjee, Tulsi; Pal, Haridas

    2005-07-01

    Photoinduced electron transfer (ET) between coumarin dyes and aromatic amine has been investigated in two cationic micelles, namely, cetyltrimethyl ammonium bromide (CTAB) and dodecyltrimethyl ammonium bromide (DTAB), and the results have been compared with those observed earlier in sodium dodecyl sulphate (SDS) and triton-X-100 (TX-100) micelles for similar donor-acceptor pairs. Due to a reasonably high effective concentration of the amines in the micellar Stern layer, the steady-state fluorescence results show significant static quenching. In the time-resolved (TR) measurements with subnanosecond time resolution, contribution from static quenching is avoided. Correlations of the dynamic quenching constants (kqTR), as estimated from the TR measurements, show the typical bell-shaped curves with the free-energy changes (ΔG0) of the ET reactions, as predicted by the Marcus outersphere ET theory. Comparing present results with those obtained earlier for similar coumarin-amine systems in SDS and TX-100 micelles, it is seen that the inversion in the present micelles occurs at an exergonicity (-ΔG0>˜1.2-1.3eV) much higher than that observed in SDS and TX-100 micelles (-ΔG0>˜0.7eV), which has been rationalized based on the relative propensities of the ET and solvation rates in different micelles. In CTAB and DTAB micelles, the kqTR values are lower than the solvation rates, which result in the full contribution of the solvent reorganization energy (λs) towards the activation barrier for the ET reaction. Contrary to this, in SDS and TX-100 micelles, kqTR values are either higher or comparable with the solvation rates, causing only a partial contribution of λs in these cases. Thus, Marcus inversion in present cationic micelles is inferred to be the true inversion, whereas that in the anionic SDS and neutral TX-100 micelles are understood to be the apparent inversion, as envisaged from two-dimensional ET theory.

  20. The bimolecular reaction of radiolysis product of hydrated electron at temperature up to 473K; Reaksi bimolekular antar produk radiolisis elektron terhidrasi pada temperatur hingga 473K

    Energy Technology Data Exchange (ETDEWEB)

    Sunaryo, G R [Reactor Safety Technology Research Centre, National Atomic Energy Agency, Serpong (Indonesia)

    1996-06-01

    Rate constant from the bimolecular reaction of hydrated electron was determined by using radiolysis method. The methanol solution with concentration of 5 x 10{sup -2} dm{sup 3} mol{sup -1} was used as a scavenger of H and OH radicals. The pH was kept by adding the buffer solution of 1.0 x 10{sup -3} dm{sup 3} mol{sup -1} Na{sub 2}HPO{sub 4} + 1.0 x 10{sup 4} dm{sup 3} mol{sup -1} NaH{sub 2}PO{sub 4}. The irradiation was done by using the electron beam which come from linear accelerator 28 MeV with pulse width 10ns and dose of 80 Gy per pulse. The absorbance of hydrated electron was observed at wavelength of 824 nm. By using the kinetic equation the rate reaction constants were obtained. The bimolecular reaction of hydrated electron increase with temperature up to 423K. The activation energy was 19.3 kJ mol{sup -1} and the 2 k (298K) was 1.1 x 10{sup 10} dm{sup 3} mol{sup -1}. Then this bimolecular reaction decrease at temperature higher than 423K and the rate reaction constant at 473K almost similar with that at 298K. (author)

  1. Switching and sensing spin states of co-porphyrin in bimolecular reactions on Au111 using scanning tunneling microscopy.

    Science.gov (United States)

    Kim, Howon; Chang, Yun Hee; Lee, Soon-Hyeong; Kim, Yong-Hyun; Kahng, Se-Jong

    2013-10-22

    Controlling and sensing spin states of magnetic molecules at the single-molecule level is essential for spintronic molecular device applications. Here, we demonstrate that spin states of Co-porphyrin on Au(111) can be reversibly switched over by binding and unbinding of the NO molecule and can be sensed using scanning tunneling microscopy and spectroscopy (STM and STS). Before NO exposure, Co-porphryin showed a clear zero-bias peak, a signature of Kondo effect in STS, whereas after NO exposures, it formed a molecular complex, NO-Co-porphyrin, that did not show any zero-bias feature, implying that the Kondo effect was switched off by binding of NO. The Kondo effect could be switched back on by unbinding of NO through single-molecule manipulation or thermal desorption. Our density functional theory calculation results explain the observations with pairing of unpaired spins in dz(2) and ppπ* orbitals of Co-porphyrin and NO, respectively. Our study opens up ways to control molecular spin state and Kondo effect by means of enormous variety of bimolecular binding and unbinding reactions on metallic surfaces.

  2. Mass spectrometric studies of bimolecular reactions in a selected ion flow tube (SIFT)

    International Nuclear Information System (INIS)

    Shul, R.J.; Upschulte, B.L.; Passarella, R.; Keesee, R.G.; Castleman, A.W.

    1985-01-01

    The rate coefficients for a number of thermal energy charge transfer reactions have been obtained with a selected ion flow tube (SIFT). The reactions studied involve Ar + and Ar 2 + with a variety of neutral molecules including: O 2 , CS 2 , CO 2 , SO 2 , H 2 S, NH 3 , and SF 6 . Such reactions have been of long-standing interest in the field of gas-phase ion-molecule chemistry from both a practical and fundamental point of view. Consideration of charge transfer reactions as possible sources of chemical lasers and their role in ionospheric and interstellar chemistry account for much of the interest. Fundamentally, the mechanism involved in these reactions has yet to be definitively established. The consumption deposition of energy into internal modes and translational degrees of freedom in such reactions has also been a topic of considerable debate. The apparatus consists of five main components: an ion source, SIFT quadrupole, ion injector, flow tube, and a mass spectrometer detection system. Ions formed in a high pressure source leak into a SIFT quadrupole where they are mass selected. The primary ion of interest is then injected into the flow tube where reactions are studied. Once in the flow tube the ions are carried downstream by an inert buffer gas, either argon, nitrogen, or helium in the present study. Neutral reactant gas is added through a reactant gas inlet (RGI) at an appropriate location downstream in the flow tube, and allowed to react with the injected ions. Ions on the flow tube axis are sampled through a 1 mm orifice where they are mass analyzed by a second quadrupole mass spectrometer and detected with a channeltron electron multiplier

  3. Enhanced bimolecular exchange reaction through programmed coordination of a five-coordinate oxovanadium complex for efficient redox mediation in dye-sensitized solar cells.

    Science.gov (United States)

    Oyaizu, Kenichi; Hayo, Noriko; Sasada, Yoshito; Kato, Fumiaki; Nishide, Hiroyuki

    2013-12-07

    Electrochemical reversibility and fast bimolecular exchange reaction found for VO(salen) gave rise to a highly efficient redox mediation to enhance the photocurrent of a dye-sensitized solar cell, leading to an excellent photovoltaic performance with a conversion efficiency of 5.4%. A heterogeneous electron-transfer rate constant at an electrode (k0) and a second-order rate constant for an electron self-exchange reaction (k(ex)) were proposed as key parameters that dominate the charge transport property, which afforded a novel design concept for the mediators based on their kinetic aspects.

  4. The influence of the "cage" effect on the mechanism of reversible bimolecular multistage chemical reactions proceeding from different sites in solutions.

    Science.gov (United States)

    Doktorov, Alexander B

    2016-08-28

    Manifestations of the "cage" effect at the encounters of reactants have been theoretically treated on the example of multistage reactions (including bimolecular exchange reactions as elementary stages) proceeding from different active sites in liquid solutions. It is shown that for reactions occurring near the contact of reactants, consistent consideration of quasi-stationary kinetics of such multistage reactions (possible in the framework of the encounter theory only) can be made on the basis of chemical concepts of the "cage complex," just as in the case of one-site model described in the literature. Exactly as in the one-site model, the presence of the "cage" effect gives rise to new channels of reactant transformation that cannot result from elementary event of chemical conversion for the given reaction mechanism. Besides, the multisite model demonstrates new (as compared to one-site model) features of multistage reaction course.

  5. A mathematical analysis of Prx2-STAT3 disulfide exchange rate constants for a bimolecular reaction mechanism.

    Science.gov (United States)

    Langford, Troy F; Deen, William M; Sikes, Hadley D

    2018-03-22

    Appreciation of peroxiredoxins as the major regulators of H 2 O 2 concentrations in human cells has led to a new understanding of redox signaling. In addition to their status as the primary reducers of H 2 O 2 to water, the oxidized peroxiredoxin byproduct of this reaction has recently been shown capable of participation in H 2 O 2 -mediated signaling pathways through disulfide exchange reactions with the transcription factor STAT3. The dynamics of peroxidase-transcription factor disulfide exchange reactions have not yet been considered in detail with respect to how these reactions fit into the larger network of competing reactions in human cells. In this study, we used a kinetic model of oxidation and reduction reactions related to H 2 O 2 metabolism in the cytosol of human cells to study the dynamics of peroxiredoxin-2 mediated oxidation of the redox-regulated transcription factor STAT3. In combination with previously reported experimental data, the model was used to estimate the rate coefficient of a biomolecular reaction between Prx2 and STAT3 for two sets of assumptions that constitute lower and upper bound cases. Using these estimates, we calculated the relative rates of the reaction of oxidized peroxiredoxin-2 and STAT3 and other competing reactions in the cytosol. These calculations revealed that peroxiredoxin-2-mediated oxidation of STAT3 likely occurs at a much slower rate than competing reactions in the cytosol. This analysis suggests the existence of more complex mechanisms, potentially involving currently unknown protein-protein recognition partners, which facilitate disulfide exchange reactions between peroxiredoxin-2 and STAT3. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Unraveling the role of entropy in tuning unimolecular vs . bimolecular reaction rates: The case of olefin polymerization catalyzed by transition metals

    KAUST Repository

    Falivene, Laura

    2018-04-24

    Olefin polymerization catalyzed by Group 4 transition metals is studied here as test case to reveal the entropy effects when bimolecular and unimolecular reactions are computed for processes occurring in solution. Catalytic systems characterized by different ligand frameworks, metal, and growing polymeric chain for which experimental data are available have been selected in order to validate the main approaches to entropy calculation. Applying the “standard” protocol results in a strong disagreement with the experimental results and the methods introducing a direct correction of the translational entropy term based on a single experimental parameter emerge as the most reliable. The general and powerful computational tool achieved in this study can represent a further step towards the “catalyst design” to control and predict the molecular mass of the resulting polymers.

  7. Bimolecular interaction of argpyrimidine (a Maillard reaction product) in in vitro non-enzymatic protein glycation model and its potential role as an antiglycating agent.

    Science.gov (United States)

    Bhattacherjee, Abhishek; Dhara, Kaliprasanna; Chakraborti, Abhay Sankar

    2017-09-01

    Non- enzymatic glycation, also known as Maillard reaction, is one of the most important and investigated reactions in biochemistry. Maillard reaction products (MRPs) like protein-derived advanced glycation end products (AGEs) are often referred to cause pathophysiological complications in human systems. On contrary, several MRPs are exogenously used as antioxidant, antimicrobial and flavouring agents. In the preset study, we have shown that argpyrimidine, a well-established AGE, interacts with bovine serum albumin (BSA) and glucose individually in standard BSA-glucose model system and successfully inhibits glycation of the protein. Bimolecular interaction of argpyrimidine with glucose or BSA has been studied independently. Chromatographic purification, different spectroscopic studies and molecular modeling have been used to evaluate the nature and pattern of interactions. Binding of argpyrimidine with BSA prevents incorporation of glucose inside the native protein. Argpyrimidine can also directly entrap glucose. Both these interactions may be associated with the antiglycation potential of argpyrimidine, indicating a beneficial function of an AGE. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Picosecond real time study of the bimolecular reaction O(3P)+C2H4 and the unimolecular photodissociation of CH3CHO and H2CO

    Science.gov (United States)

    Abou-Zied, Osama K.; McDonald, J. Douglas

    1998-07-01

    The bimolecular reaction of O(3P) with ethylene and the unimolecular photodissociation of acetaldehyde and formaldehyde have been studied using a picosecond pump/probe technique. The bimolecular reaction was initiated in a van der Waals dimer precursor, C2H4ṡNO2, and the evolution of the vinoxy radical product monitored by laser-induced fluorescence. The NO2 constituent of the complex was photodissociated at 266 nm. The triplet oxygen atom then attacks a carbon atom of C2H4 to form a triplet diradical (CH2CH2O) which subsequently dissociates to vinoxy (CH2CHO) and H. The rise time of vinoxy radical production was measured to be 217 (+75-25) ps. RRKM theory was applied and a late high exit barrier was invoked in order to fit the measured rise time. The structure and binding energy of the van der Waals complex have been modeled using Lennard-Jones type potentials and the results were compared with other systems. The unimolecular side of the potential energy surfaces of this reaction has been investigated by photodissociating acetaldehyde at the same pump energy of 266 nm. The resulting photoproducts, acetyl radical (CH3CO) and formyl radical (HCO), have been monitored by resonance enhanced multiphoton ionization (REMPI) combined with a time-of-flight mass spectrometer. The similarity in the measured evolution times of both radicals indicates the same photodissociation pathway of the parent molecule. The photodissociation rate of acetaldehyde is estimated from RRKM theory to be very fast (3×1012s-1). The T1←S1 intersystem crossing (ISC) rate is found to be the rate determining step to photodissociation and increases with energy. The REMPI mechanism for the production of CH3CO+ is proposed to be the same as that of HCO+(2+1). The HCO product from the photodissociation of formaldehyde at 266 nm reveals a faster T1←S1 ISC rate than in acetaldehyde.

  9. Bimolecular reaction of CH3 + CO in solid p-H2: Infrared absorption of acetyl radical (CH3CO) and CH3-CO complex

    Science.gov (United States)

    Das, Prasanta; Lee, Yuan-Pern

    2014-06-01

    We have recorded infrared spectra of acetyl radical (CH3CO) and CH3-CO complex in solid para-hydrogen (p-H2). Upon irradiation at 248 nm of CH3C(O)Cl/p-H2 matrices, CH3CO was identified as the major product; characteristic intense IR absorption features at 2990.3 (ν9), 2989.1 (ν1), 2915.6 (ν2), 1880.5 (ν3), 1419.9 (ν10), 1323.2 (ν5), 836.6 (ν7), and 468.1 (ν8) cm-1 were observed. When CD3C(O)Cl was used, lines of CD3CO at 2246.2 (ν9), 2244.0 (ν1), 1866.1 (ν3), 1046.7 (ν5), 1029.7 (ν4), 1027.5 (ν10), 889.1 (ν6), and 723.8 (ν7) cm-1 appeared. Previous studies characterized only three vibrational modes of CH3CO and one mode of CD3CO in solid Ar. In contrast, upon photolysis of a CH3I/CO/p-H2 matrix with light at 248 nm and subsequent annealing at 5.1 K before re-cooling to 3.2 K, the CH3-CO complex was observed with characteristic IR features at 3165.7, 3164.5, 2150.1, 1397.6, 1396.4, and 613.0 cm-1. The assignments are based on photolytic behavior, observed deuterium isotopic shifts, and a comparison of observed vibrational wavenumbers and relative IR intensities with those predicted with quantum-chemical calculations. This work clearly indicates that CH3CO can be readily produced from photolysis of CH3C(O)Cl because of the diminished cage effect in solid p-H2 but not from the reaction of CH3 + CO because of the reaction barrier. Even though CH3 has nascent kinetic energy greater than 87 kJ mol-1 and internal energy ˜42 kJ mol-1 upon photodissociation of CH3I at 248 nm, its energy was rapidly quenched so that it was unable to overcome the barrier height of ˜27 kJ mol-1 for the formation of CH3CO from the CH3 + CO reaction; a barrierless channel for formation of a CH3-CO complex was observed instead. This rapid quenching poses a limitation in production of free radicals via bimolecular reactions in p-H2.

  10. Chemical reaction dynamics using the Advanced Light Source

    International Nuclear Information System (INIS)

    Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.

    1995-01-01

    The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10(sup 16) photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source

  11. Chemical reaction dynamics using the Advanced Light Source

    International Nuclear Information System (INIS)

    Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.

    1995-09-01

    The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10 16 photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source

  12. Reformulation and solution of the master equation for multiple-well chemical reactions.

    Science.gov (United States)

    Georgievskii, Yuri; Miller, James A; Burke, Michael P; Klippenstein, Stephen J

    2013-11-21

    We consider an alternative formulation of the master equation for complex-forming chemical reactions with multiple wells and bimolecular products. Within this formulation the dynamical phase space consists of only the microscopic populations of the various isomers making up the reactive complex, while the bimolecular reactants and products are treated equally as sources and sinks. This reformulation yields compact expressions for the phenomenological rate coefficients describing all chemical processes, i.e., internal isomerization reactions, bimolecular-to-bimolecular reactions, isomer-to-bimolecular reactions, and bimolecular-to-isomer reactions. The applicability of the detailed balance condition is discussed and confirmed. We also consider the situation where some of the chemical eigenvalues approach the energy relaxation time scale and show how to modify the phenomenological rate coefficients so that they retain their validity.

  13. Title: Elucidation of Environmental Fate of Artificial Sweeteners (Aspartame, Acesulfame K and Saccharin) by Determining Bimolecular Rate Constants with Hydroxyl Radical at Various pH and Temperature Conditions and Possible Reaction By-Products

    Science.gov (United States)

    Teraji, T.; Arakaki, T.; Suzuka, T.

    2012-12-01

    Use of artificial sweeteners in beverages and food has been rapidly increasing because of their non-calorie nature. In Japan, aspartame, acesulfame K and sucralose are among the most widely used artificial sweeteners. Because the artificial sweeteners are not metabolized in human bodies, they are directly excreted into the environment without chemical transformations. We initiated a study to better understand the fate of artificial sweeteners in the marine environment. The hydroxyl radical (OH), the most potent reactive oxygen species, reacts with various compounds and determines the environmental oxidation capacity and the life-time of many compounds. The steady-state OH concentration and the reaction rate constants between the compound and OH are used to estimate the life-time of the compound. In this study, we determine the bimolecular rate constants between aspartame, acefulfame K and saccharin and OH at various pH and temperature conditions using a competition kinetics technique. We use hydrogen peroxide as a photochemical source of OH. Bimolecular rate constant we obtained so far for aspartame was (2.6±1.2)×109 M-1 s-1 at pH = 3.0 and (4.9±2.3)×109 M-1 s-1 at pH = 5.5. Little effect was seen by changing the temperatures between 15 and 40 oC. Activation energy (Ea) was calculated to be -1.0 kJ mol-1 at pH = 3.0, +8.5 kJ mol-1 at pH = 5.5, which could be regarded as zero. We will report bimolecular rate constants at different pHs and temperatures for acesulfame K and saccharin, as well. Possible reaction by-products for aspartame will be also reported. We will further discuss the fate of aspartame in the coastal environment.

  14. Stochastic modeling and simulation of reaction-diffusion system with Hill function dynamics.

    Science.gov (United States)

    Chen, Minghan; Li, Fei; Wang, Shuo; Cao, Young

    2017-03-14

    Stochastic simulation of reaction-diffusion systems presents great challenges for spatiotemporal biological modeling and simulation. One widely used framework for stochastic simulation of reaction-diffusion systems is reaction diffusion master equation (RDME). Previous studies have discovered that for the RDME, when discretization size approaches zero, reaction time for bimolecular reactions in high dimensional domains tends to infinity. In this paper, we demonstrate that in the 1D domain, highly nonlinear reaction dynamics given by Hill function may also have dramatic change when discretization size is smaller than a critical value. Moreover, we discuss methods to avoid this problem: smoothing over space, fixed length smoothing over space and a hybrid method. Our analysis reveals that the switch-like Hill dynamics reduces to a linear function of discretization size when the discretization size is small enough. The three proposed methods could correctly (under certain precision) simulate Hill function dynamics in the microscopic RDME system.

  15. Dynamics of anion-molecule reactions at low energy

    International Nuclear Information System (INIS)

    Mikosch, J.

    2007-11-01

    Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S N 2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S N 2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S N 2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S N 2 mechanism involving CH 3 -rotation. (orig.)

  16. Dynamics of anion-molecule reactions at low energy

    Energy Technology Data Exchange (ETDEWEB)

    Mikosch, J.

    2007-11-15

    Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S{sub N}2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S{sub N}2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S{sub N}2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S{sub N}2 mechanism involving CH{sub 3}-rotation. (orig.)

  17. Ion-Molecule Reaction Dynamics.

    Science.gov (United States)

    Meyer, Jennifer; Wester, Roland

    2017-05-05

    We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

  18. Semiclassical methods in chemical reaction dynamics

    International Nuclear Information System (INIS)

    Keshavamurthy, S.

    1994-12-01

    Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems

  19. Semiclassical methods in chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Keshavamurthy, Srihari [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems.

  20. Dynamic effects in fragmentation reactions

    International Nuclear Information System (INIS)

    Bertsch, G. F.; Esbensen, H.

    2002-01-01

    Fragmentation reactions offer a useful tool to study the spectroscopy of halo nuclei, but the large extent of the halo wave function makes the reaction theory more difficult. The simple reaction models based on the eikonal approximation for the nuclear interaction or first-order perturbation theory for the Coulomb interaction have systematic errors that they investigate here, comparing to the predictions of complete dynamical calculations. They find that stripping probabilities are underpredicted by the eikonal model, leading to extracted spectroscopy strengths that are two large. In contrast, the Coulomb excitation is overpredicted by the simple theory. They attribute this to a screening effect, as is well known in the Barkas effect on stopping powers. The errors decrease with beam energy as E(sub beam)(sup -1), and are not significant at beam energies above 50 MeV/u. At lower beam energies, the effects should be taken into account when extracting quantitative spectroscopic strengths

  1. A numerical study of air pollutant dispersion with bimolecular chemical reactions in an urban street canyon using large-eddy simulation

    Science.gov (United States)

    Kikumoto, Hideki; Ooka, Ryozo

    2012-07-01

    A large-eddy simulation is performed on a turbulent dispersion of chemically reactive air pollutants in a two-dimensional urban street canyon with an aspect ratio of 1.0. Nitrogen monoxide emitted from a line-source set on the bottom of the street canyon disperses and reacts with Ozone included in a free stream. The reactions have significant influences on the concentrations of pollutants in the canyon space, and they increase the concentrations of the reaction products relative to of the concentrations of the reactants. The transport of air pollutants through a free shear layer above the canyon is closely related to the structure of the turbulence. Gases in the canyon are mainly exhausted when low-speed regions appear above the canyon. In contrast, pollutants in the free stream flow into the canyon with high-speed fluid bodies. Consequently, the correlation between the time fluctuations of the reactants' concentrations strongly affects the reaction rates in the region near the free shear layer. In this calculation, the correlation term reaches to a value of 20% of the mean reaction rate at a maximum there.

  2. Effective dynamics along given reaction coordinates, and reaction rate theory.

    Science.gov (United States)

    Zhang, Wei; Hartmann, Carsten; Schütte, Christof

    2016-12-22

    In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: we first show that if we start with an ergodic diffusion process whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Mori-Zwanzig, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.

  3. Dynamics of traveling reaction pulses

    International Nuclear Information System (INIS)

    Dovzhenko, A. Yu.; Rumanov, E. N.

    2007-01-01

    The growth of activator losses is accompanied by the decay of a traveling reaction pulse. In a ring reactor, this propagation threshold is present simultaneously with a threshold related to the ring diameter. The results of numerical experiments with pulses of an exothermal reaction reveal the transition from pulse propagation to a homogeneous hot regime, established regimes with periodic variations of the pulse velocity, and oscillatory decay of the pulse. When the medium becomes 'bistable' as a result of the variation in parameters, this factor does not prevent the propagation of pulses, but leads to changes in the pulse structure

  4. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  5. A ring polymer molecular dynamics study of the isotopologues of the H + H2 reaction.

    Science.gov (United States)

    Suleimanov, Yury V; de Tudela, Ricardo Pérez; Jambrina, Pablo G; Castillo, Jesús F; Sáez-Rábanos, Vicente; Manolopoulos, David E; Aoiz, F Javier

    2013-03-14

    The inclusion of Quantum Mechanical (QM) effects such as zero point energy (ZPE) and tunneling in simulations of chemical reactions, especially in the case of light atom transfer, is an important problem in computational chemistry. In this respect, the hydrogen exchange reaction and its isotopic variants constitute an excellent benchmark for the assessment of approximate QM methods. In particular, the recently developed ring polymer molecular dynamics (RPMD) technique has been demonstrated to give very good results for bimolecular chemical reactions in the gas phase. In this work, we have performed a detailed RPMD study of the H + H(2) reaction and its isotopologues Mu + H(2), D + H(2) and Heμ + H(2), at temperatures ranging from 200 to 1000 K. Thermal rate coefficients and kinetic isotope effects have been computed and compared with exact QM calculations as well as with quasiclassical trajectories and experiment. The agreement with the QM results is good for the heaviest isotopologues, with errors ranging from 15% to 45%, and excellent for Mu + H(2), with errors below 15%. We have seen that RPMD is able to capture the ZPE effect very accurately, a desirable feature of any method based on molecular dynamics. We have also verified Richardson and Althorpe's prediction [J. O. Richardson and S. C. Althorpe, J. Chem. Phys., 2009, 131, 214106] that RPMD will overestimate thermal rates for asymmetric reactions and underestimate them for symmetric reactions in the deep tunneling regime. The ZPE effect along the reaction coordinate must be taken into account when assigning the reaction symmetry in the multidimensional case.

  6. Probing reaction dynamics with GDR decay

    International Nuclear Information System (INIS)

    Beene, J.R.

    1994-01-01

    The giant dipole resonance (GDR) has been a prolific source of information on the physics of the nucleus. Mostly it has taught us about nuclear structure, but recently experiments have utilized the GDR as a probe of nuclear reaction dynamics. In this report two examples of such investigations are discussed involving very different reactions and probing time scales that differ by a factor of ∼10 3

  7. Raman spectroscopic study of reaction dynamics

    Science.gov (United States)

    MacPhail, R. A.

    1990-12-01

    The Raman spectra of reacting molecules in liquids can yield information about various aspects of the reaction dynamics. The author discusses the analysis of Raman spectra for three prototypical unimolecular reactions, the rotational isomerization of n-butane and 1,2-difluoroethane, and the barrierless exchange of axial and equatorial hydrogens in cyclopentane via pseudorotation. In the first two cases the spectra are sensitive to torsional oscillations of the gauche conformer, and yield estimates of the torsional solvent friction. In the case of cyclopentane, the spectra can be used to discriminate between different stochastic models of the pseudorotation dynamics, and to determine the relevant friction coefficients.

  8. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu

    2013-08-10

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.

  9. Markovian dynamics on complex reaction networks

    International Nuclear Information System (INIS)

    Goutsias, J.; Jenkinson, G.

    2013-01-01

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples

  10. Reaction dynamics in polyatomic molecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

  11. Observation of correlated excitations in bimolecular collisions

    Science.gov (United States)

    Gao, Zhi; Karman, Tijs; Vogels, Sjoerd N.; Besemer, Matthieu; van der Avoird, Ad; Groenenboom, Gerrit C.; van de Meerakker, Sebastiaan Y. T.

    2018-02-01

    Although collisions between atoms and molecules are largely understood, collisions between two molecules have proven much harder to study. In both experiment and theory, our ability to determine quantum-state-resolved bimolecular cross-sections lags behind their atom-molecule counterparts by decades. For many bimolecular systems, even rules of thumb—much less intuitive understanding—of scattering cross sections are lacking. Here, we report the measurement of state-to-state differential cross sections on the collision of state-selected and velocity-controlled nitric oxide (NO) radicals and oxygen (O2) molecules. Using velocity map imaging of the scattered NO radicals, the full product-pair correlations of rotational excitation that occurs in both collision partners from individual encounters are revealed. The correlated cross sections show surprisingly good agreement with quantum scattering calculations using ab initio NO-O2 potential energy surfaces. The observations show that the well-known energy-gap law that governs atom-molecule collisions does not generally apply to bimolecular excitation processes, and reveal a propensity rule for the vector correlation of product angular momenta.

  12. Unimolecular reaction dynamics of free radicals

    International Nuclear Information System (INIS)

    Terry A. Miller

    2006-01-01

    Free radical reactions are of crucial importance in combustion and in atmospheric chemistry. Reliable theoretical models for predicting the rates and products of these reactions are required for modeling combustion and atmospheric chemistry systems. Unimolecular reactions frequently play a crucial role in determining final products. The dissociations of vinyl, CH2= CH, and methoxy, CH3O, have low barriers, about 13,000 cm-1 and 8,000 cm-1, respectively. Since barriers of this magnitude are typical of free radicals these molecules should serve as benchmarks for this important class of reactions. To achieve this goal, a detailed understanding of the vinyl and methoxy radicals is required. Results for dissociation dynamics of vinyl and selectively deuterated vinyl radical are reported. Significantly, H-atom scrambling is shown not to occur in this reaction. A large number of spectroscopic experiments for CH3O and CHD2O have been performed. Spectra recorded include laser induced fluorescence (LIF), laser excited dispersed fluorescence (LEDF), fluorescence dip infrared (FDIR) and stimulated emission pumping (SEP). Such results are critical for implementing dynamics experiments involving the dissociation of methoxy

  13. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schatz, G.C. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  14. Are Nonadiabatic Reaction Dynamics the Key to Novel Organosilicon Molecules? The Silicon (Si(3P))-Dimethylacetylene (C4H6(X1A1g)) System as a Case Study.

    Science.gov (United States)

    Thomas, Aaron M; Dangi, Beni B; Yang, Tao; Kaiser, Ralf I; Lin, Lin; Chou, Tzu-Jung; Chang, Agnes H H

    2018-06-06

    The bimolecular gas phase reaction of ground-state silicon (Si; 3 P) with dimethylacetylene (C 4 H 6 ; X 1 A 1g ) was investigated under single collision conditions in a crossed molecular beams machine. Merged with electronic structure calculations, the data propose nonadiabatic reaction dynamics leading to the formation of singlet SiC 4 H 4 isomer(s) and molecular hydrogen (H 2 ) via indirect scattering dynamics along with intersystem crossing (ISC) from the triplet to the singlet surface. The reaction may lead to distinct energetically accessible singlet SiC 4 H 4 isomers ( 1 p8- 1 p24) in overall exoergic reaction(s) (-107 -20 +12 kJ mol -1 ). All feasible reaction products are either cyclic, carry carbene analogous silylene moieties, or carry C-Si-H or C-Si-C bonds that would require extensive isomerization from the initial collision complex(es) to the fragmenting singlet intermediate(s). The present study demonstrates the first successful crossed beams study of an exoergic reaction channel arising from bimolecular collisions of silicon, Si( 3 P), with a hydrocarbon molecule.

  15. Fusion dynamics in 40Ca induced reactions

    International Nuclear Information System (INIS)

    Prasad, E.; Hinde, D.J.; Williams, E.

    2017-01-01

    Synthesis of superheavy elements (SHEs) and investigation of their properties are among the most challenging research topics in modern science. A non-compound nuclear process called quasi fission is partly responsible for the very low production cross sections of SHEs. The formation and survival probabilities of the compound nucleus (CN) strongly depend on the competition between fusion and quasi fission. A clear understanding of these processes and their dynamics is required to make reliable predictions of the best reactions to synthesise new SHEs. All elements beyond Nh are produced using hot fusion reactions and beams of 48 Ca were used in most of these experiments. In this context a series of fission measurements have been carried out at the Australian National University (ANU) using 40;48 Ca beams on various targets ranging from 142 Nd to 249 Cf. Some of the 40 Ca reactions will be discussed in this symposium

  16. Molecular beam studies of reaction dynamics

    International Nuclear Information System (INIS)

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

  17. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  18. Dynamics of the F(-) + CH3I → HF + CH2I(-) Proton Transfer Reaction.

    Science.gov (United States)

    Zhang, Jiaxu; Xie, Jing; Hase, William L

    2015-12-17

    Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 Å(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 Å(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F

  19. Exciplex formation in bimolecular photoinduced electron-transfer investigated by ultrafast time-resolved infrared spectroscopy.

    Science.gov (United States)

    Koch, Marius; Letrun, Romain; Vauthey, Eric

    2014-03-12

    The dynamics of bimolecular photoinduced electron-transfer reactions has been investigated with three donor/acceptor (D/A) pairs in tetrahydrofuran (THF) and acetonitrile (ACN) using a combination of ultrafast spectroscopic techniques, including time-resolved infrared absorption. For the D/A pairs with the highest driving force of electron transfer, all transient spectroscopic features can be unambiguously assigned to the excited reactant and the ionic products. For the pair with the lowest driving force, three additional transient infrared bands, more intense in THF than in ACN, with a time dependence that differs from those of the other bands are observed. From their frequency and solvent dependence, these bands can be assigned to an exciplex. Moreover, polarization-resolved measurements point to a relatively well-defined mutual orientation of the constituents and to a slower reorientational time compared to those of the individual reactants. Thanks to the minimal overlap of the infrared signature of all transient species in THF, a detailed reaction scheme including the relevant kinetic and thermodynamic parameters could be deduced for this pair. This analysis reveals that the formation and recombination of the ion pair occur almost exclusively via the exciplex.

  20. Quantum dynamics of fast chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, J.C. [Univ. of Chicago, IL (United States)

    1993-12-01

    The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.

  1. A network dynamics approach to chemical reaction networks

    NARCIS (Netherlands)

    van der Schaft, Abraham; Rao, S.; Jayawardhana, B.

    2016-01-01

    A treatment of chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a

  2. Self-assembled tethered bimolecular lipid membranes.

    Science.gov (United States)

    Sinner, Eva-Kathrin; Ritz, Sandra; Naumann, Renate; Schiller, Stefan; Knoll, Wolfgang

    2009-01-01

    This chapter describes some of the strategies developed in our group for designing, constructing and structurally and functionally characterizing tethered bimolecular lipid membranes (tBLM). We introduce this platform as a novel model membrane system that complements the existing ones, for example, Langmuir monolayers, vesicular liposomal dispersions and bimolecular ("black") lipid membranes. Moreover, it offers the additional advantage of allowing for studies of the influence of membrane structure and order on the function of integral proteins, for example, on how the composition and organization of lipids in a mixed membrane influence the ion translocation activity of integral channel proteins. The first strategy that we introduce concerns the preparation of tethered monolayers by the self-assembly of telechelics. Their molecular architecture with a headgroup, a spacer unit (the "tether") and the amphiphile that mimics the lipid molecule allows them to bind specifically to the solid support thus forming the proximal layer of the final architecture. After fusion of vesicles that could contain reconstituted proteins from a liposomal dispersion in contact to this monolayer the tethered bimolecular lipid membrane is obtained. This can then be characterized by a broad range of surface analytical techniques, including surface plasmon spectroscopies, the quartz crystal microbalance, fluorescence and IR spectroscopies, and electrochemical techniques, to mention a few. It is shown that this concept allows for the construction of tethered lipid bilayers with outstanding electrical properties including resistivities in excess of 10 MOmega cm2. A modified strategy uses the assembly of peptides as spacers that couple covalently via their engineered sulfhydryl or lipoic acid groups at the N-terminus to the employed gold substrate, while their C-terminus is being activated afterward for the coupling of, for example, dimyristoylphosphatidylethanol amine (DMPE) lipid molecules

  3. Inhomogeneous bimolecular recombination in partially crystallised tri-methylphenyl diamine glasses

    International Nuclear Information System (INIS)

    Goldie, D.M.

    2013-01-01

    The rise and fall dynamics of transient photocurrents induced by exposure to ultraviolet radiation have been analysed for a series of glassy tri-methylphenyl diamine films that have been partially crystallised by ageing under ambient conditions following vapour deposition. An inhomogeneous bimolecular recombination model that uses coupled rate equations is found to provide a consistent fit for the observed photocurrent dynamics provided the recombination rate of holes in the crystallised regions of the films is lower compared to the amorphous regions. Parameters returned by the bimolecular model are investigated as a function of the film age but are observed to be highly sensitive to the initial experimental estimates that are supplied for the effective hole recombination time. The effective hole recombination time generated by the model is found to be relatively independent of film age, however, and has a value of around 0.16 s for a carrier generation rate of 7 × 10 14 cm −3 s −1 . The effective recombination time and steady-state photoconductivity magnitudes are found to be consistent with experimental hole mobility and photo-carrier generation efficiency values that are obtained using complementary time-of-flight and charge collection experiments. - Highlights: ► Transient photocurrents in evaporated diamine films have fast and slow components. ► Transient photocurrents are modelled using inhomogeneous bimolecular recombination. ► Recombination rates differ between crystallised and amorphous film regions. ► Recombination parameters evolve with film age as the films crystallise

  4. Modeling non-adiabatic photoexcited reaction dynamics in condensed phases

    International Nuclear Information System (INIS)

    Coker, D.F.

    2003-01-01

    Reactions of photoexcited molecules, ions, and radicals in condensed phase environments involve non-adiabatic dynamics over coupled electronic surfaces. We focus on how local environmental symmetries can effect non-adiabatic coupling between excited electronic states and thus influence, in a possibly controllable way, the outcome of photo-excited reactions. Semi-classical and mixed quantum-classical non-adiabatic molecular dynamics methods, together with semi-empirical excited state potentials are used to probe the dynamical mixing of electronic states in different environments from molecular clusters, to simple liquids and solids, and photo-excited reactions in complex reaction environments such as zeolites

  5. Modeling Bimolecular Reactive Transport With Mixing-Limitation: Theory and Application to Column Experiments

    Science.gov (United States)

    Ginn, T. R.

    2018-01-01

    The challenge of determining mixing extent of solutions undergoing advective-dispersive-diffusive transport is well known. In particular, reaction extent between displacing and displaced solutes depends on mixing at the pore scale, that is, generally smaller than continuum scale quantification that relies on dispersive fluxes. Here a novel mobile-mobile mass transfer approach is developed to distinguish diffusive mixing from dispersive spreading in one-dimensional transport involving small-scale velocity variations with some correlation, such as occurs in hydrodynamic dispersion, in which short-range ballistic transports give rise to dispersed but not mixed segregation zones, termed here ballisticules. When considering transport of a single solution, this approach distinguishes self-diffusive mixing from spreading, and in the case of displacement of one solution by another, each containing a participant reactant of an irreversible bimolecular reaction, this results in time-delayed diffusive mixing of reactants. The approach generates models for both kinetically controlled and equilibrium irreversible reaction cases, while honoring independently measured reaction rates and dispersivities. The mathematical solution for the equilibrium case is a simple analytical expression. The approach is applied to published experimental data on bimolecular reactions for homogeneous porous media under postasymptotic dispersive conditions with good results.

  6. Reaction product imaging

    Energy Technology Data Exchange (ETDEWEB)

    Chandler, D.W. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    Over the past few years the author has investigated the photochemistry of small molecules using the photofragment imaging technique. Bond energies, spectroscopy of radicals, dissociation dynamics and branching ratios are examples of information obtained by this technique. Along with extending the technique to the study of bimolecular reactions, efforts to make the technique as quantitative as possible have been the focus of the research effort. To this end, the author has measured the bond energy of the C-H bond in acetylene, branching ratios in the dissociation of HI, the energetics of CH{sub 3}Br, CD{sub 3}Br, C{sub 2}H{sub 5}Br and C{sub 2}H{sub 5}OBr dissociation, and the alignment of the CD{sub 3} fragment from CD{sub 3}I photolysis. In an effort to extend the technique to bimolecular reactions the author has studied the reaction of H with HI and the isotopic exchange reaction between H and D{sub 2}.

  7. Electromagnetic Reactions and Few-Nucleon Dynamics

    Directory of Open Access Journals (Sweden)

    Bacca Sonia

    2014-03-01

    Full Text Available We present an update on recent theoretical studies of electromagnetic reactions obtained by using the Lorentz integral transform method. The 4He nucleus will be the main focus of this report: results for the photo-disintegration and the electro-disintegration processes will be shown, as well as a recent calculation of polarizability effects in muonic atoms. We also discuss the exciting possibility to investigate inelastic reactions for mediummass nuclei in coupled-cluster theory, highlighted by the recent application to the 16O photo-nuclear cross section.

  8. Elucidation of Environmental Fate of Artificial Sweetener, Aspartame by Determining Bimolecular Rate Constants with Hydroxyl Radical at Various pH and Temperature Conditions and Reaction By-Products Presentation type:Poster Section:Ocean Sciences Session:General Contribution Authors:Takashi Teraji (1) Takemitsu Arakaki (2) AGU# 10173629 (1) Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru Nishihara-cho, Okinawa, 903-0123, Japan (a4269bj@yahoo.co.jp), (2) Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru Nishihara-cho, Okinawa, 903-0123, Japan (arakakit@sci.u-ryukyu.ac.jp)

    Science.gov (United States)

    Teraji, T.; Arakaki, T.

    2011-12-01

    Use of artificial sweeteners in drinks and food has been rapidly increasing because of their non-calorie nature. In Japan, aspartame, acesulfame K and sucralose are among the most widely used artificial sweeteners. Because the artificial sweeteners are not metabolized in human bodies, they are directly excreted into the environment without chemical transformations. We initiated a study to better understand the fate of artificial sweeteners in the marine environment. In particular, we focused on the fate of aspartame by determining its bimolecular rate constants with hydroxyl radicals at various pH and temperature conditions and reaction by-products. The hydroxyl radical (OH), the most potent reactive oxygen species, reacts with various compounds and determines the environmental oxidation capacity and the life-time of many compounds. The steady-state OH concentration and the reaction rate constants between the compound and OH are used to estimate the life-time of the compound. In this study, we determine the bimolecular rate constants between aspartame and OH at various pH and temperature conditions using a competition kinetics technique. We use hydrogen peroxide as a photochemical source of OH. Bimolecular rate constant we obtained so far was (2.6±1.2)×109 M-1 s-1 at pH = 3.0. Little effect was seen by changing the temperatures between 15 and 40 °C. Activation energy (Ea) was calculated to be -1.0 kJ mol-1 at pH = 3.0, which could be regarded as zero. We will report reaction rate constants at different pHs and reaction by-products which will be analyzed by GC-MS. We will further discuss the fate of aspartame in the coastal environment.

  9. Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

    National Research Council Canada - National Science Library

    Johnston, K

    1998-01-01

    .... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

  10. Molecular dynamics for reactions of heterogeneous catalysis

    NARCIS (Netherlands)

    Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

    1991-01-01

    An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

  11. Dynamic CT of tuberculous meningeal reactions

    International Nuclear Information System (INIS)

    Jinkins, J.R.

    1987-01-01

    The technique of intravenous dynamic cranial computed tomography has been applied to the patient population at this location in Saudi Arabia with meningeal tuberculosis. The various manifestations and sequelae including meningitis, arteritis, infarct, and true meningeal tuberculomata all have characteristic if not specific appearances. The dynamic study enhances an otherwise static examination and reveals a great deal about the pathophysiology of tuberculosis involving the cerebral meningeal surfaces. (orig.)

  12. Testing string dynamics in lepton nucleus reactions

    International Nuclear Information System (INIS)

    Gyulassy, M.; Pluemer, M.

    1989-10-01

    The sensitivity of nuclear attenuation of 10-100 GeV lepton nucleus (ell A) reactions to space-time aspects of hadronization is investigated within the context of the Lund string model. We consider two mechanisms for attenuation in a nucleus: final state cascading and string flip excitations. Implications for the evolution of the energy density in nuclear collisions are discussed. 16 refs., 10 figs

  13. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    CERN Document Server

    Capellos, Christos

    1986-01-01

    This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys­ tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...

  14. Transverse flow reactor studies of the dynamics of radical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Macdonald, R.G. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Radical reactions are in important in combustion chemistry; however, little state-specific information is available for these reactions. A new apparatus has been constructed to measure the dynamics of radical reactions. The unique feature of this apparatus is a transverse flow reactor in which an atom or radical of known concentration will be produced by pulsed laser photolysis of an appropriate precursor molecule. The time dependence of individual quantum states or products and/or reactants will be followed by rapid infrared laser absorption spectroscopy. The reaction H + O{sub 2} {yields} OH + O will be studied.

  15. Construction of a bimolecular fluorescence complementation (BiFC ...

    African Journals Online (AJOL)

    Protein–protein interactions are essential for signal transduction in cells. Bimolecular fluorescence complementation (BiFC) is a novel technology that utilises green fluorescent proteins to visualize protein–protein interactions and subcellular protein localisation. BiFC based on pSATN vectors are a good system for ...

  16. A network dynamics approach to chemical reaction networks

    Science.gov (United States)

    van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

    2016-04-01

    A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

  17. Dynamic screening in solar and stellar nuclear reactions

    Energy Technology Data Exchange (ETDEWEB)

    Daeppen, W. [Department of Physics and Astronomy, University of Southern California, Los Angeles, CA (United States); Mussack, K. [Los Alamos National Laboratory, XTD-2, Los Alamos, NM (United States)

    2012-02-15

    In the hot, dense plasma of solar and stellar interiors, Coulomb potentials are screened, resulting in increased nuclear reaction rates. Although Salpeter's approximation for static screening is widely accepted and used in stellar modeling, the question of screening in nuclear reactions was revisited in the 1990s. In particular the issue of dynamic effects was raised by Shaviv and Shaviv, who applied the techniques of molecular dynamics to the conditions in the Sun's core in order to numerically determine the effect of screening. By directly calculating the motion of ions and electrons due to Coulomb interactions, the simulations are used to compute the effect of screening without the mean-field assumption inherent in Salpeter's approximation. In the last few years, the USC group has first reproduced Shaviv and Shaviv's numerical analysis of the screening energy, showing an effect of dynamic screening. When the consequence for the reaction-rate was computed, a rather surprising resulted, which is contrary to that from static screening theory. Our calculations showed that dynamic screening does not significantly change the reaction rate from that of the bare Coulomb potential. If this can be independently confirmed, then the effects of dynamic screening are highly relevant and should be included in stellar nuclear reaction rates (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  18. Bayesian inversion analysis of nonlinear dynamics in surface heterogeneous reactions.

    Science.gov (United States)

    Omori, Toshiaki; Kuwatani, Tatsu; Okamoto, Atsushi; Hukushima, Koji

    2016-09-01

    It is essential to extract nonlinear dynamics from time-series data as an inverse problem in natural sciences. We propose a Bayesian statistical framework for extracting nonlinear dynamics of surface heterogeneous reactions from sparse and noisy observable data. Surface heterogeneous reactions are chemical reactions with conjugation of multiple phases, and they have the intrinsic nonlinearity of their dynamics caused by the effect of surface-area between different phases. We adapt a belief propagation method and an expectation-maximization (EM) algorithm to partial observation problem, in order to simultaneously estimate the time course of hidden variables and the kinetic parameters underlying dynamics. The proposed belief propagation method is performed by using sequential Monte Carlo algorithm in order to estimate nonlinear dynamical system. Using our proposed method, we show that the rate constants of dissolution and precipitation reactions, which are typical examples of surface heterogeneous reactions, as well as the temporal changes of solid reactants and products, were successfully estimated only from the observable temporal changes in the concentration of the dissolved intermediate product.

  19. Crossed molecular beam studies of unimolecular reaction dynamics

    International Nuclear Information System (INIS)

    Buss, R.J.

    1979-04-01

    The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF 3 I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol -1 . In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum

  20. The dynamics of the Hg + Br2 reaction: elucidation of the reaction mechanism for the Br exchange reaction.

    Science.gov (United States)

    Jambrina, P G; Menéndez, M; Aoiz, F J

    2017-06-28

    In spite of its importance in the Hg atmospheric chemistry, the dynamics of the Hg + Br 2 → HgBr + Br reaction is poorly understood. In this article, we have carried out a comprehensive study of the reaction mechanism of this reaction by means of quasiclassical trajectories (QCTs) on an existing ab initio potential energy surface (PES). The reaction has a non trivial dynamics, as a consequence of its large endothermicity, the presence of a deep potential well, and the competition between the Br exchange and the collision induced dissociation processes. Our calculations demonstrate that insertion is only relevant at energies just above the reaction threshold and that, at energies above 2.3 eV, HgBr formation typically takes place via a sort of frustrated dissociation. In order to compare directly with the results obtained in extensive cross molecular beam experiments for the homologous reaction with I 2 , angular distributions in the laboratory frame for Hg + Br 2 have been simulated under similar experimental conditions. The lack of agreement at the highest energies considered suggests that either the two reactions have substantially different mechanisms or that calculations on a single PES cannot account for the dynamics at those energies.

  1. Stability and dynamics of reactors with heterogeneously catalyzed reactions

    Energy Technology Data Exchange (ETDEWEB)

    Eigenberger, G [BASF A.G., Ludwigshafen am Rhein (Germany, F.R.)

    1978-12-01

    Our knowledge of causes and consequences of problems arising from instability and dynamic effects in reactors with heterogeneously catalyzed reactions has increased remarkably in recent years. Especially thermal effects, caused by the self-acceleration of an exothermic reaction in combination with heat and mass transport, are now well understood. In addition, kinetic effects, i.e. phenomena which have to be explained by the kinetic peculiarities of surface reactions, have attracted increasing interest. For both cases the state of the art will be reviewed, highlighting the physical and chemical causes of the observed phenomena.

  2. Dependence of ICF reaction dynamics on target structure

    International Nuclear Information System (INIS)

    Kumar, Kamal; Dutt, Sunil; GulI, Muntazir; Ahmad, Tauseef; Rizvi, I.A.; Ali, Sabir; Agarwal, Avinash; Kumar, R.; Chaubey, A.K.

    2016-01-01

    The projectile structure is also found responsible for the ICF reaction processes. It is found that projectile having bigger alpha cluster is more unstable towards break up. In this context, a comparative study of 12 C and 16 O ion-beams induced reactions with different targets has been done. The deduced ICF contributions for different systems have been plotted against the target charge of different targets. It is observed that target properties may also be responsible for the interplay between CF and ICF reaction dynamics

  3. Dynamics of synchrotron VUV-induced intracluster reactions

    Energy Technology Data Exchange (ETDEWEB)

    Grover, J.R. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    Photoionization mass spectrometry (PIMS) using the tunable vacuum ultraviolet radiation available at the National Synchrotron Light Source is being exploited to study photoionization-induced reactions in small van der Waals mixed complexes. The information gained includes the observation and classification of reaction paths, the measurement of onsets, and the determination of relative yields of competing reactions. Additional information is obtained by comparison of the properties of different reacting systems. Special attention is given to finding unexpected features, and most of the reactions investigated to date display such features. However, understanding these reactions demands dynamical information, in addition to what is provided by PIMS. Therefore the program has been expanded to include the measurement of kinetic energy release distributions.

  4. Photoinduced bimolecular electron transfer kinetics in small unilamellar vesicles

    International Nuclear Information System (INIS)

    Choudhury, Sharmistha Dutta; Kumbhakar, Manoj; Nath, Sukhendu; Pal, Haridas

    2007-01-01

    Photoinduced electron transfer (ET) from N,N-dimethylaniline to some coumarin derivatives has been studied in small unilamellar vesicles (SUVs) of the phospholipid, DL-α-dimyristoyl-phosphatidylcholine, using steady-state and time-resolved fluorescence quenching, both below and above the phase transition temperature of the vesicles. The primary interest was to examine whether Marcus inversion [H. Sumi and R. A. Marcus, J. Chem. Phys. 84, 4894 (1986)] could be observed for the present ET systems in these organized assemblies. The influence of the topology of SUVs on the photophysical properties of the reactants and consequently on their ET kinetics has also been investigated. Absorption and fluorescence spectral data of the coumarins in SUVs and the variation of their fluorescence decays with temperature indicate that the dyes are localized in the bilayer of the SUVs. Time-resolved area normalized emission spectra analysis, however, reveals that the dyes are distributed in two different microenvironments in the SUVs, which we attribute to the two leaflets of the bilayer, one toward bulk water and the other toward the inner water pool. The microenvironments in the two leaflets are, however, not indicated to be that significantly different. Time-resolved anisotropy decays were biexponential for all the dyes in SUVs, and this has been interpreted in terms of the compound motion model according to which the dye molecules can experience a fast wobbling-in-cone type of motion as well as a slow overall rotating motion of the cone containing the molecule. The expected bimolecular diffusion-controlled rates in SUVs, as estimated by comparing the microviscosities in SUVs (determined from rotational correlation times) and that in acetonitrile solution, are much slower than the observed fluorescence quenching rates, suggesting that reactant diffusion (translational) does not play any role in the quenching kinetics in the present systems. Accordingly, clear inversions are

  5. Imaging the reactions of molecular dications: a new probe of dicationic reaction dynamics and energetics

    International Nuclear Information System (INIS)

    Wan-Ping Hu, S.; Harper, S.M.; Price, S.D.

    2002-01-01

    Experiments which generated angularly resolved data to prove the dynamics of dication chemical reactions were performed using a position sensitive coincidence (PSCO) apparatus, to detect in coincidence both of the charged products from such reaction. It consists of a ion source, a hemispherical energy analyser, and a time-of-flight mass spectrometer. Initial experiments to test the apparatus performance were runned on the atomic electron transfer reaction: Ne 2+ + Ar → Ne + + Ar + . Angular distributions, translational and internal energies of the product ions were extracted, as well as the scattering diagram among other data. (nevyjel)

  6. Bimolecular Master Equations for a Single and Multiple Potential Wells with Analytic Solutions.

    Science.gov (United States)

    Ghaderi, Nima

    2018-04-12

    The analytic solutions, that is, populations, are derived for the K-adiabatic and K-active bimolecular master equations, separately, for a single and multiple potential wells and reaction channels, where K is the component of the total angular momentum J along the axis of least moment of inertia of the recombination products at a given energy E. The analytic approach provides the functional dependence of the population of molecules on its K-active or K-adiabatic dissociation, association rate constants and the intermolecular energy transfer, where the approach may complement the usual numerical approaches for reactions of interest. Our previous work, Part I, considered the solutions for a single potential well, whereby an assumption utilized there is presently obviated in the derivation of the exact solutions and farther discussed. At the high-pressure limit, the K-adiabatic and K-active bimolecular master equations may each reduce, respectively, to the K-adiabatic and K-active bimolecular Rice-Ramsperger-Kassel-Marcus theory (high-pressure limit expressions) for bimolecular recombination rate constant, for a single potential well, and augmented by isomerization terms when multiple potential wells are present. In the low-pressure limit, the expression for population above the dissociation limit, associated with a single potential well, becomes equivalent to the usual presumed detailed balance between the association and dissociation rate constants, where the multiple well case is also considered. When the collision frequency of energy transfer, Z LJ , between the chemical intermediate and bath gas is sufficiently less than the dissociation rate constant k d ( E' J' K') for postcollision ( E' J' K), then the solution for population, g( EJK) + , above the critical energy further simplifies such that depending on Z LJ , the dissociation and association rate constant k r ( EJK), as g( EJK) + = k r ( EJK)A·BC/[ Z LJ + k d ( EJK)], where A and BC are the reactants, for

  7. Fractal sets generated by chemical reactions discrete chaotic dynamics

    International Nuclear Information System (INIS)

    Gontar, V.; Grechko, O.

    2007-01-01

    Fractal sets composed by the parameters values of difference equations derived from chemical reactions discrete chaotic dynamics (DCD) and corresponding to the sequences of symmetrical patterns were obtained in this work. Examples of fractal sets with the corresponding symmetrical patterns have been presented

  8. A dynamical theory of incomplete fusion reactions: The breakup-fusion reaction approach

    International Nuclear Information System (INIS)

    Udagawa, T.

    1984-01-01

    A dynamical theory of partial fusion reactions is presented, which may fill the gap between direct and compound nuclear reaction theories. With the new theory one can calculate partial fusion taking place in three-body (and many more) channels reached via direct reactions, e.g., breakup and knockout reactions. The authors present first the results for the cross section for such reactions, taking as an example breakup followed by fusion. They then discuss a physical picture which emerges from their theory, namely that the partial fusion reactions, particularly of the massive-transfer type, take place in a so-called deep peripheral region. It is also shown that the deep peripheral character of such processes diminishes as the mass of the fused system decreases, so that the reactions essentially evolve to the usual peripheral character. Finally, comparisons are made of results of numerical calculations with experimental data, taking as an example the /sup 159/Tb(/sup 14/N,α) reaction with E/sub lab/ = 95 MeV

  9. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

    NARCIS (Netherlands)

    Vijaykumar, A.; Ouldridge, T.E.; ten Wolde, P.R.; Bolhuis, P.G.

    2017-01-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic

  10. Reaction dynamics of electronically excited alkali atoms with simpler molecules

    International Nuclear Information System (INIS)

    Weiss, P.S.; Mestdagh, J.M.; Schmidt, H.; Vernon, M.F.; Covinsky, M.H.; Balko, B.A.; Lee, Y.T.

    1985-05-01

    The reactions of electronically excited sodium atoms with simple molecules have been studied in crossed molecular beams experiments. Electronically excited Na(3 2 P/sub 3/2/, 4 2 D/sub 5/2/, and 5 2 S/sub 1/2/) were produced by optical pumping using single frequency dye lasers. The effects of the symmetry, and the orientation and alignment of the excited orbital on the chemical reactivity, and detailed information on the reaction dynamics were derived from measurements of the product angular and velocity distributions. 12 refs., 9 figs

  11. Chemical memory reactions induced bursting dynamics in gene expression.

    Science.gov (United States)

    Tian, Tianhai

    2013-01-01

    Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

  12. Confining Domains Lead to Reaction Bursts: Reaction Kinetics in the Plasma Membrane

    Science.gov (United States)

    Kalay, Ziya; Fujiwara, Takahiro K.; Kusumi, Akihiro

    2012-01-01

    Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity. PMID:22479350

  13. Confining domains lead to reaction bursts: reaction kinetics in the plasma membrane.

    Directory of Open Access Journals (Sweden)

    Ziya Kalay

    Full Text Available Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity.

  14. The photodissociation and reaction dynamics of vibrationally excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    Crim, F.F. [Univ. of Wisconsin, Madison (United States)

    1993-12-01

    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  15. Switching dynamics in reaction networks induced by molecular discreteness

    International Nuclear Information System (INIS)

    Togashi, Yuichi; Kaneko, Kunihiko

    2007-01-01

    To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentrations on the system size, which is caused by transitions to discreteness-induced novel states

  16. Direct single-molecule dynamic detection of chemical reactions.

    Science.gov (United States)

    Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

    2018-02-01

    Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

  17. Microscopic study on dynamic barrier in fusion reactions

    International Nuclear Information System (INIS)

    Wu Xizhen; Tian Junlong; Zhao Kai; Li Zhuxia; Wang Ning

    2004-01-01

    The authors briefly review the fusion process of very heavy nuclear systems and some theoretical models. The authors propose a microscopic transport dynamic model, i.e. the Improved Quantum Molecular Dynamic model, for describing fusion reactions of heavy systems, in which the dynamical behavior of the fusion barrier in heavy fusion systems has been studied firstly. The authors find that with the incident energy decreasing the lowest dynamic barrier is obtained which approaches to the adiabatic static barrier and with increase of the incident energy the dynamic barrier goes up to the diabatic static barrier. The authors also indicate that how the dynamical fusion barrier is correlated with the development of the configuration of fusion partners along the fusion path. Associating the single-particle potentials obtained at different stages of fusion with the Two Center Shell Model, authors can study the time evolution of the single particle states of fusion system in configuration space of single particle orbits along the fusion path. (author)

  18. Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

    Science.gov (United States)

    Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

    2017-03-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

  19. Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

    Science.gov (United States)

    Bolhuis, Peter

    Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

  20. Cellular reprogramming dynamics follow a simple 1D reaction coordinate

    Science.gov (United States)

    Teja Pusuluri, Sai; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

    2018-01-01

    Cellular reprogramming, the conversion of one cell type to another, induces global changes in gene expression involving thousands of genes, and understanding how cells globally alter their gene expression profile during reprogramming is an ongoing problem. Here we reanalyze time-course data on cellular reprogramming from differentiated cell types to induced pluripotent stem cells (iPSCs) and show that gene expression dynamics during reprogramming follow a simple 1D reaction coordinate. This reaction coordinate is independent of both the time it takes to reach the iPSC state as well as the details of the experimental protocol used. Using Monte-Carlo simulations, we show that such a reaction coordinate emerges from epigenetic landscape models where cellular reprogramming is viewed as a ‘barrier-crossing’ process between cell fates. Overall, our analysis and model suggest that gene expression dynamics during reprogramming follow a canonical trajectory consistent with the idea of an ‘optimal path’ in gene expression space for reprogramming.

  1. Nuclear dynamics in heavy ion induced fusion-fission reactions

    International Nuclear Information System (INIS)

    Kapoor, S.S.

    1992-01-01

    Heavy ion induced fission and fission-like reactions evolve through a complex nuclear dynamics encountered in the medium energy nucleus-nucleus collisions. In the recent years, measurements of the fragment-neutron and fragment-charged particle angular correlations in heavy ion induced fusion-fission reactions, have provided new information on the dynamical times of nuclear deformations of the initial dinuclear complex to the fission saddle point and the scission point. From the studies of fragment angular distributions in heavy ion induced fission it has been possible to infer the relaxation times of the dinuclear complex in the K-degree of freedom and our recent measurements on the entrance channel dependence of fragment anisotropies have provided an experimental signature of the presence of fissions before K-equilibration. This paper reviews recent experimental and theoretical status of the above studies with particular regard to the questions relating to dynamical times, nuclear dissipation and the effect of nuclear dissipation on the K-distributions at the fission saddle in completely equilibrated compound nucleus. (author). 19 refs., 9 figs

  2. Dynamical constraints and adiabatic invariants in chemical reactions.

    Science.gov (United States)

    Lorquet, J C

    2007-08-23

    For long-range electrostatic potentials and, more generally, when the topography of the potential energy surface is locally simple, the reaction path coordinate is adiabatically separable from the perpendicular degrees of freedom. For the ion-permanent dipole and ion-quadrupole interactions, the Poisson bracket of the adiabatic invariant decreases with the interfragment distance more rapidly than the electrostatic potential. The smaller the translational momentum, the moment of inertia of the neutral fragment, and the dipole or quadrupole moments are, the more reliable the adiabatic approximation is, as expected from the usual argumentation. Closed-form expressions for an effective one-dimensional potential in an adiabatic Hamiltonian are given. Connection with a model where the decoupling is exact is obtained in the limit of an infinitely heavy dipole. The dynamics is also constrained by adiabatic invariance for a harmonic valley about a curved reaction path, as shown by the reaction path Hamiltonian method. The maximum entropy method reveals that, as a result of the invariance properties of the entropy, constraints whose validity has been demonstrated locally only subsist in all parts of phase space. However, their form varies continuously, and they are not necessarily expressed in simple terms as they are in the asymptotic region. Therefore, although the influence of adiabatic invariance has been demonstrated at asymptotically large values of the reaction coordinate only, it persists in more interesting ranges.

  3. Fission dynamics of superheavy nuclei formed in uranium induced reactions

    International Nuclear Information System (INIS)

    Gurjit Kaur; Sandhu, Kirandeep; Sharma, Manoj K.

    2017-01-01

    The compound nuclear system follows symmetric fission if the competing processes such as quasi-elastic, deep inelastic, quasi-fission etc are absent. The contribution of quasi fission events towards the fusion-fission mechanism depends on the entrance channel asymmetry of reaction partners, deformations and orientations of colliding nuclei beside the dependence on energy and angular momentum. Usually the 209 Bi and 208 Pb targets are opted for the production of superheavy nuclei with Z CN =104-113. The nuclei in same mass/charge range can also be synthesized using actinide targets + light projectiles (i.e. asymmetric reaction partners) via hot fusion interactions. These actinide targets are prolate deformed which prefer the compact configurations at above barrier energies, indicating the occurrence of symmetric fission events. Here an attempt is made to address the dynamics of light superheavy system (Z CN =104-106), formed via hot fusion interactions involving actinide targets

  4. Crossed-beam studies of the dynamics of radical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Liu, K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    The objective of this program is to characterize the detailed dynamics of elementary radical reactions and to provide a better understanding of radical reactivity in general. The radical beam is typically generated by a laser photolysis method. After colliding with the reacting molecule in a crossed-beam apparatus, the reaction product state distribution is interrogated by laser spectroscopic techniques. Several radicals of combustion significance, such as O, CH, OH, CN and NCO have been successfully generated and their collisional behavior at the state-to-state integral cross section level of detail has been studied in this manner. During the past year, the detection system has been converted from LIF to REMPI schemes, and the emphasis of this program shifted to investigate the product angular distributions. Both inelastic and reactive processes have been studied.

  5. Dynamic phase transition in diffusion-limited reactions

    International Nuclear Information System (INIS)

    Tauber, U.C.

    2002-01-01

    Many non-equilibrium systems display dynamic phase transitions from active to absorbing states, where fluctuations cease entirely. Based on a field theory representation of the master equation, the critical behavior can be analyzed by means of the renormalization group. The resulting universality classes for single-species systems are reviewed here. Generically, the critical exponents are those of directed percolation (Reggeon field theory), with critical dimension d c = 4. Yet local particle number parity conservation in even-offspring branching and annihilating random walks implies an inactive phase (emerging below d c = 4/3) that is characterized by the power laws of the pair annihilation reaction, and leads to different critical exponents at the transition. For local processes without memory, the pair contact process with diffusion represents the only other non-trivial universality class. The consistent treatment of restricted site occupations and quenched random reaction rates are important open issues (Author)

  6. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    Truhlar, Donald G.

    1993-01-01

    Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

  7. Dynamics of GeV light-ion-induced reactions

    International Nuclear Information System (INIS)

    Kwiatkowski, K.; Bracken, D.S.; Foxford, E.R.; Ginger, D.S.; Hsi, W.C.; Morley, K.B.; Viola, V.E.; Wang, G.; Korteling, R.G.; Legrain, R.

    1996-09-01

    Recent results from studies of the 1.8 - 4.8 GeV 3 He + nat Ag, 197 Au reactions at LNS with the ISiS detector array have shown evidence for a saturation in deposition energy and multifragmentation from a low-density source. The collision dynamics have been examined in the context of intranuclear cascade and BUU models, while breakup phenomena have been compared with EES and SMM models. Fragment-fragment correlations and isotope ratios are also investigated. (K.A.)

  8. Pattern dynamics of the reaction-diffusion immune system.

    Science.gov (United States)

    Zheng, Qianqian; Shen, Jianwei; Wang, Zhijie

    2018-01-01

    In this paper, we will investigate the effect of diffusion, which is ubiquitous in nature, on the immune system using a reaction-diffusion model in order to understand the dynamical behavior of complex patterns and control the dynamics of different patterns. Through control theory and linear stability analysis of local equilibrium, we obtain the optimal condition under which the system loses stability and a Turing pattern occurs. By combining mathematical analysis and numerical simulation, we show the possible patterns and how these patterns evolve. In addition, we establish a bridge between the complex patterns and the biological mechanism using the results from a previous study in Nature Cell Biology. The results in this paper can help us better understand the biological significance of the immune system.

  9. Dynamical isospin effects in nucleon-induced reactions

    International Nuclear Information System (INIS)

    Ou Li; Li Zhuxia; Wu Xizhen

    2008-01-01

    The isospin effects in proton-induced reactions on isotopes of 112-132 Sn and the corresponding β-stable isobars are studied by means of the improved quantum molecular dynamics model and some sensitive probes for the density dependence of the symmetry energy at subnormal densities are proposed. The beam energy range is chosen to be 100-300 MeV. Our study shows that the system size dependence of the reaction cross sections for p+ 112-132 Sn deviates from the Carlson's empirical expression obtained by fitting the reaction cross sections for proton on nuclei along the β-stability line and sensitively depends on the stiffness of the symmetry energy. We also find that the angular distribution of elastic scattering for p+ 132 Sn at large impact parameters is very sensitive to the density dependence of the symmetry energy, which is uniquely due to the effect of the symmetry potential with no mixture of the effect from the isospin dependence of the nucleon-nucleon cross sections. The isospin effects in neutron-induced reactions are also studied and it is found that the effects are just opposite to that in proton-induced reactions. We find that the difference between the peaks of the angular distributions of elastic scattering for p+ 132 Sn and n+ 132 Sn at E p,n =100 MeV and b=7.5 fm is positive for soft symmetry energy U sym sf and negative for super-stiff symmetry energy U sym nlin and close to zero for linear density dependent symmetry energy U sym lin , which seems very useful for constraining the density dependence of the symmetry energy at subnormal densities

  10. Bimodal Exciplex Formation in Bimolecular Photoinduced Electron Transfer Revealed by Ultrafast Time-Resolved Infrared Absorption.

    Science.gov (United States)

    Koch, Marius; Licari, Giuseppe; Vauthey, Eric

    2015-09-03

    The dynamics of a moderately exergonic photoinduced charge separation has been investigated by ultrafast time-resolved infrared absorption with the dimethylanthracene/phthalonitrile donor/acceptor pair in solvents covering a broad range of polarity. A distinct spectral signature of an exciplex could be identified in the -C≡N stretching region. On the basis of quantum chemistry calculations, the 4-5 times larger width of this band compared to those of the ions and of the locally excited donor bands is explained by a dynamic distribution of exciplex geometry with different mutual orientations and distances of the constituents and, thus, with varying charge-transfer character. Although spectrally similar, two types of exciplexes could be distinguished by their dynamics: short-lived, "tight", exciplexes generated upon static quenching and longer-lived, "loose", exciplexes formed upon dynamic quenching in parallel with ion pairs. Tight exciplexes were observed in all solvents, except in the least polar diethyl ether where quenching is slower than diffusion. The product distribution of the dynamic quenching depends strongly on the solvent polarity: whereas no significant loose exciplex population could be detected in acetonitrile, both exciplex and ion pair are generated in less polar solvents, with the relative population of exciplex increasing with decreasing solvent polarity. These results are compared with those reported previously with donor/acceptor pairs in different driving force regimes to obtain a comprehensive picture of the role of the exciplexes in bimolecular photoinduced charge separation.

  11. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

    2015-12-07

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  12. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    International Nuclear Information System (INIS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

    2015-01-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

  13. Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics

    KAUST Repository

    Franz, Benjamin

    2013-06-19

    Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.

  14. Dynamical calculations of nuclear fission and heavy-ion reactions

    International Nuclear Information System (INIS)

    Nix, J.R.; Sierk, A.J.

    1984-01-01

    With the goal of determining the magnitude and mechanism of nuclear dissipation from comparisons of predictions with experimental data, we describe recent calculations in a unified macroscopic-microscopic approach to large-amplitude collective nuclear motion such as occurs in fission and heavy-ion reactions. We describe the time dependence of the distribution function in phase space of collective coordinates and momenta by a generalized Fokker-Planck equation. The nuclear potential energy of deformation is calculated as the sum of repulsive Coulomb and centrifugal energies and an attractive Yukawa-plus-exponential potential, the inertia tensor is calculated for a superposition of rigid-body rotation and incompressible, nearly irrotational flow by use of the Werner-Wheeler method, and the dissipation ensor that describes the conversion of collective energy into single-particle excitation energy is calculated for two prototype mechanisms that represent opposite extremes of large and small dissipation. We solve the generalized Hamilton equations of motion for the first moments of the distribution function to obtain the mean translational fission-fragment kinetic energy and mass of a third fragment that sometimes forms between the two end fragments, as well as dynamical thresholds, capture cross sections, and ternary events in heavy-ion reactions. 33 references

  15. AFD: an application for bi-molecular interaction using axial frequency distribution.

    Science.gov (United States)

    Raza, Saad; Azam, Syed Sikander

    2018-03-06

    Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

  16. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N

    2013-01-01

    Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

  17. Very Low Rate Constants of Bimolecular CO Adsorption on Anionic Gold Clusters: Implications for Catalytic Activity

    Czech Academy of Sciences Publication Activity Database

    Balteanu, I.; Balaj, O. P.; Fox, B. S.; Beyer, M. K.; Bastl, Zdeněk; Bondybey, V. E.

    2003-01-01

    Roč. 5, - (2003), s. 1213-1218 ISSN 1463-9076 Institutional research plan: CEZ:AV0Z4040901 Keywords : bimolecular * adsorption * catalytic activity Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.959, year: 2003

  18. Exploiting Fission Chain Reaction Dynamics to Image Fissile Materials

    Science.gov (United States)

    Chapman, Peter Henry

    Radiation imaging is one potential method to verify nuclear weapons dismantlement. The neutron coded aperture imager (NCAI), jointly developed by Oak Ridge National Laboratory (ORNL) and Sandia National Laboratories (SNL), is capable of imaging sources of fast (e.g., fission spectrum) neutrons using an array of organic scintillators. This work presents a method developed to discriminate between non-multiplying (i.e., non-fissile) neutron sources and multiplying (i.e., fissile) neutron sources using the NCAI. This method exploits the dynamics of fission chain-reactions; it applies time-correlated pulse-height (TCPH) analysis to identify neutrons in fission chain reactions. TCPH analyzes the neutron energy deposited in the organic scintillator vs. the apparent neutron time-of-flight. Energy deposition is estimated from light output, and time-of-flight is estimated from the time between the neutron interaction and the immediately preceding gamma interaction. Neutrons that deposit more energy than can be accounted for by their apparent time-of-flight are identified as fission chain-reaction neutrons, and the image is reconstructed using only these neutron detection events. This analysis was applied to measurements of weapons-grade plutonium (WGPu) metal and 252Cf performed at the Nevada National Security Site (NNSS) Device Assembly Facility (DAF) in July 2015. The results demonstrate it is possible to eliminate the non-fissile 252Cf source from the image while preserving the fissileWGPu source. TCPH analysis was also applied to additional scenes in which theWGPu and 252Cf sources were measured individually. The results of these separate measurements further demonstrate the ability to remove the non-fissile 252Cf source and retain the fissileWGPu source. Simulations performed using MCNPX-PoliMi indicate that in a one hour measurement, solid spheres ofWGPu are retained at a 1sigma level for neutron multiplications M -˜ 3.0 and above, while hollowWGPu spheres are

  19. Dynamics of nuclear fission and heavy-ion reactions

    International Nuclear Information System (INIS)

    Nix, J.R.; Sierk, A.J.

    1979-01-01

    Large-amplitude collective motion in fission and heavy-ion reactions is studied by solving classical equations of motion for the time evolution of the nuclear shape. In the nuclear potential energy of deformation, the generalized surface energy was calculated by means of a double volume integral of a Yukawa-plus-exponential function, which was obtained by requiring that two semi-infinite slabs of constant-density nuclear matter have minimum energy at zero separation. The collective kinetic energy is calculated for nuclear flow that is a superposition of incompressible, nearly irrotational collective-shape motion and rigid-body rotation. Nuclear dissipation is included by means of the Rayleigh dissipation function, which depends upon the physical mechanism that converts collective energy into internal energy. For both ordinary two-body viscosity and a combined wall and window one-body dissipation, fission-fragment kinetic energies are calculated for the fission of nuclei throughout the periodic table and compare with experimental results. Finally, the one-body dynamics of nucleons inside a cylinder colliding with a moving piston is explicitly studied by solving exactly the collisionless Boltzmann equation for the distribution function. By examining the relative phases of the pressure at the piston and the piston's velocity, a dissipative force and an elastic restoring force can be separately identified. 9 references

  20. Bimolecular Rate Constants for FAD-Dependent Glucose Dehydrogenase from Aspergillus terreus and Organic Electron Acceptors.

    Science.gov (United States)

    Tsuruoka, Nozomu; Sadakane, Takuya; Hayashi, Rika; Tsujimura, Seiya

    2017-03-10

    The flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH) from Aspergillus species require suitable redox mediators to transfer electrons from the enzyme to the electrode surface for the application of bioelectrical devices. Although several mediators for FAD-GDH are already in use, they are still far from optimum in view of potential, kinetics, sustainability, and cost-effectiveness. Herein, we investigated the efficiency of various phenothiazines and quinones in the electrochemical oxidation of FAD-GDH from Aspergillus terreus . At pH 7.0, the logarithm of the bimolecular oxidation rate constants appeared to depend on the redox potentials of all the mediators tested. Notably, the rate constant of each molecule for FAD-GDH was approximately 2.5 orders of magnitude higher than that for glucose oxidase from Aspergillus sp. The results suggest that the electron transfer kinetics is mainly determined by the formal potential of the mediator, the driving force of electron transfer, and the electron transfer distance between the redox active site of the mediator and the FAD, affected by the steric or chemical interactions. Higher k ₂ values were found for ortho-quinones than for para-quinones in the reactions with FAD-GDH and glucose oxidase, which was likely due to less steric hindrance in the active site in the case of the ortho-quinones.

  1. Bimolecular Rate Constants for FAD-Dependent Glucose Dehydrogenase from Aspergillus terreus and Organic Electron Acceptors

    Directory of Open Access Journals (Sweden)

    Nozomu Tsuruoka

    2017-03-01

    Full Text Available The flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH from Aspergillus species require suitable redox mediators to transfer electrons from the enzyme to the electrode surface for the application of bioelectrical devices. Although several mediators for FAD-GDH are already in use, they are still far from optimum in view of potential, kinetics, sustainability, and cost-effectiveness. Herein, we investigated the efficiency of various phenothiazines and quinones in the electrochemical oxidation of FAD-GDH from Aspergillus terreus. At pH 7.0, the logarithm of the bimolecular oxidation rate constants appeared to depend on the redox potentials of all the mediators tested. Notably, the rate constant of each molecule for FAD-GDH was approximately 2.5 orders of magnitude higher than that for glucose oxidase from Aspergillus sp. The results suggest that the electron transfer kinetics is mainly determined by the formal potential of the mediator, the driving force of electron transfer, and the electron transfer distance between the redox active site of the mediator and the FAD, affected by the steric or chemical interactions. Higher k2 values were found for ortho-quinones than for para-quinones in the reactions with FAD-GDH and glucose oxidase, which was likely due to less steric hindrance in the active site in the case of the ortho-quinones.

  2. Cellular and molecular dynamics in the foreign body reaction

    NARCIS (Netherlands)

    Luttikhuizen, Daniel T.; Harmsen, Martin C.; Van Luyn, Marja J. A.

    Intracorporally implanted materials, such as medical devices, will provoke the body to initiate an inflammatory reaction. This inflammatory reaction to implanted materials is known as the foreign body reaction (FBR) and is characterized by 3 distinct phases: onset, progression, and resolution. The

  3. Langevin dynamics of A+A reactions in one dimension

    International Nuclear Information System (INIS)

    Sancho, J M; Romero, A H; Lacasta, A M; Lindenberg, Katja

    2007-01-01

    We propose a set of Langevin equations of motion together with a reaction rule for the study of binary reactions. Our scheme is designed to address this problem for arbitrary friction γ and temperature T. It easily accommodates the inclusion of a substrate potential, and it lends itself to straightforward numerical integration. We test this approach on diffusion-limited (γ → ∞) as well as ballistic (γ = 0) A+A → P reactions for which there are extensive exact and approximate theoretical results as well as extensive Monte Carlo results. We reproduce the known results using our integration scheme, and also present new results for the ballistic reactions

  4. Development of a quantum chemical molecular dynamics tribochemical simulator and its application to tribochemical reaction dynamics of lubricant additives

    International Nuclear Information System (INIS)

    Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M

    2010-01-01

    Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives

  5. Physical Chemistry of Reaction Dynamics in Ionic Liquid

    Energy Technology Data Exchange (ETDEWEB)

    Maroncelli, Mark [Pennsylvania State Univ., University Park, PA (United States)

    2016-10-02

    Work completed over the past year mainly involves finishing studies related to solvation dynamics in ionic liquids, amplifying and extending our initial PFG-NMR work on solute diffusion, and learning how to probe rotational dynamics in ionic liquids.

  6. The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van 't Hoff.

    Science.gov (United States)

    Yang, Zhongyue; Houk, K N

    2018-03-15

    Jacobus Henricus van 't Hoff was the first Nobel Laureate in Chemistry. He pioneered in the study of chemical dynamics, which referred at that time to chemical kinetics and thermodynamics. The term has evolved in modern times to refer to the exploration of chemical transformations in a time-resolved fashion. Chemical dynamics has been driven by the development of molecular dynamics trajectory simulations, which provide atomic visualization of chemical processes and illuminate how dynamic effects influence chemical reactivity and selectivity. In homage to the legend of van 't Hoff, we review the development of the chemical dynamics of organic reactions, our area of research. We then discuss our trajectory simulations of pericyclic reactions, and our development of dynamic criteria for concerted and stepwise reaction mechanisms. We also describe a method that we call environment-perturbed transition state sampling, which enables trajectory simulations in condensed-media using quantum mechanics and molecular mechanics (QM/MM). We apply the method to reactions in solvent and in enzyme. Jacobus Henricus van 't Hoff (1852, Rotterdam-1911, Berlin) received the Nobel Prize for Chemistry in 1901 "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". van 't Hoff was born the Netherlands, and earned his doctorate in Utrecht in 1874. In 1896 he moved to Berlin, where he was offered a position with more research and less teaching. van 't Hoff is considered one of the founders of physical chemistry. A key step in establishing this new field was the start of Zeitschrift für Physikalische Chemie in 1887. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Reaction dynamics of small molecules at metal surfaces

    International Nuclear Information System (INIS)

    Samson, P.A.

    1999-09-01

    The dissociation-desorption dynamics of D 2 upon the Sn/Pt(111) surface alloy are dependent on the surface concentration of Sn. The p(2 x 2) Sn/Pt(111) alloy surface (Θ Sn = 0.25 ML), is initially ∼30 times less reactive towards D 2 adsorption than clean Pt(111). On the (√3 x √3) R30 deg Sn/Pt(111) alloy surface (Θ Sn = 0.33 ML), increased inhibition of D 2 adsorption is reported, with S o ∼ 10 -5 at low energy, coinciding with the loss of stable Pt 3 hollow sites and a significant reduction in the D atom binding energy. Sticking on the √3 alloy is activated with an increased energy threshold of ∼280 meV, with no evidence that vibration enhances dissociation. The barrier to dissociation remains in the entrance channel before the D 2 bond begins to stretch. Vibrational excitation is, however, observed in nitrogen desorption from the catalytic reaction of NO + H 2 over Pd(110). For a surface at 600 K, N 2 vibrational state population ratios of P(v=1/v=0) = 0.50 ± 0.05 and P(v=2/v=0) = 0.60 ± 0.20 are reported. Desorption occurs via the N(ad) + N(ad) recombination channel with little energy released into translation and rotation. The translational energy release observed is dependent on the N 2 vibrational state, with translational temperatures of 425 K, 315 K and 180 K reported for the v=0, 1 and 2 states respectively. Sub-thermal energy releases and normally directed angular distributions suggest the influence of a trapping mechanism, recombining molecules scattering through a molecularly adsorbed state, with a transition state of large d NN responsible for the product vibrational excitation. Although N 2 dissociation on Fe(100) forms a simple overlayer structure, on Fe(110), molecular chemisorption does not occur at or above room temperature and the sticking is extremely small (∼10 -6 to 10 -7 ). Activated nitrogen bombardment can be used to prepare a 'surface nitride' with a structure related to the geometry of bulk Fe 4 N. Scanning tunnelling

  8. Rate kernel theory for pseudo-first-order kinetics of diffusion-influenced reactions and application to fluorescence quenching kinetics.

    Science.gov (United States)

    Yang, Mino

    2007-06-07

    Theoretical foundation of rate kernel equation approaches for diffusion-influenced chemical reactions is presented and applied to explain the kinetics of fluorescence quenching reactions. A many-body master equation is constructed by introducing stochastic terms, which characterize the rates of chemical reactions, into the many-body Smoluchowski equation. A Langevin-type of memory equation for the density fields of reactants evolving under the influence of time-independent perturbation is derived. This equation should be useful in predicting the time evolution of reactant concentrations approaching the steady state attained by the perturbation as well as the steady-state concentrations. The dynamics of fluctuation occurring in equilibrium state can be predicted by the memory equation by turning the perturbation off and consequently may be useful in obtaining the linear response to a time-dependent perturbation. It is found that unimolecular decay processes including the time-independent perturbation can be incorporated into bimolecular reaction kinetics as a Laplace transform variable. As a result, a theory for bimolecular reactions along with the unimolecular process turned off is sufficient to predict overall reaction kinetics including the effects of unimolecular reactions and perturbation. As the present formulation is applied to steady-state kinetics of fluorescence quenching reactions, the exact relation between fluorophore concentrations and the intensity of excitation light is derived.

  9. Studies in the reaction dynamics of beam-gas chemiluminescent reactions

    International Nuclear Information System (INIS)

    Prisant, M.G.

    1984-01-01

    This thesis develops techniques for the analysis and interpretation of data obtained from beam-gas chemiluminescence experiments. These techniques are applied to experimental studies of atom transfer reactions of the type A + BC → AB + C. A procedure is developed for determining the product rotational alignment in the center-of-mass frame from polarization measurements of chemiluminescent atom-diatom exchange reactions under beam-gas conditions. Knowledge of a vector property of a reaction, such as product alignment, provides information on the disposition of angular momentum by a chemical reaction. Fluorescence polarization and hence product alignment are measured for two prototype reactions. The reaction of metastable calcium atoms with hydrogen-chloride gas yields highly aligned calcium-chloride product which exhibits little variation of alignment with vibrational state. The reaction of ground-state calcium with fluorine gas yields moderately aligned product which shows strong variation of alignment with vibration. A multi-surface direct-interaction model is developed to interpret product alignment and population data. The predictions of this model for the reaction of calcium with fluorine show reasonable agreement with experiment

  10. Structural parameter identifiability analysis for dynamic reaction networks

    DEFF Research Database (Denmark)

    Davidescu, Florin Paul; Jørgensen, Sten Bay

    2008-01-01

    method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...

  11. Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

    DEFF Research Database (Denmark)

    Costa, Rafael S.; Machado, Daniel; Rocha, Isabel

    2010-01-01

    , represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis–Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action......The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters...

  12. Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

    Science.gov (United States)

    Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

    2012-03-29

    Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

  13. Analysis of the nucleon-nucleus reactions by the quantum molecular dynamics

    International Nuclear Information System (INIS)

    Chiba, Satoshi; Niita, Koji; Maruyama, Toshiki; Fukahori, Tokio; Takada, Hiroshi; Iwamoto, Akira

    1995-01-01

    The quantum molecular dynamics + statistical decay model has been applied to analyze the nucleon-induced nuclear reactions in the energy range from 50 to 3 GeV in order to verify its applicability to light-ion induced nuclear reactions. It was found that the present approach could give a quantitative description of various cross sections such as (p,p'), (p,n), (n,p) reactions from a wide range of targets and also target-like isotope production cross sections from p+Fe reaction, showing its basic ability as a tool for the study of intermediate energy nuclear reactions and nuclear data evaluation. (author)

  14. Chemistry in interstellar space. [environment characteristics influencing reaction dynamics

    Science.gov (United States)

    Donn, B.

    1973-01-01

    The particular characteristics of chemistry in interstellar space are determined by the unique environmental conditions involved. Interstellar matter is present at extremely low densities. Large deviations from thermodynamic equilibrium are, therefore, to be expected. A relatively intense ultraviolet radiation is present in many regions. The temperatures are in the range from 5 to 200 K. Data concerning the inhibiting effect of small activation energies in interstellar clouds are presented in a table. A summary of measured activation energies or barrier heights for exothermic exchange reactions is also provided. Problems of molecule formation are discussed, taking into account gas phase reactions and surface catalyzed processes.

  15. Isotope yield ratios as a probe of the reaction dynamics

    International Nuclear Information System (INIS)

    Trautmann, W.; Hildenbrand, K.D.; Lynen, U.; Mueller, W.F.J.; Rabe, H.J.; Sann, H.; Stelzer, H.; Trockel, R.; Wada, R.; Brummund, N.; Glasow, R.; Kampert, K.H.; Santo, R.; Eckert, E.M.; Pochodzalla, J.; Bock, I.; Pelte, D.

    1987-04-01

    Isotopically resolved yields of particles and complex fragments from 12 C and 18 O induced reactions on 53 Ni, 54 Ni, Ag, and 197 Au in the intermediate range of bombarding energies 30 MeV ≤ E/A ≤ 84 MeV were measured. The systematic variation of the deduced isotope yield ratios with projectile and target is used to determine the degree of N/Z equilibration achieved and to establish time scales for the reaction process. A quantum statistical model is employed in order to derive entropies of the emitting systems from the measured isotope yield ratios. (orig.)

  16. Dynamics of ion–molecule reactions from beam experiments: A historical survey

    Czech Academy of Sciences Publication Activity Database

    Herman, Zdeněk; Futrell, J. H.

    2015-01-01

    Roč. 377, FEB 2015 (2015), s. 84-92 ISSN 1387-3806 Institutional support: RVO:61388955 Keywords : Ion–molecule reactions * Dynamics * Beam scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.183, year: 2015

  17. Triangular Diagrams Teach Steady and Dynamic Behaviour of Catalytic Reactions.

    Science.gov (United States)

    Klusacek, K.; And Others

    1989-01-01

    Illustrates how triangular diagrams can aid in presenting some of the rather complex transient interactions that occur among gas and surface species during heterogeneous catalytic reactions. The basic equations and numerical examples are described. Classroom use of the triangular diagram is discussed. Several diagrams and graphs are provided. (YP)

  18. Dynamic Modelling and Identification of Precipitation Reactions in Full-Scale WWTP

    DEFF Research Database (Denmark)

    Mbamba, Christian Kazadi; Tait, Stephan; Flores-Alsina, Xavier

    , this paper evaluates plant-wide modelling of precipitation reactions using a generic approach integrated within activated sludge and anaerobic models. Preliminary results of anaerobic digester sludge in batch system suggest that the model is able to simulate the dynamics of precipitation reactions. Kinetic...

  19. Reaction dynamics of inflammation proteins and T lymphocytes during radon balneotherapy

    International Nuclear Information System (INIS)

    Peter, A.; Vulpe, B.

    1989-01-01

    During a three-week radon treatment with daily administration of baths a periodical course of reaction with antidromic dynamics of inflammation proteins and T lymphocytes could be shown. A conspicuous reaction of the organism (moment of the treatment reaction) is to be observed one week after the beginning of the treatment. At the end of the cure a decrease of the activity of inflammation as well as of individual acute-phase proteins and immunoglobulins it to be proved. (author)

  20. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    KAUST Repository

    Miller, Nichole Cates

    2012-09-05

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    KAUST Repository

    Miller, Nichole Cates; Cho, Eunkyung; Junk, Matthias J N; Gysel, Roman; Risko, Chad; Kim, Dongwook; Sweetnam, Sean; Miller, Chad E.; Richter, Lee J.; Kline, Regis Joseph; Heeney, Martin J.; McCulloch, Iain A.; Amassian, Aram; Acevedo-Feliz, Daniel; Knox, Christopher; Hansen, Michael Ryan; Dudenko, Dmytro V.; Chmelka, Bradley F.; Toney, Michael F.; Bré das, Jean Luc; McGehee, Michael D.

    2012-01-01

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.

    1996-01-01

    of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

  3. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  4. Resonances and reactions from mean-field dynamics

    Directory of Open Access Journals (Sweden)

    Stevenson P. D.

    2016-01-01

    Full Text Available The time-dependent version of nuclear density functional theory, using functionals derived from Skyrme interactions, is able to approximately describe nuclear dynamics. We present time-dependent results of calculations of dipole resonances, concentrating on excitations of valence neutrons against a proton plus neutron core in the neutron-rich doubly-magic 132Sn nucleus, and results of collision dynamics, highlighting potential routes to ternary fusion, with the example of a collision of 48Ca+48Ca+208Pb resulting in a compound nucleus of element 120 stable against immediate fission.

  5. Gas dynamic reaction process and system for laser chemistry

    International Nuclear Information System (INIS)

    Garbuny, M.

    1979-01-01

    A reaction system is disclosed wherein a moving, unidirectional stream of an activatable gaseous species is produced, the individual members of which have the forward components of their velocities at least 10 times greater than the lateral components of their velocities. The stream is irradiated with substantially monochromatic light having a frequency which activates at least some of the individual members of the species. The activated members can then be reacted with another stream or otherwise utilized

  6. Reaction and Aggregation Dynamics of Cell Surface Receptors

    Science.gov (United States)

    Wang, Michelle Dong

    This dissertation is composed of both theoretical and experimental studies of cell surface receptor reaction and aggregation. Project I studies the reaction rate enhancement due to surface diffusion of a bulk dissolved ligand with its membrane embedded target, using numerical calculations. The results show that the reaction rate enhancement is determined by ligand surface adsorption and desorption kinetic rates, surface and bulk diffusion coefficients, and geometry. In particular, we demonstrate that the ligand surface adsorption and desorption kinetic rates, rather than their ratio (the equilibrium constant), are important in rate enhancement. The second and third projects are studies of acetylcholine receptor clusters on cultured rat myotubes using fluorescence techniques after labeling the receptors with tetramethylrhodamine -alpha-bungarotoxin. The second project studies when and where the clusters form by making time-lapse movies. The movies are made from overlay of the pseudocolored total internal reflection fluorescence (TIRF) images of the cluster, and the schlieren images of the cell cultures. These movies are the first movies made using TIRF, and they clearly show the cluster formation from the myoblast fusion, the first appearance of clusters, and the eventual disappearance of clusters. The third project studies the fine structural features of individual clusters observed under TIRF. The features were characterized with six parameters by developing a novel fluorescence technique: spatial fluorescence autocorrelation. These parameters were then used to study the feature variations with age, and with treatments of drugs (oligomycin and carbachol). The results show little variation with age. However, drug treatment induced significant changes in some parameters. These changes were different for oligomycin and carbachol, which indicates that the two drugs may eliminate clusters through different mechanisms.

  7. Global dynamics of a reaction-diffusion system

    Directory of Open Access Journals (Sweden)

    Yuncheng You

    2011-02-01

    Full Text Available In this work the existence of a global attractor for the semiflow of weak solutions of a two-cell Brusselator system is proved. The method of grouping estimation is exploited to deal with the challenge in proving the absorbing property and the asymptotic compactness of this type of coupled reaction-diffusion systems with cubic autocatalytic nonlinearity and linear coupling. It is proved that the Hausdorff dimension and the fractal dimension of the global attractor are finite. Moreover, the existence of an exponential attractor for this solution semiflow is shown.

  8. Comparison of dynamical aspects of nonadiabatic electron, proton, and proton-coupled electron transfer reactions

    International Nuclear Information System (INIS)

    Hatcher, Elizabeth; Soudackov, Alexander; Hammes-Schiffer, Sharon

    2005-01-01

    The dynamical aspects of a model proton-coupled electron transfer (PCET) reaction in solution are analyzed with molecular dynamics simulations. The rate for nonadiabatic PCET is expressed in terms of a time-dependent probability flux correlation function. The impact of the proton donor-acceptor and solvent dynamics on the probability flux is examined. The dynamical behavior of the probability flux correlation function is dominated by a solvent damping term that depends on the energy gap correlation function. The proton donor-acceptor motion does not impact the dynamical behavior of the probability flux correlation function but does influence the magnitude of the rate. The approximations previously invoked for the calculation of PCET rates are tested. The effects of solvent damping on the proton donor-acceptor vibrational motion are found to be negligible, and the short-time solvent approximation, in which only equilibrium fluctuations of the solvent are considered, is determined to be valid for these types of reactions. The analysis of PCET reactions is compared to previous analyses of single electron and proton transfer reactions. The dynamical behavior is qualitatively similar for all three types of reactions, but the time scale of the decay of the probability flux correlation function is significantly longer for single proton transfer than for PCET and single electron transfer due to a smaller solvent reorganization energy for proton transfer

  9. Competitive Pressure: Competitive Dynamics as Reactions to Multiple Rivals

    OpenAIRE

    Zucchini, Leon; Kretschmer, Tobias

    2011-01-01

    Competitive dynamics research has focused primarily on interactions between dyads of firms. Drawing on the awareness-motivation-capability framework and strategic group theory we extend this by proposing that firms’ actions are influenced by perceived competitive pressure resulting from actions by several rivals. We predict that firms’ action magnitude is influenced by the total number of rival actions accumulating in the market, and that this effect is moderated by strategic group membership...

  10. Electron transfer reactions of metal complexes in solution

    International Nuclear Information System (INIS)

    Sutin, N.

    1977-01-01

    A few representative electron-transfer reactions are selected and their kinetic parameters compared with the predictions of activated complex models. Since Taube has presented an elegant treatment of intramolecular electron-transfer reactions, emphasis is on bimolecular reactions. The latter electron-transfer reactions are more complicated to treat theoretically since the geometries of their activated complexes are not as well known as for the intramolecular case. In addition in biomolecular reactions, the work required to bring the two reactants together needs to be calculated. Since both reactants generally carry charges this presents a non-trivial problem at the ionic strengths usually used to study bimolecular electron transfer

  11. Nucleon induced reaction by anti-symmetrized molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tosaka, Yoshiharu [Fujitsu Labs. Ltd., Kawasaki, Kanagawa (Japan); Ono, Akira; Horiuchi, Hisashi

    1998-07-01

    Neutron soft error is a phenomenon, for example, to change memory information of LSI from 0 to 1 by introducing a lot of charge depend on product ions by nuclear reaction between neutrons of second cosmic rays and nuclei of Si in LSI. To study the phenomena, the information such as energy, angular and mass distribution of product ions by n+{sup 28}Si reaction from 20 to 500 MeV incident energy were necessary. 180 MeV p+{sup 27}Al, having large amount of data of heavy recoil nucleus, was investigated. On AMD, A = 1,24-27 ion were produced at the initial collision (before 100 fm/c), after that the mass distribution was not changed, indicating stable excited nucleus. However, on AMD-V, the excited nuclei were destructed in course of time. A = 1,2,4,18 and 21-27 ion were produced at 120 fm/c, but almost kinds of ions less than 27 produced at 320 fm/c. After decay, difference between results of AMD and AMD-V was small and both reproduced the experimental values. AMD-V gave better result of product cross section and differential cross section. (S.Y.)

  12. Development of tight-binding, chemical-reaction-dynamics simulator for combinatorial computational chemistry

    International Nuclear Information System (INIS)

    Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira

    2004-01-01

    Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated

  13. Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure

    Directory of Open Access Journals (Sweden)

    Recchia F.

    2011-10-01

    Full Text Available Multinucleon transfer reactions have been investigated in 40Ar+208Pb with the Prisma+Clara set-up. The experimental differential cross sections of different neutron transfer channels have been obtained at three different angular settings taking into account the transmission through the spectrometer. The experimental yields of the excited states have been determined via particle-γ coincidences. In odd Ar isotopes, we reported a signif cant population of 11/2− states, reached via neutron transfer. Their structure matches a stretched conf guration of the valence neutron coupled to vibration quanta.

  14. Biodegradation at Dynamic Plume Fringes: Mixing Versus Reaction Control

    Science.gov (United States)

    Cirpka, O. A.; Eckert, D.; Griebler, C.; Haberer, C.; Kürzinger, P.; Bauer, R.; Mellage, A.

    2014-12-01

    Biodegradation of continuously emitted plumes is known to be most pronounced at the plume fringe, where mixing of contaminated water and ambient groundwater, containing dissolved electron acceptors, stimulates microbial activity. Under steady-state conditions, physical mixing of contaminant and electron acceptor by transverse dispersion was shown to be the major bottleneck for biodegradation, with plume lengths scaling inversely with the bulk transverse dispersivity in quasi two-dimensional settings. Under these conditions, the presence of suitable microbes is essential but the biokinetic parameters do not play an important role. When the location of the plume shifts (caused, e.g., by a fluctuating groundwater table), however, the bacteria are no more situated at the plume fringe and biomass growth, decay, activation and deactivation determine the time lag until the fringe-controlled steady state is approached again. During this time lag, degradation is incomplete. The objective of the presented study was to analyze to which extent flow and transport dynamics diminish effectiveness of fringe-controlled biodegradation and which microbial processes and related biokinetic parameters determine the system response in overall degradation to hydraulic fluctuations. We performed experiments in quasi-two-dimensional flow through microcosms on aerobic toluene degradation by Pseudomonas putida F1. Plume dynamics were simulated by vertical alteration of the toluene plume position and experimental results were analyzed by reactive-transport modeling. We found that, even after disappearance of the toluene plume for two weeks, the majority of microorganisms stayed attached to the sediment and regained their full biodegradation potential within two days after reappearance of the toluene plume. Our results underline that besides microbial growth and maintenance (often subsumed as "biomass decay") microbial dormancy (that is, change into a metabolically inactive state) and

  15. Transcriptional dynamics with time-dependent reaction rates

    Science.gov (United States)

    Nandi, Shubhendu; Ghosh, Anandamohan

    2015-02-01

    Transcription is the first step in the process of gene regulation that controls cell response to varying environmental conditions. Transcription is a stochastic process, involving synthesis and degradation of mRNAs, that can be modeled as a birth-death process. We consider a generic stochastic model, where the fluctuating environment is encoded in the time-dependent reaction rates. We obtain an exact analytical expression for the mRNA probability distribution and are able to analyze the response for arbitrary time-dependent protocols. Our analytical results and stochastic simulations confirm that the transcriptional machinery primarily act as a low-pass filter. We also show that depending on the system parameters, the mRNA levels in a cell population can show synchronous/asynchronous fluctuations and can deviate from Poisson statistics.

  16. Transcriptional dynamics with time-dependent reaction rates

    International Nuclear Information System (INIS)

    Nandi, Shubhendu; Ghosh, Anandamohan

    2015-01-01

    Transcription is the first step in the process of gene regulation that controls cell response to varying environmental conditions. Transcription is a stochastic process, involving synthesis and degradation of mRNAs, that can be modeled as a birth–death process. We consider a generic stochastic model, where the fluctuating environment is encoded in the time-dependent reaction rates. We obtain an exact analytical expression for the mRNA probability distribution and are able to analyze the response for arbitrary time-dependent protocols. Our analytical results and stochastic simulations confirm that the transcriptional machinery primarily act as a low-pass filter. We also show that depending on the system parameters, the mRNA levels in a cell population can show synchronous/asynchronous fluctuations and can deviate from Poisson statistics. (paper)

  17. Dynamical hindrance to compound nucleus formation in heavy ion reactions

    International Nuclear Information System (INIS)

    Blocki, J.; Feldmeier, H.; Swiatecki, W.J.

    1987-01-01

    A large number of dynamical trajectories corresponding to colliding nuclei, as represented by an idealized, sharp-surfaced liquid-drop model with one-body dissipation are examined. The objective was to delineate quantitatively, within this model, the behaviour of the extra-extra-push energy E XX in its dependence on the mass /or charge/ numbers of the colliding nuclei. Qualitatively, the results are as anticipated on the basis of earlier studies: the appearance of a dynamical limitation on compound nucleus formation beyond a certain threshold locus in the A 1 . A 2 plane, with the energy E XX rising smoothly but rapidly beyond the threshold. The reduction of the two-dimensional function E XX /A 1 ,A 2 / to a one-dimensional function of a mean fissility x m appears possible as a rough approximation. As expected, the mean fissility x and the entrance channel fissility x 0 . The optimum choice appears to be one in which x is given about twice the weight of x 0

  18. Nonlinear electromechanical modelling and dynamical behavior analysis of a satellite reaction wheel

    Science.gov (United States)

    Aghalari, Alireza; Shahravi, Morteza

    2017-12-01

    The present research addresses the satellite reaction wheel (RW) nonlinear electromechanical coupling dynamics including dynamic eccentricity of brushless dc (BLDC) motor and gyroscopic effects, as well as dry friction of shaft-bearing joints (relative small slip) and bearing friction. In contrast to other studies, the rotational velocity of the flywheel is considered to be controllable, so it is possible to study the reaction wheel dynamical behavior in acceleration stages. The RW is modeled as a three-phases BLDC motor as well as flywheel with unbalances on a rigid shaft and flexible bearings. Improved Lagrangian dynamics for electromechanical systems is used to obtain the mathematical model of the system. The developed model can properly describe electromechanical nonlinear coupled dynamical behavior of the satellite RW. Numerical simulations show the effectiveness of the presented approach.

  19. Time-resolved imaging of purely valence-electron dynamics during a chemical reaction

    DEFF Research Database (Denmark)

    Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods...... such as electron(7-10) or X-ray diffraction(11) and X-ray absorption(12) yield complementary information about the atomic motions. Time-resolved methods that are directly sensitive to both valence-electron dynamics and atomic motions include photoelectron spectroscopy(13-15) and high-harmonic generation(16......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...

  20. Spectroscopy and reaction dynamics of collision complexes containing hydroxyl radicals

    Energy Technology Data Exchange (ETDEWEB)

    Lester, M.I. [Univ. of Pennsylvania, Philadelphia (United States)

    1993-12-01

    The DOE supported work in this laboratory has focused on the spectroscopic characterization of the interaction potential between an argon atom and a hydroxyl radical in the ground X{sup 2}II and excited A {sup 2}{summation}{sup +} electronic states. The OH-Ar system has proven to be a test case for examining the interaction potential in an open-shell system since it is amenable to experimental investigation and theoretically tractable from first principles. Experimental identification of the bound states supported by the Ar + OH (X {sup 2}II) and Ar + OH(A {sup 2}{summation}{sup +}) potentials makes it feasible to derive realistic potential energy surfaces for these systems. The experimentally derived intermolecular potentials provide a rigorous test of ab initio theory and a basis for understanding the dramatically different collision dynamics taking place on the ground and excited electronic state surfaces.

  1. Pico-second laser spectroscopy and reaction dynamics in liquids

    International Nuclear Information System (INIS)

    Mialocq, Jean-Claude

    1984-01-01

    The dynamic relaxation of excited singlet states of molecules and ions in liquid solution is investigated using picosecond laser spectroscopy. The more efficient process for the deactivation of the first excited singlet state of pinacyanol is internal conversion S 1 → S 0 between iso-energetic states. At low viscosity, the rate constant is inversely proportional to the macroscopic viscosity and depends on the relaxation of the angle between the quinoline end groups around the polymethinic chain. Electron photodetachment by 265 nm excitation of the ferrocyanide and phenolate anions and photoionisation of neutral molecules, phenol, indole and tryptophan in polar solvents give rise to the solvated electron formation. The mono-or bi-photonic nature of the ejection process and the solvent relaxation around the excess electron are analyzed. (author) [fr

  2. Ground Reaction Forces Generated During Rhythmical Squats as a Dynamic Loads of the Structure

    Science.gov (United States)

    Pantak, Marek

    2017-10-01

    Dynamic forces generated by moving persons can lead to excessive vibration of the long span, slender and lightweight structure such as floors, stairs, stadium stands and footbridges. These dynamic forces are generated during walking, running, jumping and rhythmical body swaying in vertical or horizontal direction etc. In the paper the mathematical models of the Ground Reaction Forces (GRFs) generated during squats have been presented. Elaborated models was compared to the GRFs measured during laboratory tests carried out by author in wide range of frequency using force platform. Moreover, the GRFs models were evaluated during dynamic numerical analyses and dynamic field tests of the exemplary structure (steel footbridge).

  3. Dynamical resonances in the fluorine atom reaction with the hydrogen molecule.

    Science.gov (United States)

    Yang, Xueming; Zhang, Dong H

    2008-08-01

    [Reaction: see text]. The concept of transition state has played a crucial role in the field of chemical kinetics and reaction dynamics. Resonances in the transition state region are important in many chemical reactions at reaction energies near the thresholds. Detecting and characterizing isolated reaction resonances, however, have been a major challenge in both experiment and theory. In this Account, we review the most recent developments in the study of reaction resonances in the benchmark F + H 2 --> HF + H reaction. Crossed molecular beam scattering experiments on the F + H 2 reaction have been carried out recently using the high-resolution, highly sensitive H-atom Rydberg tagging technique with HF rovibrational states almost fully resolved. Pronounced forward scattering for the HF (nu' = 2) product has been observed at the collision energy of 0.52 kcal/mol in the F + H 2 (j = 0) reaction. Quantum dynamical calculations based on two new potential energy surfaces, the Xu-Xie-Zhang (XXZ) surface and the Fu-Xu-Zhang (FXZ) surface, show that the observed forward scattering of HF (nu' = 2) in the F + H 2 reaction is caused by two Feshbach resonances (the ground resonance and first excited resonance). More interestingly, the pronounced forward scattering of HF (nu' = 2) at 0.52 kcal/mol is enhanced considerably by the constructive interference between the two resonances. In order to probe the resonance potential more accurately, the isotope substituted F + HD --> HF + D reaction has been studied using the D-atom Rydberg tagging technique. A remarkable and fast changing dynamical picture has been mapped out in the collision energy range of 0.3-1.2 kcal/mol for this reaction. Quantum dynamical calculations based on the XXZ surface suggest that the ground resonance on this potential is too high in comparison with the experimental results of the F + HD reaction. However, quantum scattering calculations on the FXZ surface can reproduce nearly quantitatively the resonance

  4. Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zahn, Dirk

    2004-01-01

    The rate-determining step of acid catalyzed peptide hydrolysis is the nucleophilic attack of a water molecule to the carbon atom of the amide group. Therein the addition of the hydroxyl group to the amide carbon atom involves the association of a water molecule transferring one of its protons to an adjacent water molecule. The protonation of the amide nitrogen atom follows as a separate reaction step. Since the nucleophilic attack involves the breaking and formation of several bonds, the underlying reaction coordinate is rather complex. We investigate this reaction step from path sampling Car-Parrinello molecular dynamics simulations. This approach does not require the predefinition of reaction coordinates and is thus particularly suited for investigating reaction mechanisms. From our simulations the most relevant components of the reaction coordinate are elaborated. Though the C···O distance of the oxygen atom of the water molecule performing the nucleophilic attack and the corresponding amide carbon atom is a descriptor of the reaction progress, a complete picture of the reaction coordinate must include all three molecules taking part in the reaction. Moreover, the proton transfer is found to depend on favorable solvent configurations. Thus, also the arrangement of non-reacting, i.e. solvent water molecules needs to be considered in the reaction coordinate

  5. Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics.

    Science.gov (United States)

    Lee, Sangyun; Kim, Ji-Hyun; Lee, Sangyoub

    2012-02-14

    Acetylcholinesterase is an enzyme with a very high turnover rate; it quenches the neurotransmitter, acetylcholine, at the synapse. We have investigated the kinetics of the enzyme reaction by calculating the diffusion rate of the substrate molecule along an active site channel inside the enzyme from atomic-level molecular dynamics simulations. In contrast to the previous works, we have found that the internal substrate diffusion is the determinant of the acetylcholinesterase kinetics in the low substrate concentration limit. Our estimate of the overall bimolecular reaction rate constant for the enzyme is in good agreement with the experimental data. In addition, the present calculation provides a reasonable explanation for the effects of the ionic strength of solution and the mutation of surface residues of the enzyme. The study suggests that internal diffusion of the substrate could be a key factor in understanding the kinetics of enzymes of similar characteristics.

  6. Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Gray, S.K. [Argonne National Laboratory, IL (United States)

    1993-12-01

    A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.

  7. The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Tully, John C. [Yale Univ., New Haven, CT (United States)

    2017-06-10

    Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opens up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.

  8. Convection and reaction in a diffusive boundary layer in a porous medium: nonlinear dynamics.

    Science.gov (United States)

    Andres, Jeanne Therese H; Cardoso, Silvana S S

    2012-09-01

    We study numerically the nonlinear interactions between chemical reaction and convective fingering in a diffusive boundary layer in a porous medium. The reaction enhances stability by consuming a solute that is unstably distributed in a gravitational field. We show that chemical reaction profoundly changes the dynamics of the system, by introducing a steady state, shortening the evolution time, and altering the spatial patterns of velocity and concentration of solute. In the presence of weak reaction, finger growth and merger occur effectively, driving strong convective currents in a thick layer of solute. However, as the reaction becomes stronger, finger growth is inhibited, tip-splitting is enhanced and the layer of solute becomes much thinner. Convection enhances the mass flux of solute consumed by reaction in the boundary layer but has a diminishing effect as reaction strength increases. This nonlinear behavior has striking differences to the density fingering of traveling reaction fronts, for which stronger chemical kinetics result in more effective finger merger owing to an increase in the speed of the front. In a boundary layer, a strong stabilizing effect of reaction can maintain a long-term state of convection in isolated fingers of wavelength comparable to that at onset of instability.

  9. A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

    2015-01-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Dynamic Characteristics and Model for Centralization Reaction of Acidic Tailings From Heap Leaching of Uranium Ore

    International Nuclear Information System (INIS)

    Ding Dexin; Liu Yulong; Li Guangyue; Wang Youtuan

    2010-01-01

    Centralization tests were carried out on acidic tailings from heap leaching of uranium ore by using CaO, NaOH and NH 4 OH. The variations of pH with time were measured for the three centralization systems and the dynamic models for the systems were set up by regressing the measured data. The centralization process consists of the fast reaction phase representing the reaction between the centralization agent and the acid on the surface of the tailing's particles and the slow diffusion-reaction phase representing the diffusion-reaction between the centralization agent and the acid within the tailing's particles. The non-linear coupling and feedback function model for the diffusion-reaction of the centralization agent can reflect the process and mode of the centralization reaction. There is a non-linear oscillation in the variation of pH within the centralization systems. The dynamic model for the tailing's centralization reaction can fit the pH variation within the centralization systems. (authors)

  11. Proceedings of the Workshop on open problems in heavy ion reaction dynamics at VIVITRON energies

    International Nuclear Information System (INIS)

    Beck, F.A.

    1993-01-01

    Some problems of heavy ion reaction dynamics at the VIVITRON tandem accelerator and the experimental facilities are discussed at the meeting. Topics include light dinuclear systems, collision dynamics at low energies, fission evaporation and fusion of heavy nuclei and others. Most documents consist of transparencies presented at the workshop, texts of papers are missing. All items are indexed and abstracted for the INIS database. (K.A.)

  12. Proceedings of the Workshop on open problems in heavy ion reaction dynamics at VIVITRON energies

    Energy Technology Data Exchange (ETDEWEB)

    Beck, F. A.

    1993-07-01

    Some problems of heavy ion reaction dynamics at the VIVITRON tandem accelerator and the experimental facilities are discussed at the meeting. Topics include light dinuclear systems, collision dynamics at low energies, fission evaporation and fusion of heavy nuclei and others. Most documents consist of transparencies presented at the workshop, texts of papers are missing. All items are indexed and abstracted for the INIS database. (K.A.).

  13. Vibrational-rotational excitation: chemical reactions of vibrationally excited molecules

    International Nuclear Information System (INIS)

    Moore, C.B.; Smith, I.W.M.

    1979-03-01

    This review considers a limited number of systems, particularly gas-phase processes. Excited states and their preparation, direct bimolecular reactions, reactions of highly excited molecules, and reactions in condensed phases are discussed. Laser-induced isotope separation applications are mentioned briefly. 109 references

  14. Uncertainty for calculating transport on Titan: A probabilistic description of bimolecular diffusion parameters

    Science.gov (United States)

    Plessis, S.; McDougall, D.; Mandt, K.; Greathouse, T.; Luspay-Kuti, A.

    2015-11-01

    Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's upper atmosphere. Our results show that, after propagating uncertainty through the Massman model, the uncertainty in molecular diffusion is highly correlated to temperature and we observe no noticeable correlation with pressure. We propagate the calibrated molecular diffusion estimate and associated uncertainty to obtain an estimate with uncertainty due to bimolecular diffusion for the methane molar fraction as a function of altitude. Results show that the uncertainty in methane abundance due to molecular diffusion is in general small compared to eddy diffusion and the chemical kinetics description. However, methane abundance is most sensitive to uncertainty in molecular diffusion above 1200 km where the errors are nontrivial and could have important implications for scientific research based on diffusion models in this altitude range.

  15. Soft tissue deformation modelling through neural dynamics-based reaction-diffusion mechanics.

    Science.gov (United States)

    Zhang, Jinao; Zhong, Yongmin; Gu, Chengfan

    2018-05-30

    Soft tissue deformation modelling forms the basis of development of surgical simulation, surgical planning and robotic-assisted minimally invasive surgery. This paper presents a new methodology for modelling of soft tissue deformation based on reaction-diffusion mechanics via neural dynamics. The potential energy stored in soft tissues due to a mechanical load to deform tissues away from their rest state is treated as the equivalent transmembrane potential energy, and it is distributed in the tissue masses in the manner of reaction-diffusion propagation of nonlinear electrical waves. The reaction-diffusion propagation of mechanical potential energy and nonrigid mechanics of motion are combined to model soft tissue deformation and its dynamics, both of which are further formulated as the dynamics of cellular neural networks to achieve real-time computational performance. The proposed methodology is implemented with a haptic device for interactive soft tissue deformation with force feedback. Experimental results demonstrate that the proposed methodology exhibits nonlinear force-displacement relationship for nonlinear soft tissue deformation. Homogeneous, anisotropic and heterogeneous soft tissue material properties can be modelled through the inherent physical properties of mass points. Graphical abstract Soft tissue deformation modelling with haptic feedback via neural dynamics-based reaction-diffusion mechanics.

  16. The Crossed-Beam Scattering Method in Studies of Ion-Molecule Reaction Dynamics

    Czech Academy of Sciences Publication Activity Database

    Herman, Zdeněk

    2001-01-01

    Roč. 212, - (2001), s. 413-443 ISSN 1387-3806 R&D Projects: GA ČR GA203/00/0632 Institutional research plan: CEZ:AV0Z4040901 Keywords : ion-molecule reaction dynamics * ion scattering * experimental methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.176, year: 2001

  17. Dynamics of chemical reactions of multiply-charged cations: Information from beam scattering experiments

    Czech Academy of Sciences Publication Activity Database

    Herman, Zdeněk

    2015-01-01

    Roč. 378, FEB 2015 (2015), s. 113-126 ISSN 1387-3806 Institutional support: RVO:61388955 Keywords : Multiply-charged ions * Dynamics of chemical reactions * Beam scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.183, year: 2015

  18. Optically Controlled Electron-Transfer Reaction Kinetics and Solvation Dynamics : Effect of Franck-Condon States

    NARCIS (Netherlands)

    Gupta, Kriti; Patra, Aniket; Dhole, Kajal; Samanta, Alok Kumar; Ghosh, Swapan K.

    2017-01-01

    Experimental results for optically controlled electron-transfer reaction kinetics (ETRK) and nonequilibrium solvation dynamics (NESD) of Coumarin 480 in DMPC vesicle show their dependence on excitation wavelength λex. However, the celebrated Marcus theory and linear-response-theory-based approaches

  19. Dynamical Behaviors of Stochastic Reaction-Diffusion Cohen-Grossberg Neural Networks with Delays

    Directory of Open Access Journals (Sweden)

    Li Wan

    2012-01-01

    Full Text Available This paper investigates dynamical behaviors of stochastic Cohen-Grossberg neural network with delays and reaction diffusion. By employing Lyapunov method, Poincaré inequality and matrix technique, some sufficient criteria on ultimate boundedness, weak attractor, and asymptotic stability are obtained. Finally, a numerical example is given to illustrate the correctness and effectiveness of our theoretical results.

  20. National array of neutron detectors (NAND) a versatile setup for studies on reaction dynamics

    International Nuclear Information System (INIS)

    Golda, K.S.; Singh, R.P.; Zacharias, J.; Archunan, M.; Kothari, A.; Barua, P.; Gupta, Arti; Venkataramanan, S.; Suman, S.K.; Kumar, Rajesh; Kumar, Pankaj; Jhingan, A.; Sugathan, P.; Datta, S.K.; Chatterjee, Mihir; Bhowmik, R.K.; Singh, Hardev; Behera, B.; Kumar, A.; Singh, G.; Ranjit; Mandal, S.

    2006-01-01

    National Array of Neutron Detectors (NAND) is a large array of neutron detectors being setup at Inter University Accelerator Centre. The primary motive behind the development of this array, is the study of reaction dynamics in the energy domain near the Coulomb barrier

  1. Molecular dynamics simulation of the first electron transfer step in the oxygen reduction reaction

    NARCIS (Netherlands)

    Hartnig, C.B.; Koper, M.T.M.

    2002-01-01

    We present a molecular dynamics simulation of solvent reorganization in the first electron transfer step in the oxygen reduction reaction, i.e. O2+e-¿O2-, modeled as taking place in the outer Helmholtz plane. The first electron transfer step is usually considered the rate-determining step from many

  2. Ultrafast Photoinduced Electron Transfer in Bimolecular Donor-Acceptor Systems

    KAUST Repository

    Alsulami, Qana A.

    2016-11-30

    The efficiency of photoconversion systems, such as organic photovoltaic (OPV) cells, is largely controlled by a series of fundamental photophysical processes occurring at the interface before carrier collection. A profound understanding of ultrafast interfacial charge transfer (CT), charge separation (CS), and charge recombination (CR) is the key determinant to improving the overall performances of photovoltaic devices. The discussion in this dissertation primarily focuses on the relevant parameters that are involved in photon absorption, exciton separation, carrier transport, carrier recombination and carrier collection in organic photovoltaic devices. A combination of steady-state and femtosecond broadband transient spectroscopies was used to investigate the photoinduced charge carrier dynamics in various donor-acceptor systems. Furthermore, this study was extended to investigate some important factors that influence charge transfer in donor-acceptor systems, such as the morphology, energy band alignment, electronic properties and chemical structure. Interestingly, clear correlations among the steady-state measurements, time-resolved spectroscopy results, grain alignment of the electron transporting layer (ETL), carrier mobility, and device performance are found. In this thesis, we explored the significant impacts of ultrafast charge separation and charge recombination at donor/acceptor (D/A) interfaces on the performance of a conjugated polymer PTB7-Th device with three fullerene acceptors: PC71BM, PC61BM and IC60BA. Time-resolved laser spectroscopy and high-resolution electron microscopy can illustrate the basis for fabricating solar cell devices with improved performances. In addition, we studied the effects of the incorporation of heavy metals into π-conjugated chromophores on electron transfer by monitoring the triplet state lifetime of the oligomer using transient absorption spectroscopy, as understanding the mechanisms controlling intersystem crossing and

  3. Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen Li [Department of Dynamics at Surfaces, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen (Germany); Ueta, Hirokazu; Beck, Rainer D. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Federale de Lausanne (Switzerland); Bisson, Regis [Aix-Marseille Universite, PIIM, CNRS, UMR 7345, 13397 Marseille (France)

    2013-05-15

    We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S({theta}). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.

  4. Predictors of chronic ankle instability: Analysis of peroneal reaction time, dynamic balance and isokinetic strength.

    Science.gov (United States)

    Sierra-Guzmán, Rafael; Jiménez, Fernando; Abián-Vicén, Javier

    2018-05-01

    Previous studies have reported the factors contributing to chronic ankle instability, which could lead to more effective treatments. However, factors such as the reflex response and ankle muscle strength have not been taken into account in previous investigations. Fifty recreational athletes with chronic ankle instability and 55 healthy controls were recruited. Peroneal reaction time in response to sudden inversion, isokinetic evertor muscle strength and dynamic balance with the Star Excursion Balance Test and the Biodex Stability System were measured. The relationship between the Cumberland Ankle Instability Tool score and performance on each test was assessed and a backward multiple linear regression analysis was conducted. Participants with chronic ankle instability showed prolonged peroneal reaction time, poor performance in the Biodex Stability System and decreased reach distance in the Star Excursion Balance Test. No significant differences were found in eversion and inversion peak torque. Moderate correlations were found between the Cumberland Ankle Instability Tool score and the peroneal reaction time and performance on the Star Excursion Balance Test. Peroneus brevis reaction time and the posteromedial and lateral directions of the Star Excursion Balance Test accounted for 36% of the variance in the Cumberland Ankle Instability Tool. Dynamic balance deficits and delayed peroneal reaction time are present in participants with chronic ankle instability. Peroneus brevis reaction time and the posteromedial and lateral directions of the Star Excursion Balance Test were the main contributing factors to the Cumberland Ankle Instability Tool score. No clear strength impairments were reported in unstable ankles. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Effect of loading rate on dynamic fracture of reaction bonded silicon nitride

    Science.gov (United States)

    Liaw, B. M.; Kobayashi, A. S.; Emery, A. F.

    1986-01-01

    Wedge-loaded, modified tapered double cantilever beam (WL-MTDCB) specimens under impact loading were used to determine the room temperature dynamic fracture response of reaction bonded silicon nitride (RBSN). The crack extension history, with the exception of the terminal phase, was similar to that obtained under static loading. Like its static counterpart, a distinct crack acceleration phase, which was not observed in dynamic fracture of steel and brittle polymers, was noted. Unlike its static counterpart, the crack continued to propagate at nearly its terminal velocity under a low dynamic stress intensity factor during the terminal phase of crack propagation. These and previously obtained results for glass and RBSN show that dynamic crack arrest under a positive dynamic stress intensity factor is unlikely in static and impact loaded structural ceramics.

  6. Reaction

    African Journals Online (AJOL)

    abp

    19 oct. 2017 ... Reaction to Mohamed Said Nakhli et al. concerning the article: "When the axillary block remains the only alternative in a 5 year old child". .... Bertini L1, Savoia G, De Nicola A, Ivani G, Gravino E, Albani A et al ... 2010;7(2):101-.

  7. Capturing Chemistry in Action with Electrons: Realization of Atomically Resolved Reaction Dynamics.

    Science.gov (United States)

    Ischenko, Anatoly A; Weber, Peter M; Miller, R J Dwayne

    2017-08-23

    One of the grand challenges in chemistry has been to directly observe atomic motions during chemical processes. The depiction of the nuclear configurations in space-time to understand barrier crossing events has served as a unifying intellectual theme connecting the different disciplines of chemistry. This challenge has been cast as an imaging problem in which the technical issues reduce to achieving not only sufficient simultaneous space-time resolution but also brightness for sufficient image contrast to capture the atomic motions. This objective has been met with electrons as the imaging source. The review chronicles the first use of electron structural probes to study reactive intermediates, to the development of high bunch charge electron pulses with sufficient combined spatial-temporal resolution and intensity to literally light up atomic motions, as well as the means to characterize the electron pulses in terms of temporal brightness and image reconstruction. The use of femtosecond Rydberg spectroscopy as a novel means to use internal electron scattering within the molecular reference frame to obtain similar information on reaction dynamics is also discussed. The focus is on atomically resolved chemical reaction dynamics with pertinent references to work in other areas and forms of spectroscopy that provide additional information. Effectively, we can now directly observe the far-from-equilibrium atomic motions involved in barrier crossing and categorize chemistry in terms of a power spectrum of a few dominant reaction modes. It is this reduction in dimensionality that makes chemical reaction mechanisms transferrable to seemingly arbitrarily complex (large N) systems, up to molecules as large as biological macromolecules (N > 1000 atoms). We now have a new way to reformulate reaction mechanisms using an experimentally determined dynamic mode basis that in combination with recent theoretical advances has the potential to lead to a new conceptual basis for

  8. Coarse-grained molecular dynamics simulations of polymerization with forward and backward reactions.

    Science.gov (United States)

    Krajniak, Jakub; Zhang, Zidan; Pandiyan, Sudharsan; Nies, Eric; Samaey, Giovanni

    2018-06-11

    We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e.g. water molecules or development of polymer morphology during the process of splitting off byproduct molecules. Another concept that could be studied is the degradation of polymeric materials, a very important topic in a recycling of polymer waste. We illustrate the method by simulating the polymerization of polyethylene terephthalate (PET) at the coarse-grained level as an example of a polycondensation reaction with water as a byproduct. The algorithms are implemented in a publicly available software package and are easily accessible using a domain-specific language that describes chemical reactions in an input configuration file. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  9. Classical molecular dynamics simulation of weakly-bound projectile heavy-ion reactions

    Directory of Open Access Journals (Sweden)

    Morker Mitul R.

    2015-01-01

    Full Text Available A 3-body classical molecular dynamics approach for heavy-ion reactions involving weakly bound projectiles is developed. In this approach a weakly bound projectile is constructed as a two-body cluster of the constituent tightly bound nuclei in a configuration corresponding to the observed breakup energy. This 3-body system with their individual nucleon configuration in their ground state is dynamically evolved for given initial conditions using the three-stage classical molecular dynamics approach (3S-CMD. Various levels of rigidbody constraints on the projectile constituents and the target are considered at appropriate stages. This 3-dimensional approach explicitly takes into account not only the long range Coulomb reorientation of the deformed collision partner but internal excitations and breakup probabilities at distances close to the barrier also. Dynamical simulations of 6Li+209Bi show all the possible reaction mechanism like complete fusion, incomplete fusion, scattering and breakup scattering. Complete fusion cross sections of 6Li+209Bi and 7Li+209Bi reactions are calculated in this approach with systematic relaxations of the rigid-body constraints on one or more constituent nuclei.

  10. Competition between abstraction and exchange channels in H + HCN reaction: Full-dimensional quantum dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Bin; Guo, Hua, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2013-12-14

    Dynamics of the title reaction is investigated on an ab initio based potential energy surface using a full-dimensional quantum wave packet method within the centrifugal sudden approximation. It is shown that the reaction between H and HCN leads to both the hydrogen exchange and hydrogen abstraction channels. The exchange channel has a lower threshold and larger cross section than the abstraction channel. It also has more oscillations due apparently to quantum resonances. Both channels are affected by long-lived resonances supported by potential wells. Comparison with experimental cross sections indicates underestimation of the abstraction barrier height.

  11. Low energy ion-molecule reaction dynamics and chemiionization kinetics: Progress report, February 1, 1985-January 31, 1988

    International Nuclear Information System (INIS)

    Farrar, J.M.

    1988-01-01

    The research program at Rochester is devoted to an understanding of the dynamics of elementary gas phase ionic reactions by using the molecular beam methods. We seek to elucidate pathways for energy disposal in elementary reactions, with the goal of using this information to understand the topology of the potential surfaces which govern the reaction, applying the results to ionic channels in combustion systems. We have made significant accomplishments in several distinct areas of research in crossed beam studies of ion-neutral reaction dynamics in the past three years. Our research has focused on the following topics and has resulted in 15 publications and submissions to major journals, with several additional manuscripts in preparation: dynamics of gas phase proton transfer reactions, gas phase carbon and methyl cation chemistry, reactive scattering from double minimum potentials, reactions of highly vibrationally excited ions: NH 3 + + D 2 , and electron and proton transfer reactions of anions. 9 refs

  12. Dynamics of interface in three-dimensional anisotropic bistable reaction-diffusion system

    International Nuclear Information System (INIS)

    He Zhizhu; Liu, Jing

    2010-01-01

    This paper presents a theoretical investigation of dynamics of interface (wave front) in three-dimensional (3D) reaction-diffusion (RD) system for bistable media with anisotropy constructed by means of anisotropic surface tension. An equation of motion for the wave front is derived to carry out stability analysis of transverse perturbations, which discloses mechanism of pattern formation such as labyrinthine in 3D bistable media. Particularly, the effects of anisotropy on wave propagation are studied. It was found that, sufficiently strong anisotropy can induce dynamical instabilities and lead to breakup of the wave front. With the fast-inhibitor limit, the bistable system can further be described by a variational dynamics so that the boundary integral method is adopted to study the dynamics of wave fronts.

  13. Reaction Ensemble Molecular Dynamics: Direct Simulation of the Dynamic Equilibrium Properties of Chemically Reacting Mixtures

    Czech Academy of Sciences Publication Activity Database

    Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.

    2004-01-01

    Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004

  14. Full Dynamic Reactions in the Basic Shaft Bearings of Big Band Saw Machines

    Science.gov (United States)

    Marinov, Boycho

    2013-03-01

    The band saws machines are a certain class woodworking machines for longitudinal or transversal cutting as well as for curvilinear wood cutting. These machines saw the wood through a band-saw blade and two feeding wheels. These wheels usually are very large and they are produced with inaccuracies. The centre of mass of the disc is displaced from the axis of rotation of the distance e (eccentricity) and the axis of the disk makes an angle with the axis of rotation. In this paper, the dy- namic reactions in the bearings of the basic shaft, which drives the band saw machines, are analyzed. These reactions are caused by the external loading and the kinematics and the mass characteristics of the rotating disk. The expressions for the full dynamic reactions are obtained. These expressions allow the parameters of the machines to be chosen in such a way that the loading in the shaft and the bearings to be minimal.

  15. Incident angle dependence of reactions between graphene and hydrogen atom by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Saito, Seiki; Nakamura, Hiroaki; Ito, Atsushi

    2010-01-01

    Incident angle dependence of reactions between graphene and hydrogen atoms are obtained qualitatively by classical molecular dynamics simulation under the NVE condition with modified Brenner reactive empirical bond order (REBO) potential. Chemical reaction depends on two parameters, i.e., polar angle θ and azimuthal angle φ of the incident hydrogen. From the simulation results, it is found that the reaction rates strongly depend on polar angle θ. Reflection rate becomes larger with increasing θ, and the θ dependence of adsorption rate is also found. The θ dependence is caused by three dimensional structure of the small potential barrier which covers adsorption sites. φ dependence of penetration rate is also found for large θ. (author)

  16. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

    Science.gov (United States)

    Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

    2014-10-14

    The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a

  17. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    International Nuclear Information System (INIS)

    Lespade, Laure

    2016-01-01

    Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH · or ABTS ·+ is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  18. Heavy ion collision dynamics of 10,11B+10,11B reactions

    Directory of Open Access Journals (Sweden)

    Singh BirBikram

    2015-01-01

    Full Text Available The dynamical cluster-decay model (DCM of Gupta and collaborators has been applied successfully to the decay of very-light (A ∼ 30, light (A ∼ 40−80, medium, heavy and super-heavy mass compound nuclei for their decay to light particles (evaporation residues, ER, fusion-fission (ff, and quasi-fission (qf depending on the reaction conditions. We intend to extend here the application of DCM to study the extreme case of decay of very-light nuclear systems 20,21,22Ne∗ formed in 10,11B+10,11B reactions, for which experimental data is available for their binary symmetric decay (BSD cross sections, i.e., σBSD. For the systems under study, the calculations are presented for the σBSD in terms of their preformation and barrier penetration probabilities P0 and P. Interesting results are that in the decay of such lighter systems there is a competing reaction mechanism (specifically, the deep inelastic orbiting of non-compound nucleus (nCN origin together with ff. We have emipirically estimated the contribution of σnCN. Moreover, the important role of nuclear structure characteristics via P0 as well as angular momentum ℓ in the reaction dynamics are explored in the study.

  19. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Energy Technology Data Exchange (ETDEWEB)

    Lespade, Laure, E-mail: l.lespade@ism.u-bordeaux1.fr

    2016-08-22

    Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH{sup ·} or ABTS{sup ·+} is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  20. Study of dynamics of glucose-glucose oxidase-ferricyanide reaction

    Science.gov (United States)

    Nováková, A.; Schreiberová, L.; Schreiber, I.

    2011-12-01

    This work is focused on dynamics of the glucose-glucose oxidase-ferricyanide enzymatic reaction with or without sodium hydroxide in a continuous-flow stirred tank reactor (CSTR) and in a batch reactor. This reaction exhibits pH-variations having autocatalytic character and is reported to provide nonlinear dynamic behavior (bistability, excitability). The dynamical behavior of the reaction was examined within a wide range of inlet parameters. The main inlet parameters were the ratio of concentrations of sodium hydroxide and ferricyanide and the flow rate. In a batch reactor we observed an autocatalytic drop of pH from slightly basic to medium acidic values. In a CSTR our aim was to find bistability in the presence of sodium hydroxide. However, only a basic steady state was found. In order to reach an acidic steady state, we investigated the system in the absence of sodium hydroxide. Under these conditions the transition from the basic to the acidic steady state was observed when inlet glucose concentration was increased.

  1. Molecular-dynamics analysis of mobile helium cluster reactions near surfaces of plasma-exposed tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D. [Department of Chemical Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)

    2015-10-28

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.

  2. Theory of the reaction dynamics of small molecules on metal surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Bret [Univ. of Massachusetts, Amherst, MA (United States)

    2016-09-09

    The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H2, H2O and CH4 on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimental data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C-covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).

  3. Turing instability and bifurcation analysis in a diffusive bimolecular system with delayed feedback

    Science.gov (United States)

    Wei, Xin; Wei, Junjie

    2017-09-01

    A diffusive autocatalytic bimolecular model with delayed feedback subject to Neumann boundary conditions is considered. We mainly study the stability of the unique positive equilibrium and the existence of periodic solutions. Our study shows that diffusion can give rise to Turing instability, and the time delay can affect the stability of the positive equilibrium and result in the occurrence of Hopf bifurcations. By applying the normal form theory and center manifold reduction for partial functional differential equations, we investigate the stability and direction of the bifurcations. Finally, we give some simulations to illustrate our theoretical results.

  4. Dynamical Dipole and Equation of State in N/Z Asymmetric Fusion Reactions

    Directory of Open Access Journals (Sweden)

    Giaz Agnese

    2014-03-01

    Full Text Available In heavy ion reactions, in the case of N/Z asymmetry between projectile and target, the process leading to complete fusion is expected to produce pre-equilibrium dipole γ-ray emission. It is generated during the charge equilibration process and it is known as Dynamical Dipole. A new measurement of the dynamical dipole emission was performed by studying 16O + 116Sn at 12 MeV/u. These data, together with those measured at 8.1 MeV/u and 15.6 MeV/u for the same reaction, provide the dependence on the Dynamical Dipole total emission yield with beam energy and they can be compared with theoretical expectations. The experimental results show a weak increase of the Dynamical Dipole total yield with beam energies and are in agreement with the prediction of a theoretical model based on the Boltzmann–Nordheim–Vlasov (BNV approach. The measured trend with beam energy does not confirm the rise and fall behavior previously reported for the same fused compound but with a much higher dipole moment.

  5. Global dynamics of a nonlocal delayed reaction-diffusion equation on a half plane

    Science.gov (United States)

    Hu, Wenjie; Duan, Yueliang

    2018-04-01

    We consider a delayed reaction-diffusion equation with spatial nonlocality on a half plane that describes population dynamics of a two-stage species living in a semi-infinite environment. A Neumann boundary condition is imposed accounting for an isolated domain. To describe the global dynamics, we first establish some a priori estimate for nontrivial solutions after investigating asymptotic properties of the nonlocal delayed effect and the diffusion operator, which enables us to show the permanence of the equation with respect to the compact open topology. We then employ standard dynamical system arguments to establish the global attractivity of the nontrivial equilibrium. The main results are illustrated by the diffusive Nicholson's blowfly equation and the diffusive Mackey-Glass equation.

  6. Role of rotational energy component in the dynamics of 16O+198Pt reaction

    Directory of Open Access Journals (Sweden)

    Sharma Manoj K.

    2017-01-01

    Full Text Available The role of rotational energy is investigated in reference to the dynamics of 16O+198Pt →214Rn∗ reaction using the sticking (IS and the non-sticking (INS limits of moment of inertia within the framework of dynamical cluster decay model. The decay barrier height and barrier position get significantly modified for the use of sticking or non-sticking choice, which in turn reproduce the evaporation residue and the fusion-fission cross-sections nicely by the IS approach, while the INS approach provides feasible addressal of data only for evaporation residue channel. Moreover, the fragmentation path of decaying fragments of 214Rn∗ compound nucleus gets influenced for different choices of moment of inertia. Beside this, the role of nuclear deformations i.e. static, dynamic quadurpole (β2 and higher order static deformation up to β4 are duly investigated for both choices of the moment of inertia.

  7. Reaction of hydrogen atoms with acrylaldehyde

    International Nuclear Information System (INIS)

    Koda, Seiichiro; Nakamura, Kazumoto; Hoshino, Takashi; Hikita, Tsutomu

    1978-01-01

    The reaction of hydrogen atoms with acrylaldehyde was investigated in a fast flow reactor equipped with a time-of-flight type mass spectrometer under reduced pressure. Main reaction products were carbon monoxide, ethylene, ethane, methane, and propanal. Consideration of the distributions of the reaction products under various reaction conditions showed that hydrogen atoms attacked the C=C double bond, especially its inner carbon side under reduced pressure. Resulting hot radicals caused subsequent reactions. The relative value of the apparent bimolecular rate constant of the reaction against that of trans-2-butene with hydrogen atoms was 1.6+-0.2, which supported the above-mentioned initial reaction. (auth.)

  8. Dynamically adjustable foot-ground contact model to estimate ground reaction force during walking and running.

    Science.gov (United States)

    Jung, Yihwan; Jung, Moonki; Ryu, Jiseon; Yoon, Sukhoon; Park, Sang-Kyoon; Koo, Seungbum

    2016-03-01

    Human dynamic models have been used to estimate joint kinetics during various activities. Kinetics estimation is in demand in sports and clinical applications where data on external forces, such as the ground reaction force (GRF), are not available. The purpose of this study was to estimate the GRF during gait by utilizing distance- and velocity-dependent force models between the foot and ground in an inverse-dynamics-based optimization. Ten males were tested as they walked at four different speeds on a force plate-embedded treadmill system. The full-GRF model whose foot-ground reaction elements were dynamically adjusted according to vertical displacement and anterior-posterior speed between the foot and ground was implemented in a full-body skeletal model. The model estimated the vertical and shear forces of the GRF from body kinematics. The shear-GRF model with dynamically adjustable shear reaction elements according to the input vertical force was also implemented in the foot of a full-body skeletal model. Shear forces of the GRF were estimated from body kinematics, vertical GRF, and center of pressure. The estimated full GRF had the lowest root mean square (RMS) errors at the slow walking speed (1.0m/s) with 4.2, 1.3, and 5.7% BW for anterior-posterior, medial-lateral, and vertical forces, respectively. The estimated shear forces were not significantly different between the full-GRF and shear-GRF models, but the RMS errors of the estimated knee joint kinetics were significantly lower for the shear-GRF model. Providing COP and vertical GRF with sensors, such as an insole-type pressure mat, can help estimate shear forces of the GRF and increase accuracy for estimation of joint kinetics. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Effects of geminate and bimolecular recombination on the performance of polymeric-small molecular solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Schubert, Marcel; Yin, Chunhong; Castellani, Mauro; Neher, Dieter [University of Potsdam, Institute of Physics and Astronomy, 14476 Potsdam-Golm (Germany); Sellinger, Alan [IMRE, 3 Research Link, 117602 Singapore (Singapore)

    2009-07-01

    Many physical properties of organic photovoltaics are related to the nature of the geminate pair, an intermediate state that forms after dissociation of photogenerated excitons and prior to free charge carrier generation. Whereas it was found that photocurrent generation is dominated by the strong field dependent process of geminate pair dissociation, the recombination of uncorrelated free charge carriers and the formation of space charge seem to play a minor role in the prominent P3HT/PCBM combination. The situation may change, when using different D/A combinations or other soluble acceptor molecules. We present organic solar cells comprising a novel small molecule based on 2-vinyl-4,5-dicyanoimidazole (Vinazene) as acceptor and M3EH-PPV as donor. While bilayer devices show promising results with a fill factor up to 57 %, the IU-characteristics of bulk heterojunction devices are dominated by bimolecular recombination and space charge effects even at moderate illumination intensities. Photo-CELIV measurements were performed to study the bimolecular recombination in detail. By combining photo-CELIV results with PL and IU measurements we are able to analyze the interrelation of recombination losses, free charge carrier generation and exciplex formation.

  10. ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.

    Directory of Open Access Journals (Sweden)

    Johannes Schöneberg

    Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.

  11. Effect of vibrational excitation on the dynamics of ion-molecule reactions

    International Nuclear Information System (INIS)

    Anderson, S.L.

    1981-11-01

    A new experimental technique for the study of vibrational effects on ion-molecule reaction cross sections is described. Vibrational and collision energy dependent cross sections are presented for proton and H atom transfer, charge transfer and collision induced dissociation reactions in various isotopic H 2 + + H 2 systems. Charge and proton transfer cross sections are presented for the reactions of H 2 + and D 2 + with Ar, N 2 , CO, and O 2 . All the reactions are shown to be highly influenced by avoided crossings between the ground and first excited potential energy surfaces. Because of the nature of the crossings, vibrational motion of the systems can cause both adiabatic and non-adiabatic behavior of the system. This makes the vibrational dependences of the various cross sections a very sensitive probe of the dynamics of the collisions particularly, their behavior in the region of the crossings. Evidence is seen for charge transfer between reagents as they approach each other, transition to and in some cases reactions on excited potential energy surfaces, competition between different channels, and strong coupling of proton and charge transfer channels which occurs only for two of the systems studied (H 2 + + Ar, N 2 ). Oscillatory structure is observed in the collision energy dependence of the endoergic H 2 + (v = 0) + Ar charge transfer reaction for the first time, and a simple model which is commonly used for atom-atom charge transfer is used to fit the peaks. Finally a simple model is used to assess the importance of energy resonance and Franck-Condon effects on molecular charge transfer

  12. Fast fission phenomenon, deep inelastic reactions and compound nucleus formation described within a dynamical macroscopic model

    International Nuclear Information System (INIS)

    Gregoire, C.; Ngo, C.; Remaud, B.

    1982-01-01

    We present a dynamical model to describe dissipative heavy ion reactions. It treats explicitly the relative motion of the two ions, the mass asymmetry of the system and the projection of the isospin of each ion. The deformations, which are induced during the collision, are simulated with a time-dependent interaction potential. This is done by a time-dependent transition between a sudden interaction potential in the entrance channel and an adiabatic potential in the exit channel. The model allows us to compute the compound-nucleus cross section and multidifferential cross-sections for deep inelastic reactions. In addition, for some systems, and under certain conditions which are discussed in detail, a new dissipative heavy ion collision appears: fast-fission phenomenon which has intermediate properties between deep inelastic and compound nucleus reactions. The calculated properties concerning fast fission are compared with experimental results and reproduce some of those which could not be understood as belonging to deep inelastic or compound-nucleus reactions. (orig.)

  13. Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Battaglia, Francine [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Agblevor, Foster [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Klein, Michael [Univ. of Delaware, Newark, DE (United States); Sheikhi, Reza [Northeastern Univ., Boston, MA (United States)

    2015-12-31

    A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.

  14. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multizone Reaction Kinetics: Modeling of Decarburization

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoffrey; Akbar Rhamdhani, M.; Li, Zushu; Schrama, Frank N. H.; Overbosch, Aart

    2018-03-01

    In a previous study by the authors (Rout et al. in Metall Mater Trans B 49:537-557, 2018), a dynamic model for the BOF, employing the concept of multizone kinetics was developed. In the current study, the kinetics of decarburization reaction is investigated. The jet impact and slag-metal emulsion zones were identified to be primary zones for carbon oxidation. The dynamic parameters in the rate equation of decarburization such as residence time of metal drops in the emulsion, interfacial area evolution, initial size, and the effects of surface-active oxides have been included in the kinetic rate equation of the metal droplet. A modified mass-transfer coefficient based on the ideal Langmuir adsorption equilibrium has been proposed to take into account the surface blockage effects of SiO2 and P2O5 in slag on the decarburization kinetics of a metal droplet in the emulsion. Further, a size distribution function has been included in the rate equation to evaluate the effect of droplet size on reaction kinetics. The mathematical simulation indicates that decarburization of the droplet in the emulsion is a strong function of the initial size and residence time. A modified droplet generation rate proposed previously by the authors has been used to estimate the total decarburization rate by slag-metal emulsion. The model's prediction shows that about 76 pct of total carbon is removed by reactions in the emulsion, and the remaining is removed by reactions at the jet impact zone. The predicted bath carbon by the model has been found to be in good agreement with the industrially measured data.

  15. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multizone Reaction Kinetics: Modeling of Decarburization

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoffrey; Akbar Rhamdhani, M.; Li, Zushu; Schrama, Frank N. H.; Overbosch, Aart

    2018-06-01

    In a previous study by the authors (Rout et al. in Metall Mater Trans B 49:537-557, 2018), a dynamic model for the BOF, employing the concept of multizone kinetics was developed. In the current study, the kinetics of decarburization reaction is investigated. The jet impact and slag-metal emulsion zones were identified to be primary zones for carbon oxidation. The dynamic parameters in the rate equation of decarburization such as residence time of metal drops in the emulsion, interfacial area evolution, initial size, and the effects of surface-active oxides have been included in the kinetic rate equation of the metal droplet. A modified mass-transfer coefficient based on the ideal Langmuir adsorption equilibrium has been proposed to take into account the surface blockage effects of SiO2 and P2O5 in slag on the decarburization kinetics of a metal droplet in the emulsion. Further, a size distribution function has been included in the rate equation to evaluate the effect of droplet size on reaction kinetics. The mathematical simulation indicates that decarburization of the droplet in the emulsion is a strong function of the initial size and residence time. A modified droplet generation rate proposed previously by the authors has been used to estimate the total decarburization rate by slag-metal emulsion. The model's prediction shows that about 76 pct of total carbon is removed by reactions in the emulsion, and the remaining is removed by reactions at the jet impact zone. The predicted bath carbon by the model has been found to be in good agreement with the industrially measured data.

  16. Dynamics of the fusion reaction in the dtμ- system

    International Nuclear Information System (INIS)

    Belyaev, V.B.; Revai, J.; Zubarev, A.L.

    1988-08-01

    A dynamical scheme based on the (td,αn) two-channel model is derived for the description of the fusion reaction in the dtμ - system. Special attention is paid to the correct specification of the final states. Several possibilities are pointed out for the systematic improvement of the sudden approximation for the sticking coefficient. It seems to be useful to outline a general formulation of these processes which would allow a clear comparison of existing approaches. The lack of satisfactory agreement between experimental and theoretical values of the sticking coefficient is a further argument in favour of the programme. (R.P.) 10 refs

  17. Collective flow as a probe of heavy-ion reaction dynamics

    International Nuclear Information System (INIS)

    Awes, T.C.

    1997-01-01

    Collective flow of nuclear matter probes the dynamics of heavy-ion reactions and can provide information about the nuclear-matter equation of state. In particular, the incident energy dependences of collective flow may be a sensitive means to deduce the existence of a Quark Gluon Plasma phase in the equation of state. Collective flow measurements from 30 A MeV to 200 A GeV incident energies are briefly reviewed. Preliminary results on collective flow from the WA98 experiment at the CERN SPS are presented

  18. CHEMICAL REACTIONS ON ADSORBING SURFACE: KINETIC LEVEL OF DESCRIPTION

    Directory of Open Access Journals (Sweden)

    P.P.Kostrobii

    2003-01-01

    Full Text Available Based on the effective Hubbard model we suggest a statistical description of reaction-diffusion processes for bimolecular chemical reactions of gas particles adsorbed on the metallic surface. The system of transport equations for description of particles diffusion as well as reactions is obtained. We carry out the analysis of the contributions of all physical processes to the formation of diffusion coefficients and chemical reactions constants.

  19. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems—an analytical theory

    International Nuclear Information System (INIS)

    Qian, Hong

    2011-01-01

    The nonlinear dynamics of biochemical reactions in a small-sized system on the order of a cell are stochastic. Assuming spatial homogeneity, the populations of n molecular species follow a multi-dimensional birth-and-death process on Z n . We introduce the Delbrück–Gillespie process, a continuous-time Markov jump process, whose Kolmogorov forward equation has been known as the chemical master equation, and whose stochastic trajectories can be computed via the Gillespie algorithm. Using simple models, we illustrate that a system of nonlinear ordinary differential equations on R n emerges in the infinite system size limit. For finite system size, transitions among multiple attractors of the nonlinear dynamical system are rare events with exponentially long transit times. There is a separation of time scales between the deterministic ODEs and the stochastic Markov jumps between attractors. No diffusion process can provide a global representation that is accurate on both short and long time scales for the nonlinear, stochastic population dynamics. On the short time scale and near deterministic stable fixed points, Ornstein–Uhlenbeck Gaussian processes give linear stochastic dynamics that exhibit time-irreversible circular motion for open, driven chemical systems. Extending this individual stochastic behaviour-based nonlinear population theory of molecular species to other biological systems is discussed. (invited article)

  20. Boron atom reactions

    International Nuclear Information System (INIS)

    Estes, R.; Tabacco, M.B.; Digiuseppe, T.G.; Davidovits, P.

    1982-01-01

    The reaction rates of atomic boron with various epoxides have been measured in a flow tube apparatus. The bimolecular rate constants, in units of cm 3 molecule -1 s -1 , are: 1,2-epoxypropane (8.6 x 10 -11 ), 1,2-epoxybutane (8.8 x 10 -11 ), 1,2,3,4-diepoxybutane (5.5 x 10 -11 ), 1-chloro-2,3-epoxypropane (5.7 x 10 -11 ), and 1,2-epoxy-3,3,3-trichloropropane (1.5 x 10 -11 ). (orig.)

  1. Vibrational transitions in hydrogen bonded bimolecular complexes – A local mode perturbation theory approach to transition frequencies and intensities

    DEFF Research Database (Denmark)

    Mackeprang, Kasper; Kjærgaard, Henrik Grum

    2017-01-01

    The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded...

  2. Interplay between excitation kinetics and reaction-center dynamics in purple bacteria

    International Nuclear Information System (INIS)

    Caycedo-Soler, Felipe; RodrIguez, Ferney J; Quiroga, Luis; Johnson, Neil F

    2010-01-01

    Photosynthesis is arguably the fundamental process of life, since it enables energy from the Sun to enter the food chain on the Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations, which traverse a complex biomolecular membrane, where they are captured and fuel chemical reactions within a reaction center (RC) in order to produce nutrients. The precise nature of these dynamical processes-which lie at the interface between quantum and classical behavior and involve both noise and coordination-is still being explored. Here, we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of the purple bacteria Rsp. photometricum. Using stochastic realizations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the RC dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.

  3. Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

    Science.gov (United States)

    Wang, Ting; Plecháč, Petr

    2017-12-01

    Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

  4. Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis.

    Science.gov (United States)

    Wang, Ting; Plecháč, Petr

    2017-12-21

    Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

  5. Cluster dynamics models of irradiation damage accumulation in ferritic iron. II. Effects of reaction dimensionality

    Energy Technology Data Exchange (ETDEWEB)

    Kohnert, Aaron A.; Wirth, Brian D. [University of Tennessee, Knoxville, Tennessee 37996-2300 (United States)

    2015-04-21

    The black dot damage features which develop in iron at low temperatures exhibit significant mobility during in situ irradiation experiments via a series of discrete, intermittent, long range hops. By incorporating this mobility into cluster dynamics models, the temperature dependence of such damage structures can be explained with a surprising degree of accuracy. Such motion, however, is one dimensional in nature. This aspect of the physics has not been fully considered in prior models. This article describes one dimensional reaction kinetics in the context of cluster dynamics and applies them to the black dot problem. This allows both a more detailed description of the mechanisms by which defects execute irradiation-induced hops while allowing a full examination of the importance of kinetic assumptions in accurately assessing the development of this irradiation microstructure. Results are presented to demonstrate whether one dimensional diffusion alters the dependence of the defect population on factors such as temperature and defect hop length. Finally, the size of interstitial loops that develop is shown to depend on the extent of the reaction volumes between interstitial clusters, as well as the dimensionality of these interactions.

  6. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data

    Directory of Open Access Journals (Sweden)

    Kansuporn eSriyudthsak

    2016-05-01

    Full Text Available The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.

  7. Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data.

    Science.gov (United States)

    Sriyudthsak, Kansuporn; Shiraishi, Fumihide; Hirai, Masami Yokota

    2016-01-01

    The high-throughput acquisition of metabolome data is greatly anticipated for the complete understanding of cellular metabolism in living organisms. A variety of analytical technologies have been developed to acquire large-scale metabolic profiles under different biological or environmental conditions. Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in the metabolic reaction network. Considerable effort has been undertaken to utilize these data for constructing a mathematical model merging system properties and quantitatively characterizing a whole metabolic system in toto. However, there are technical difficulties between benchmarking the provision and utilization of data. Although, hundreds of metabolites can be measured, which provide information on the metabolic reaction system, simultaneous measurement of thousands of metabolites is still challenging. In addition, it is nontrivial to logically predict the dynamic behaviors of unmeasurable metabolite concentrations without sufficient information on the metabolic reaction network. Yet, consolidating the advantages of advancements in both metabolomics and mathematical modeling remain to be accomplished. This review outlines the conceptual basis of and recent advances in technologies in both the research fields. It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the systems level.

  8. The Reaction Mechanism of Claisen Rearrangement Obtained by Transition State Spectroscopy and Single Direct-Dynamics Trajectory

    Directory of Open Access Journals (Sweden)

    Takayoshi Kobayashi

    2013-02-01

    Full Text Available Chemical bond breaking and formation during chemical reactions can be observed using “transition state spectroscopy”. Comparing the measurement result of the transition state spectroscopy with the simulation result of single direct-dynamics trajectory, we have elucidated the reaction dynamics of Claisen rearrangement of allyl vinyl ether. Observed the reaction of the neat sample liquid, we have estimated the time constants of transformation from straight-chain structure to aromatic-like six-membered ring structure forming the C1-C6 bond. The result clarifies that the reaction proceeds via three steps taking longer time than expected from the gas phase calculation. This finding provides new hypothesis and discussions, helping the development of the field of reaction mechanism analysis.

  9. Ultrafast infrared studies of chemical reaction dynamics in room-temperature liquids

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Haw [Univ. of California, Berkeley, CA (United States)

    1999-11-01

    Femtosecond infrared spectroscopy provides sufficient spectral and temporal resolution to support a detailed investigation of the early events of a photochemical reaction. Previously unreported transient species that arise as intermediates during the course of a reaction may have lifetimes that are too short for conventional characterization. For these species, quantum-mechanical (density functional theoretical and ab initio) electronic structure calculations provide invaluable insight into chemical properties including molecular structure and energetic. With the combination of experimental and theoretical results, it is possible to assemble a comprehensive picture of the reaction dynamics of a system that is intricately influenced by the surrounding solvent molecules. The mechanisms of several important organometallic reactions, such as alkane C– H bond activation by η3-Tp*Rh(CO), silane Si–H bond activation by η5-CpMn(CO)2 and η5-CpRe(CO)2, as well as chlorinated methane C–Cl bond cleavage by the Re(CO)5 radical are elucidated. The results demonstrate the importance of molecular morphology change (C–H and Si–H act ivat ion), solvent rearrangement (Si–H activation), intersystem crossing (Si–H activation), and solvent caging (C–Cl cleavage) in understanding the reactivity of the organometallic species, The nature of the apparent free-energy barrier for C–H, Si–H, and C–Cl bond activation reaction is found to be- cleavage of an alkane C–H bond, rearrangement of a silane molecule HSiR3 (R = alkyl group) from a nonreactive alkyl site to the reactive Si–H bond, and Cl atom transfer from a chlorinated methane molecule to Re(CO)5, respectively. These results support previous d initio calculations for C–H and Si–H bond activation reaction profiles which suggest that cleavage of an alkane C–H bond by a transition metal center, unlike that of a silane

  10. Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

    Science.gov (United States)

    Srinivas, Niranjan

    Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for

  11. The Lower Extremities Exoskeleton Actuator Dynamics Research Taking into Account Support Reaction

    Directory of Open Access Journals (Sweden)

    A. A. Vereikin

    2014-01-01

    Full Text Available The article shows high relevance of research, aimed at the robotic exoskeleton creation. It defines some problems related to the process of their designing; including a lack of power supply to provide enough autonomy, and difficulties of man-machine complex control. There is a review of literature on the walking robots with tree-like kinematic structure development. This work reflects the continuing investigations, currently conducted by the authors, and relies heavily on the results of previous works, devoted to this subject.The article presents the exoskeleton dynamics equation, taking into account the impact of external forces and torques, as well as external relations imposed. Using a model of lower extremities exoskeleton developed in SolidWorks software complex, baricentric parameters of the actuator links were found. The different types of movements, committed due to harmonic changes of generalized coordinates in exoskeleton degrees of mobility, equipped with electrohydraulic actuators, were analyzed. The laws of generalized coordinate changes in time, corresponding to the worst case loading, were found. All the necessary input data for the exoskeleton dynamics equation solution were determined.The numerical values of all components of the dynamics equation were obtained as result of the dynamics equation simulation. In this case, the exoskeleton actuator load capacity was assumed to be 50 kg. The article shows dependences of torque and power in the actuator degrees of mobility on the time, as well as a curve of total capacity of all drives both, ignoring and taking into consideration the support surface reactions. Obtained dependences are the initial data for the calculation of the drive system.The proposed method for determination of exoskeleton energy parameters allows developer to perform a prompt evaluation of various options for the actuator design in accordance with the selected criteria. As a main evaluation criterion, a minimum

  12. Dual level reaction-path dynamics calculations on the C2H6 + OH → C2H5 + H2O reaction

    International Nuclear Information System (INIS)

    Coitino, E.L.; Truhlar, D.G.

    1996-01-01

    Interpolated Variational Transition State Theory with Multidimensional Tunneling contributions (IVTST/MT) has been applied to the reaction of C 2 H 6 + OH, and it yields rate constants that agree well with the available experimental information. The main disadvantage of this method is the difficulty of interpolating all required information from a few points along the reaction path. A more recent alternative is Variational Transition State Theory with Multidimensional Tunneling and Interpolated Corrections (VTST/MT-IC, also called dual-level direct dynamics), in which the reaction-path properties are first determined at an economical (lower) level of theory and then open-quotes correctedclose quotes using more accurate information obtained at a higher level for a selected number of points on the reaction path. The VTST/MT-IC method also allows for interpolation through die wider reaction swath when large-curvature tunneling occurs. In the present work we examine the affordability/accuracy tradeoff for several combinations of higher and lower levels for VTST/MT-IC reaction rate calculations on the C 2 H 6 + OH process. Various levels of theory (including NDDO-SRP and ab initio ROMP2, UQCISD, UQCISD(T), and UCCSD) have been employed for the electronic structure calculations. We also compare several semiclassical approaches implemented in the POLYRATE and MORATE programs for taking tunneling effects into account

  13. Investigation of the Three-Nucleon System Dynamics in the Deuteron-Proton Breakup Reaction

    Science.gov (United States)

    Ciepał, I.; Kłos, B.; Kistryn, St.; Stephan, E.; Biegun, A.; Bodek, K.; Deltuva, A.; Epelbaum, E.; Eslami-Kalantari, M.; Fonseca, A. C.; Golak, J.; Jha, V.; Kalantar-Nayestanaki, N.; Kamada, H.; Khatri, G.; Kirillov, Da.; Kirillov, Di.; Kliczewski, St.; Kozela, A.; Kravcikova, M.; Machner, H.; Magiera, A.; Martinska, G.; Messchendorp, J.; Nogga, A.; Parol, W.; Ramazani-Moghaddam-Arani, A.; Roy, B. J.; Sakai, H.; Sekiguchi, K.; Sitnik, I.; Siudak, R.; Skibiński, R.; Sworst, R.; Urban, J.; Witała, H.; Zejma, J.

    2014-08-01

    Precise and large sets of cross section, vector A x , A y and tensor A xx , A xy , A yy analyzing power data for the 1 H( d, pp) n breakup reactions were measured at 100 and 130 MeV deuteron beam energies with the SALAD and BINA detectors at KVI and the Germanium Wall setup at FZ-Jülich. Results are compared with various theoretical approaches which model the three-nucleon system dynamics. The cross section data reveal a sizable three-nucleon force (3NF) and Coulomb force influence. In case of the analyzing powers very low sensitivity to these effects was found and the data are well describe by 2N models only. For A xy at 130 MeV, serious disagreements were observed when 3NF models are included in the calculations.

  14. Impact of transamination reactions and protein turnover on labeling dynamics in C-13-labeling experiments

    DEFF Research Database (Denmark)

    Grotkjær, Thomas; Åkesson, M.; Christensen, Bjarke

    2004-01-01

    A dynamic model describing carbon atom transitions in the central metabolism of Saccharomyces cerevisiae is used to investigate the influence of transamination reactions and protein turnover on the transient behavior of C-13-labeling chemostat experiments. The simulations performed suggest...... that carbon exchange due to transamination and protein turnover can significantly increase the required time needed for metabolites in the TCA cycle to reach isotopic steady state, which is in agreement with published experimental observations. On the other hand, transamination and protein turnover will speed...... behavior until after three residence times. These observations suggest that greater caution should be used while also pointing to new opportunities in the design and interpretation of C-13-labeling experiments....

  15. Exciton model and quantum molecular dynamics in inclusive nucleon-induced reactions

    International Nuclear Information System (INIS)

    Bevilacqua, Riccardo; Pomp, Stephan; Watanabe, Yukinobu

    2011-01-01

    We compared inclusive nucleon-induced reactions with two-component exciton model calculations and Kalbach systematics; these successfully describe the production of protons, whereas fail to reproduce the emission of composite particles, generally overestimating it. We show that the Kalbach phenomenological model needs to be revised for energies above 90 MeV; agreement improves introducing a new energy dependence for direct-like mechanisms described by the Kalbach model. Our revised model calculations suggest multiple preequilibrium emission of light charged particles. We have also compared recent neutron-induced data with quantum molecular dynamics (QMD) calculations complemented by the surface coalescence model (SCM); we observed that the SCM improves the predictive power of QMD. (author)

  16. Neural network approach to time-dependent dividing surfaces in classical reaction dynamics

    Science.gov (United States)

    Schraft, Philippe; Junginger, Andrej; Feldmaier, Matthias; Bardakcioglu, Robin; Main, Jörg; Wunner, Günter; Hernandez, Rigoberto

    2018-04-01

    In a dynamical system, the transition between reactants and products is typically mediated by an energy barrier whose properties determine the corresponding pathways and rates. The latter is the flux through a dividing surface (DS) between the two corresponding regions, and it is exact only if it is free of recrossings. For time-independent barriers, the DS can be attached to the top of the corresponding saddle point of the potential energy surface, and in time-dependent systems, the DS is a moving object. The precise determination of these direct reaction rates, e.g., using transition state theory, requires the actual construction of a DS for a given saddle geometry, which is in general a demanding methodical and computational task, especially in high-dimensional systems. In this paper, we demonstrate how such time-dependent, global, and recrossing-free DSs can be constructed using neural networks. In our approach, the neural network uses the bath coordinates and time as input, and it is trained in a way that its output provides the position of the DS along the reaction coordinate. An advantage of this procedure is that, once the neural network is trained, the complete information about the dynamical phase space separation is stored in the network's parameters, and a precise distinction between reactants and products can be made for all possible system configurations, all times, and with little computational effort. We demonstrate this general method for two- and three-dimensional systems and explain its straightforward extension to even more degrees of freedom.

  17. DYNAMIC DEUTERIUM ENRICHMENT IN COMETARY WATER VIA ELEY–RIDEAL REACTIONS

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Yunxi; Giapis, Konstantinos P., E-mail: giapis@cheme.caltech.edu [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 (United States)

    2017-01-20

    The deuterium-to-hydrogen ratio (D/H) in water found in the coma of Jupiter family comet (JFC) 67P/Churyumov–Gerasimenko was reported to be (5.3 ± 0.7) × 10{sup −4}, the highest among comets and three times the value for other JFCs with an ocean-like ratio. This discrepancy suggests the diverse origins of JFCs and clouds the issue of the origin of Earth’s oceanic water. Here we demonstrate that Eley–Rideal reactions between accelerated water ions and deuterated cometary surface analogs can lead to instantaneous deuterium enrichment in water scattered from the surface. The reaction proceeds with H{sub 2}O{sup +} abstracting adsorbed D atoms, forming an excited H{sub 2}DO* state, which dissociates subsequently to produce energetic HDO. Hydronium ions are also produced readily by the abstraction of H atoms, consistent with H{sub 3}O{sup +} detection and abundance in various comets. Experiments with water isotopologs and kinematic analysis on deuterated platinum surfaces confirmed the dynamic abstraction mechanism. The instantaneous fractionation process is independent of the surface temperature and may operate on the surface of cometary nuclei or dust grains, composed of deuterium-rich silicates and carbonaceous chondrites. The requisite energetic water ions have been detected in the coma of 67P in two populations. This dynamic fractionation process may temporarily increase the water D/H ratio, especially as the comet gets closer to the Sun. The magnitude of the effect depends on the water ion energy-flux and the deuterium content of the exposed cometary surfaces.

  18. Elderly fallers enhance dynamic stability through anticipatory postural adjustments during a choice stepping reaction time

    Directory of Open Access Journals (Sweden)

    Romain Tisserand

    2016-11-01

    Full Text Available In the case of disequilibrium, the capacity to step quickly is critical to avoid falling for elderly. This capacity can be simply assessed through the choice stepping reaction time test (CSRT, where elderly fallers (F take longer to step than elderly non-fallers (NF. However, reasons why elderly F elongate their stepping time remain unclear. The purpose of this study is to assess the characteristics of anticipated postural adjustments (APA that elderly F develop in a stepping context and their consequences on the dynamic stability. 44 community-dwelling elderly subjects (20 F and 22 NF performed a CSRT where kinematics and ground reaction forces were collected. Variables were analyzed using two-way repeated measures ANOVAs. Results for F compared to NF showed that stepping time is elongated, due to a longer APA phase. During APA, they seem to use two distinct balance strategies, depending on the axis: in the anteroposterior direction, we measured a smaller backward movement and slower peak velocity of the center of pressure (CoP; in the mediolateral direction, the CoP movement was similar in amplitude and peak velocity between groups but lasted longer. The biomechanical consequence of both strategies was an increased margin of stability (MoS at foot-off, in the respective direction. By elongating their APA, elderly F use a safer balance strategy that prioritizes dynamic stability conditions instead of the objective of the task. Such a choice in balance strategy probably comes from muscular limitations and/or a higher fear of falling and paradoxically indicates an increased risk of fall.

  19. The algorithm of numerical calculation of constraints reactions in a dynamic system of transport machine

    Science.gov (United States)

    Akhtulov, A. L.

    2018-01-01

    The questions of construction and practical application of the automation system for the design of components and aggregates for the construction of transport vehicles are considered, taking into account their dynamic characteristics. Based on the results of the studies, a unified method for determining the reactions of bonds of a complex spatial structure is proposed. The technique, based on the method of substructures, allows us to determine the values of the transfer functions taking into account the reactions of the bonds. After the carried out researches it is necessary to note, that such approach gives the most satisfactory results and can be used for calculations of complex mechanical systems of machines and units of different purposes. The directions of increasing the degree of validity of technical decisions are shown, especially in the early stages of design, when the cost of errors is high, with careful thorough working out of all the elements of the design, which is really feasible only on the basis of automation of design and technological work.

  20. Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

    Science.gov (United States)

    Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

    2014-04-11

    Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming

  1. Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization.

    Science.gov (United States)

    Tachikawa, Hiroto

    2017-06-30

    Reactions of water dimer cation (H2O)2+ following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of (H2O)2+: ground state ( 2 A″-like state) and the first excited state ( 2 A'-like state). All trajectories on the ground-state PES lead to the proton-transferred product: H 2 O + (Wd)-H 2 O(Wa) → OH(Wd)-H 3 O + (Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited-state PES gave two products: an intermediate complex with a face-to-face structure (H 2 O-OH 2 ) + and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited-state PES: H 2 O(Wd)-H 2 O + (Wa) → H 3 O + (Wd)-OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of (H2O)2+ and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  2. Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions.

    Science.gov (United States)

    Yang, Linlin; Jing, Xu; An, Bowen; He, Cheng; Yang, Yang; Duan, Chunying

    2018-01-28

    By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.

  3. Initial dynamics of the Norrish Type I reaction in acetone: probing wave packet motion.

    Science.gov (United States)

    Brogaard, Rasmus Y; Sølling, Theis I; Møller, Klaus B

    2011-02-10

    The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results.

  4. Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model

    NARCIS (Netherlands)

    Bickelhaupt, F. Matthias; Houk, Kendall N.

    2017-01-01

    The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction

  5. Femtosecond laser induced and controlled chemical reaction of carbon monoxide and hydrogen

    CSIR Research Space (South Africa)

    Du Plessis, A

    2011-07-01

    Full Text Available Results from experiments aimed at bimolecular chemical reaction control of CO and H2 at room temperature and pressure, without any catalyst, using shaped femtosecond laser pulses are presented. A stable reaction product (CO2) was measured after...

  6. Dynamics of Db isotopes formed in reactions induced by 238U, 248Cm, and 249Bk across the Coulomb barrier

    Science.gov (United States)

    Kaur, Gurjit; Sandhu, Kirandeep; Kaur, Amandeep; Sharma, Manoj K.

    2018-05-01

    The dynamical cluster decay model is employed to investigate the decay of *265Db and *267Db nuclei, formed in the 27Al+238U , 18O+249Bk , and 19F+248Cm hot fusion reactions at energies around the Coulomb barrier. First, the fission dynamics of the 27Al+238U reaction is explored by investigating the fragmentation and preformation yield of the reaction. The symmetric mass distribution of the fission fragments is observed for *265Db nucleus, when static β2 i deformations are used within hot optimum orientation approach. However, the mass split gets broaden for the use of β2 i-dynamical hot configuration of the fragments and becomes clearly asymmetric for the cold-static-deformed approach. Within the application of cold orientations of fragments, a new fission channel is observed at mass asymmetry η =0.29 . In addition to 238U-induced reaction, the work is carried out to address the fission and neutron evaporation cross sections of *267Db nucleus formed via 19F+248Cm and 18O+249Bk reactions, besides a comprehensive analysis of fusion and capture processes. Higher fusion cross sections and compound nucleus formation probabilities (PCN) are obtained for the 18O+249Bk reaction, as larger mass asymmetry in the entrance channel leads to reduced Coulomb factor. Finally, the role of sticking (IS) and nonsticking (INS) moments of inertia is analyzed for the 4 n and 5 n channels of *267Db nuclear system.

  7. Uranium analysis in urine by inductively coupled plasma dynamic reaction cell mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Ejnik, John W. [Northern Michigan University, Chemistry Department, Marquette, MI (United States); Todorov, Todor I.; Mullick, Florabel G.; Centeno, Jose A. [Armed Forces Institute of Pathology (AFIP), Division of Biophysical Toxicology, Washington, DC (United States); Squibb, Katherine; McDiarmid, Melissa A. [University of Maryland, School of Medicine, Baltimore, MD (United States)

    2005-05-01

    Urine uranium concentrations are the best biological indicator for identifying exposure to depleted uranium (DU). Internal exposure to DU causes an increased amount of urine uranium and a decreased ratio of {sup 235}U/{sup 238}U in urine samples, resulting in measurements that vary between 0.00725 and 0.002 (i.e., natural and depleted uranium's {sup 235}U/{sup 238}U ratios, respectively). A method based on inductively coupled plasma dynamic reaction cell mass spectrometry (ICP-DRC-MS) was utilized to identify DU in urine by measuring the quantity of total U and the {sup 235}U/{sup 238}U ratio. The quantitative analysis was achieved using {sup 233}U as an internal standard. The analysis was performed both with and without the reaction gas oxygen. The reaction gas converted ionized {sup 235}U{sup +} and {sup 238}U{sup +} into {sup 235}UO{sub 2}{sup +} (m/z=267) and {sup 238}UO{sub 2}{sup +} (m/z=270). This conversion was determined to be over 90% efficient. A polyatomic interference at m/z 234.8 was successfully removed from the {sup 235}U signal under either DRC operating conditions (with or without oxygen as a reaction gas). The method was validated with 15 urine samples of known uranium compositions. The method detection limit for quantification was determined to be 0.1 pg U mL{sup -1} urine and an average coefficient of variation (CV) of 1-2% within the sample measurements. The method detection limit for determining {sup 235}U/{sup 238}U ratio was 3.0 pg U mL{sup -1} urine. An additional 21 patient samples were analyzed with no information about medical history. The measured {sup 235}U/{sup 238}U ratio within the urine samples correctly identified the presence or absence of internal DU exposure in all 21 patients. (orig.)

  8. Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

    Science.gov (United States)

    2013-11-25

    reaction time, the core of the flow was sampled through a small orifice in a rounded nose cone, while the bulk of the gas was pumped by an oil free...with direct dynamics simulations,6’ 10’ 11’ 13- 17 have provided an atomistic understanding of the dynamics of gas phase x- + CH3Y reactions. In...OH- was mass selected using a quadrupole mass filter, injected into the flow tube through a Venturi inlet, and carried downstream by a helium

  9. Magnetically levitated railway with common reaction rail for a linear motor drive and an electro dynamic side guidance arrangement

    Energy Technology Data Exchange (ETDEWEB)

    Friedrich, R

    1977-04-07

    The invention concerns a magnetically levitated railway with common reaction rail for the linear motor drive and the electrical side guidance arrangement. While the electro-dynamic hovering process requires a high electrical conductivity of the reaction rails in order to reduce eddy current losses, these should show a relatively high resistance for the asynchronous linear motor to reduce losses of propelling force. These contradictory requirements can be fulfilled for a common reaction rail made of homogeneous material of high electrical conductivity according to the invention, by providing slits at right angles to the driving axis in the part of the reaction rail allocated to the linear motor. Thus the guidance system retains a low ohmic resistance, while the part of the reaction rail allocated to the windings of the linear motor has a relatively low ohmic secondary resistance, by which the border and end effects which reduce the propelling force can be appreciably reduced.

  10. Ab initio molecular dynamics study of thermite reaction at Al and CuO nano-interfaces at different temperatures

    Science.gov (United States)

    Tang, Cui-Ming; Chen, Xiao-Xu; Cheng, Xin-Lu; Zhang, Chao-Yang; Lu, Zhi-Peng

    2018-05-01

    The thermite reaction at Al/CuO nano-interfaces is investigated with ab initio molecular dynamics calculations in canonical ensemble at 500 K, 800 K, 1200 K and 1500 K, respectively. The reaction process and reaction products are analyzed in terms of chemical bonds, average charge, time constants and total potential energy. The activity of the reactants enhances with increasing temperature, which induces a faster thermite reaction. The alloy reaction obviously expands outward at Cu-rich interface of Al/CuO system, and the reaction between Al and O atoms obviously expands outward at O-rich interface as temperature increases. Different reaction products are found at the outermost layer of different interfaces in the Al/CuO system. In generally, the average charge of the outer layer aluminum atoms (i.e., Al1, Al2, Al5 and Al6) increases with temperature. The potential energy of Al/CuO system decreases significantly, which indicates that drastic exothermic reaction occurs at the Al/CuO system. This research enhances fundamental understanding in temperature effect on the thermite reaction at atomic level, which can potentially open new possibilities for its industrial application.

  11. Self-propagating exothermic reaction analysis in Ti/Al reactive films using experiments and computational fluid dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Sen, Seema, E-mail: seema.sen@tu-ilmenau.de [Technical University of Ilmenau, Department of Materials for Electronics, Gustav-Kirchhoff-Str. 5, 98693 Ilmenau (Germany); Niederrhein University of Applied Science, Department of Mechanical and Process Engineering, Reinarzstraße 49, 47805 Krefeld (Germany); Lake, Markus; Kroppen, Norman; Farber, Peter; Wilden, Johannes [Niederrhein University of Applied Science, Department of Mechanical and Process Engineering, Reinarzstraße 49, 47805 Krefeld (Germany); Schaaf, Peter [Technical University of Ilmenau, Department of Materials for Electronics, Gustav-Kirchhoff-Str. 5, 98693 Ilmenau (Germany)

    2017-02-28

    Highlights: • Development of nanoscale Ti/Al multilayer films with 1:1, 1:2 and 1:3 molar ratios. • Characterization of exothermic reaction propagation by experiments and simulation. • The reaction velocity depends on the ignition potentials and molar ratios of the films. • Only 1Ti/3Al films exhibit the unsteady reaction propagation with ripple formation. • CFD simulation shows the time dependent atom mixing and temperature flow during exothermic reaction. - Abstract: This study describes the self-propagating exothermic reaction in Ti/Al reactive multilayer foils by using experiments and computational fluid dynamics simulation. The Ti/Al foils with different molar ratios of 1Ti/1Al, 1Ti/2Al and 1Ti/3Al were fabricated by magnetron sputtering method. Microstructural characteristics of the unreacted and reacted foils were analyzed by using electronic and atomic force microscopes. After an electrical ignition, the influence of ignition potentials on reaction propagation has been experimentally investigated. The reaction front propagates with a velocity of minimum 0.68 ± 0.4 m/s and maximum 2.57 ± 0.6 m/s depending on the input ignition potentials and the chemical compositions. Here, the 1Ti/3Al reactive foil exhibits both steady state and unsteady wavelike reaction propagation. Moreover, the numerical computational fluid dynamics (CFD) simulation shows the time dependent temperature flow and atomic mixing in a nanoscale reaction zone. The CFD simulation also indicates the potentiality for simulating exothermic reaction in the nanoscale Ti/Al foil.

  12. Interactions among the early Escherichia coli divisome proteins revealed by bimolecular fluorescence complementation.

    Science.gov (United States)

    Pazos, Manuel; Natale, Paolo; Margolin, William; Vicente, Miguel

    2013-12-01

    We used bimolecular fluorescence complementation (BiFC) assays to detect protein-protein interactions of all possible pairs of the essential Escherichia coli proto-ring components, FtsZ, FtsA and ZipA, as well as the non-essential FtsZ-associated proteins ZapA and ZapB. We found an unexpected interaction between ZipA and ZapB at potential cell division sites, and when co-overproduced, they induced long narrow constrictions at division sites that were dependent on FtsZ. These assays also uncovered an interaction between ZipA and ZapA that was mediated by FtsZ. BiFC with ZapA and ZapB showed that in addition to their expected interaction at midcell, they also interact at the cell poles. BiFC detected interaction between FtsZ and ZapB at midcell and close to the poles. Results from the remaining pairwise combinations confirmed known interactions between FtsZ and ZipA, and ZapB with itself. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Bimolecular Excited-State Electron Transfer with Surprisingly Long-Lived Radical Ions

    KAUST Repository

    Alsam, Amani Abdu

    2015-09-02

    We explored the excited-state interactions of bimolecular, non-covalent systems consisting of cationic poly[(9,9-di(3,3’-N,N’-trimethyl-ammonium) propyl fluorenyl-2,7-diyl)-alt-co-(9,9-dioctyl-fluorenyl-2,7-diyl)] diiodide salt (PFN) and 1,4-dicyanobenzene (DCB) using steady-state and time-resolved techniques, including femto- and nanosecond transient absorption and femtosecond infrared spectroscopies with broadband capabilities. The experimental results demonstrated that photo-induced electron transfer from PFN to DCB occurs on the picosecond time scale, leading to the formation of PFN+• and DCB-• radical ions. Interestingly, real-time observations of the vibrational marker modes on the acceptor side provided direct evidence and insight into the electron transfer process indirectly inferred from UV-Vis experiments. The band narrowing on the picosecond time scale observed on the antisymmetric C-N stretching vibration of the DCB radical anion provides clear experimental evidence that a substantial part of the excess energy is channeled into vibrational modes of the electron transfer product and that the geminate ion pairs dissociate. More importantly, our nanosecond time-resolved data indicate that the charge-separated state is very long lived ( 30 ns) due to the dissociation of the contact radical ion pair into free ions. Finally, the fast electron transfer and slow charge recombination anticipate the current donor−acceptor system with potential applications in organic solar cells.

  14. Bimolecular Excited-State Electron Transfer with Surprisingly Long-Lived Radical Ions

    KAUST Repository

    Alsam, Amani Abdu; Aly, Shawkat Mohammede; Usman, Anwar; Parida, Manas R.; Del Gobbo, Silvano; Alarousu, Erkki; Mohammed, Omar F.

    2015-01-01

    We explored the excited-state interactions of bimolecular, non-covalent systems consisting of cationic poly[(9,9-di(3,3’-N,N’-trimethyl-ammonium) propyl fluorenyl-2,7-diyl)-alt-co-(9,9-dioctyl-fluorenyl-2,7-diyl)] diiodide salt (PFN) and 1,4-dicyanobenzene (DCB) using steady-state and time-resolved techniques, including femto- and nanosecond transient absorption and femtosecond infrared spectroscopies with broadband capabilities. The experimental results demonstrated that photo-induced electron transfer from PFN to DCB occurs on the picosecond time scale, leading to the formation of PFN+• and DCB-• radical ions. Interestingly, real-time observations of the vibrational marker modes on the acceptor side provided direct evidence and insight into the electron transfer process indirectly inferred from UV-Vis experiments. The band narrowing on the picosecond time scale observed on the antisymmetric C-N stretching vibration of the DCB radical anion provides clear experimental evidence that a substantial part of the excess energy is channeled into vibrational modes of the electron transfer product and that the geminate ion pairs dissociate. More importantly, our nanosecond time-resolved data indicate that the charge-separated state is very long lived ( 30 ns) due to the dissociation of the contact radical ion pair into free ions. Finally, the fast electron transfer and slow charge recombination anticipate the current donor−acceptor system with potential applications in organic solar cells.

  15. Bimolecular Fluorescence Complementation of Alpha-synuclein Demonstrates its Oligomerization with Dopaminergic Phenotype in Mice

    Directory of Open Access Journals (Sweden)

    Waijiao Cai

    2018-03-01

    Full Text Available Alpha-synuclein (αSyn is encoded by the first causal gene identified in Parkinson's disease (PD and is the main component of Lewy bodies, a pathological hallmark of PD. aSyn-based animal models have contributed to our understanding of PD pathophysiology and to the development of therapeutics. Overexpression of human wildtype αSyn by viral vectors in rodents recapitulates the loss of dopaminergic neurons from the substantia nigra, another defining pathological feature of the disease. The development of a rat model exhibiting bimolecular fluorescence complementation (BiFC of αSyn by recombinant adeno-associated virus facilitates detection of the toxic αSyn oligomers species. We report here neurochemical, neuropathological and behavioral characterization of BiFC of αSyn in mice. Overexpression and oligomerization of αSyn through BiFC is detected by conjugated fluorescence. Reduced striatal dopamine and loss of nigral dopaminergic neurons are accompanied neuroinflammation and abnormal motor activities. Our mouse model may provide a valuable tool to study the role of αSyn in PD and to explore therapeutic approaches. Keywords: Parkinson's disease, Alpha-synuclein, Mouse model, Oligomers, Neuroinflammation

  16. [Hypothesis and application of bimolecular marking methods in Chinese materia medica].

    Science.gov (United States)

    Huang, Lu-qi; Qian, Dan; Deng, Chao

    2015-01-01

    Based on the current shortage of genuine/false authentication and quality evaluation in the molecular identification, and the weak functional gene research in the establishment of two-dimensional molecular markering methods for Chinese materia medica, the authors proposed a new method, the bimolecular marking methods (BIMM) for Chinese materia medica, combining DNA marker and metabolomics marker, that could simultaneously research the species and quality differences at the molecular level at the present stage. The authors introduced the concept, principle, methods, and technical process of BIMM, and summarized the technical advantages in this paper. Meanwhile, the application of BIMM in the identification of multiple sources of Chinese materia medica, years-identification, different locations, elite germplasm research, discovery of new drugs resources, protection of new varieties was also discussed. As a supplement of two-dimensional molecular markering method for Chinese materia medica, BIMM would not only expand connotation of identification of Chinese materia medica but also provide another effective way for quality evaluating.

  17. Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism

    Science.gov (United States)

    Zhao, Zhiqiang; Zhang, Zhaojun; Liu, Shu; Zhang, Dong H.

    2017-02-01

    Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

  18. Occurrence, dynamics and reactions of organic pollutants in the indoor environment

    Energy Technology Data Exchange (ETDEWEB)

    Salthammer, Tunga [Material Analysis and Indoor Chemistry, Fraunhofer Wilhelm-Klauditz Institut (WKI), Braunschweig (Germany); Bahadir, Muefit [Institut fuer Oekologische Chemie und Abfallanalytik, Technische Universitaet Braunschweig, Braunschweig (Germany)

    2009-06-15

    The indoor environment is a multidisciplinary scientific field involving chemistry, physics, biology, health sciences, architecture, building sciences and civil engineering. The need for reliable assessment of human exposure to indoor pollutants is attracting increasing attention. This, however, requires a detailed understanding of the relevant compounds, their sources, physical and chemical properties, dynamics, reactions, their distribution among the gas phase, airborne particles and settled dust as well as the availability of modern measurement techniques. Building products, furnishings and other indoor materials often emit volatile and semi-volatile organic compounds. With respect to a healthy indoor environment, only low emitting products, which do not influence indoor air quality in a negative way, should be used in a building. Therefore, materials and products for indoor use need to be evaluated for their chemical emissions. This is routinely done in test chambers and cells. Many studies have shown that the types of sources in occupational and residential indoor environments, the spectrum of emitting compounds and the duration of emission cover a wide range. The demand for standardized test methods under laboratory conditions has resulted in several guidelines for determination of emission rates. Furthermore, it has now been recognized that both primary and secondary emissions may affect indoor air quality. The problem may become more dominant when components of different materials can react with each other or when catalytic materials are applied. Such products derived from indoor related reactions may have a negative impact on indoor air quality due to their low odor threshold, health related properties or the formation of ultrafine particles. Several factors can influence the emission characteristics and numerous investigations have shown that indoor chemistry is of particular importance for the indoor related characterization of building product emissions

  19. Development of a new molecular dynamics method for tribochemical reaction and its application to formation dynamics of MoS2 tribofilm

    International Nuclear Information System (INIS)

    Morita, Yusuke; Onodera, Tasuku; Suzuki, Ai; Sahnoun, Riadh; Koyama, Michihisa; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A.; Shin-yoshi, Takatoshi; Nishino, Noriaki; Suzuki, Atsushi; Miyamoto, Akira

    2008-01-01

    Recently we have developed a novel molecular dynamics program NEW-RYUDO-CR, which can deal with chemical reactions. The developed method has been applied to the study of tribochemical reaction dynamics of MoS 2 tribofilm on iron surface. The initially amorphous MoS 2 layer self-organized its structure as result of the tribochemical reactions and formed layered MoS 2 tribofilm. The friction coefficient significantly decreased as the MoS 2 tribofilm was formed. Besides, sliding was observed between sulfur layers of MoS 2 tribofilms which occurred due to repulsive Coulombic interaction forces between sulfur atoms. This indicates that the formation of the layered MoS 2 tribofilm is important to achieve better lubrication properties

  20. Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation

    International Nuclear Information System (INIS)

    Higuchi, Yuji; Ishikawa, Takeshi; Ozawa, Nobuki; Chazeau, Laurent; Cavaillé, Jean-Yves; Kubo, Momoji

    2015-01-01

    Highlights: • We study the different dynamics of dissociation and recombination processes. • Hydrogen at the chain ends collides each other in the recombination process. • Dissociation and recombination processes take different pathway. - Abstract: We investigate the different dynamics of the stress-induced dissociation and recombination reactions in a model of polyethylene by a first-principles molecular dynamics simulation at the B3LYP/6-31g(d) level. The dissociation under external forces acting on the chemical reaction site at 300 K follows the same pathway as the one calculated by the static first-principles method because it has a similar activation barrier to that of the static first-principles calculation. On the other hand, in the recombination process, thermal fluctuations causes collisions between hydrogen atoms at the chain ends. Furthermore, when external forces do not directly act on the chemical reaction site, two different dissociation processes are observed. On the other hand, recombination process is not observed due to rarely contact of the radical carbon. These results indicate that dissociation and recombination dynamics are very different, showing the importance of the dynamic calculation.

  1. Dynamic thermal reaction analysis of wall structures in various cooling operation conditions

    International Nuclear Information System (INIS)

    Yan, Biao; Long, Enshen; Meng, Xi

    2015-01-01

    Highlights: • Four different envelop structures are separately built in the same test building. • Cooling temperature and operation time were chosen as perturbations. • State Space Method is used to analyze the influence of wall sequence order. • The numerical models are validated by the comparisons of theory and test results. • The contrast of temperature change of different envelop structures was stark. - Abstract: This paper proposes a methodology of performance assessing of envelops under different cooling operation conditions, by focusing on indoor temperature change and dynamic thermal behavior performance of walls. To obtain a general relationship between the thermal environment change and the reaction of envelop, variously insulated walls made with the same insulation material are separately built in the same wall of a testing building with the four different structures, namely self-heat insulation (full insulation material), exterior insulation, internal insulation and intermediate insulation. The advantage of this setting is that the test targets are exposed to the same environmental variables, and the tests results are thus comparable. The target responses to two types of perturbations, cooling temperature and operation time were chosen as the important variations in the tests. Parameters of cooling set temperature of 22 °C and 18 °C, operation and restoring time 10 min and 15 min are set in the test models, and discussed with simulation results respectively. The results reveal that the exterior insulation and internal insulation are more sensitive to thermal environment change than self-heat insulation and intermediate insulation.

  2. Fission dynamics of 240Cf* formed in 34,36S induced reactions

    Directory of Open Access Journals (Sweden)

    Jain Deepika

    2015-01-01

    Full Text Available We have studied the entrance channel effects in the decay of Compound nucleus 240Cf* formed in 34S+206Pb and 36S+204Pb reactions by using energy density dependent nuclear proximity potential in the framework of dynamical cluster-decay model (DCM. At different excitation energies, the fragmentation potential and preformation probability of decaying fragments are almost identical for both the entrance channels, which seem to suggest that decay is independent of its formation and entrance channel excitation energy. It is also observed that, with inclusion of deformation effects upto quadrupole within the optimum orientation approach, the fragmentation path governing potential energy surfaces gets modified significantly. Beside this, the fission mass distribution of Cf* isotopes is also investigated. The calculated fission cross-sections using SIII force for both the channels find nice agreement with the available experimental data for deformed choice of fragments, except at higher energies. In addition to this, the comparative analysis with Blocki based nuclear attraction is also worked out. It is observed that Blocki proximity potential accounts well for the CN decay at all energies whereas the use of EDF based nuclear potential suggests the presence of some non-compound nucleus process (such as quasi-fission (qf at higher energies.

  3. Studies of the Three-Nucleon System Dynamics in the Deuteron-Proton Breakup Reaction

    Science.gov (United States)

    Ciepał, I.; Kłos, B.; Stephan, E.; Kistryn, St.; Biegun, A.; Bodek, K.; Deltuva, A.; Epelbaum, E.; Eslami-Kalantari, M.; Fonseca, A. C.; Golak, J.; Jha, V.; Kalantar-Nayestanaki, N.; Kamada, H.; Khatri, G.; Kirillov, Da.; Kirillov, Di.; Kliczewski, St.; Kozela, A.; Kravcikova, M.; Machner, H.; Magiera, A.; Martinska, G.; Messchendorp, J.; Nogga, A.; Parol, W.; Ramazani-Moghaddam-Arani, A.; Roy, B. J.; Sakai, H.; Sekiguchi, K.; Sitnik, I.; Siudak, R.; Skibiński, R.; Sworst, R.; Urban, J.; Witała, H.; Zejma, J.

    2014-03-01

    One of the most important goals of modern nuclear physics is to contruct nuclear force model which properly describes the experimental data. To develop and test predictions of current models the breakup 1H(overrightarrow d, pp)n reaction was investigated experimentally at 100 and 130 MeV deuteron beam energies. Rich set of data for cross section, vector and tensor analyzing powers was obtained with the use of the SALAD and BINA detectors at KVI and Germanium Wall setup at FZ-Jülich. Results are compared with various theoretical approaches which describe the three-nucleon (3N) system dynamics. For correct description of the cross section data both, three-nucleon force (3NF) and Coulomb force, have to be included into calculations and influence of those ingredients is seizable at specific parts of the phase space. In case of the vector analyzing powers very low sensitivity to any effects beyond nucleon-nucleon interaction was found. At 130 MeV, the Axy data are not correctly described when 3NF models are included into calculations.

  4. Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald, E-mail: gerald.mathias@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-03-14

    In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call “Hamiltonian dielectric solvent” (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

  5. Energy transfer and reaction dynamics of matrix-isolated 1,2-difluoroethane-d4

    Science.gov (United States)

    Raff, Lionel M.

    1990-09-01

    The molecular dynamics of vibrationally excited 1,2-difluoroethane-d4 isolated in Ar, Kr, and Xe matrices at 12 K are investigated using trajectory methods. The matrix model is an fcc crystal containing 125 unit cells with 666 atoms in a cubic (5×5×5) arrangement. It is assumed that 1,2-difluoroethane-d4 is held interstitially within the volume bounded by the innermost unit cell of the crystal. The transport effects of the bulk are simulated using the velocity reset method introduced by Riley, Coltrin, and Diestler [J. Chem. Phys. 88, 5934 (1988)]. The system potential is written as the separable sum of a lattice potential, a lattice-molecule interaction and a gas-phase potential for 1,2-difluoroethane. The first two of these are assumed to have pairwise form while the molecular potential is a modified form of the global potential previously developed for 1,2-difluoroethane [J. Phys. Chem. 91, 3266 (1987)]. Calculated sublimation energies for the pure crystals are in good accord with the experimental data. The distribution of metastable-state energies for matrix-isolated 1,2-difluoroethane-d4 is Gaussian in form. In krypton, the full width at half maximum for the distribution is 0.37 eV. For a total excitation energy of 6.314 eV, the observed dynamic processes are vibrational relaxation, orientational exchange, and four-center DF elimination reactions. The first of these processes is characterized by a near linear, first-order decay curve with rate coefficients in the range 1.30-1.48×1011 s-1. The average rates in krypton and xenon are nearly equal. The process is slightly slower in argon. The decay curves exhibit characteristic high-frequency oscillations that are generally seen in energy transfer studies. It is demonstrated that these oscillations are associated with the frequencies for intramolecular energy transfer so that the entire frequency spectrum for such transfer processes can be obtained from the Fourier transform of the decay curve. Orientational

  6. Dynamics of O(3P) Reactions with Gaseous Liquid and Solid Hydrocarbons

    National Research Council Canada - National Science Library

    Hase, William L

    2006-01-01

    ...) were applied to model reactions, including 0 + ethane and related reactions. In the second phase, a semiempirical quantum chemistry method, PM3-SRP, was developed by modifying and reparametrizing the standard PM3 method to fit the ab initio data...

  7. Exact substitute processes for diffusion-reaction systems with local complete exclusion rules

    International Nuclear Information System (INIS)

    Schulz, Michael; Reineker, Peter

    2005-01-01

    Lattice systems with one species diffusion-reaction processes under local complete exclusion rules are studied analytically starting from the usual master equations with discrete variables and their corresponding representation in a Fock space. On this basis, a formulation of the transition probability as a Grassmann path integral is derived in a straightforward manner. It will be demonstrated that this Grassmann path integral is equivalent to a set of Ito stochastic differential equations. Averages of arbitrary variables and correlation functions of the underlying diffusion-reaction system can be expressed as weighted averages over all solutions of the system of stochastic differential equations. Furthermore, these differential equations are equivalent to a Fokker-Planck equation describing the probability distribution of the actual Ito solutions. This probability distribution depends on continuous variables in contrast to the original master equation, and their stochastic dynamics may be interpreted as a substitute process which is completely equivalent to the original lattice dynamics. Especially, averages and correlation functions of the continuous variables are connected to the corresponding lattice quantities by simple relations. Although the substitute process for diffusion-reaction systems with exclusion rules has some similarities to the well-known substitute process for the same system without exclusion rules, there exists a set of remarkable differences. The given approach is not only valid for the discussed single-species processes. We give sufficient arguments to show that arbitrary combinations of unimolecular and bimolecular lattice reactions under complete local exclusions may be described in terms of our approach

  8. Utilizing the dynamic stark shift as a probe for dielectric relaxation in photosynthetic reaction centers during charge separation.

    Science.gov (United States)

    Guo, Zhi; Lin, Su; Woodbury, Neal W

    2013-09-26

    In photosynthetic reaction centers, the electric field generated by light-induced charge separation produces electrochromic shifts in the transitions of reaction center pigments. The extent of this Stark shift indirectly reflects the effective field strength at a particular cofactor in the complex. The dynamics of the effective field strength near the two monomeric bacteriochlorophylls (BA and BB) in purple photosynthetic bacterial reaction centers has been explored near physiological temperature by monitoring the time-dependent Stark shift during charge separation (dynamic Stark shift). This dynamic Stark shift was determined through analysis of femtosecond time-resolved absorbance change spectra recorded in wild type reaction centers and in four mutants at position M210. In both wild type and the mutants, the kinetics of the dynamic Stark shift differ from those of electron transfer, though not in the same way. In wild type, the initial electron transfer and the increase in the effective field strength near the active-side monomer bacteriochlorophyll (BA) occur in synchrony, but the two signals diverge on the time scale of electron transfer to the quinone. In contrast, when tyrosine is replaced by aspartic acid at M210, the kinetics of the BA Stark shift and the initial electron transfer differ, but transfer to the quinone coincides with the decay of the Stark shift. This is interpreted in terms of differences in the dynamics of the local dielectric environment between the mutants and the wild type. In wild type, comparison of the Stark shifts associated with BA and BB on the two quasi-symmetric halves of the reaction center structure confirm that the effective dielectric constants near these cofactors are quite different when the reaction center is in the state P(+)QA(-), as previously determined by Steffen et al. at 1.5 K (Steffen, M. A.; et al. Science 1994, 264, 810-816). However, it is not possible to determine from static, low-temperature measurments if the

  9. Ferrocyanide Safety Project Dynamic X-Ray Diffraction studies of sodium nickel ferrocyanide reactions with equimolar nitrate/nitrite salts

    International Nuclear Information System (INIS)

    Dodds, J.N.; UNOCAL, Brea, CA

    1994-07-01

    Dynamic X-ray Diffraction (DXRD) has been to used to identify and quantify the solid state reactions that take place between sodium nickel ferrocyanide, Na 2 NiFe(CN) 6 , and equimolar concentrations of sodium nitrate/nitrite, reactions of interest to the continued environmental safety of several large underground waste storage tanks at the Hanford site in eastern Washington. The results are supportive of previous work, which indicated that endothermic dehydration and melting of the nitrates take place before the occurrence of exothermic reactions that being about 300 degrees C. The DXRD results show that a major reaction set at these temperatures is the occurrence of a series reaction that produces sodium cyanate, NaCNO, as an intermediate in a mildly exothermic first step. In the presence of gaseous oxygen, NaCNO subsequently reacts exothermally and at a faster rate to form metal oxides. Measurements of the rate of this reaction are used to estimate the heat release. Comparisons of this estimated heat release rate with heat transfer rates from a hypothetical ''hot spot'' show that, even in a worst-case scenario, the heat transfer rates are approximately eight times higher than the rate of energy release from the exothermic reactions

  10. Formation of Bimolecular Membranes from Lipid Monolayers and a Study of Their Electrical Properties

    Science.gov (United States)

    Montal, M.; Mueller, P.

    1972-01-01

    Bimolecular membranes are formed from two lipid monolayers at an air-water interface by the apposition of their hydrocarbon chains when an aperture in a Teflon partition separating two aqueous phases is lowered through the interface. Formation of the membrane is monitored by an increase of the electrical capacity, as measured with a voltage clamp. Electrical resistance of the unmodified membrane is analogous to that of conventional planar bilayers (black lipid membranes) prepared in the presence of a hydrocarbon solvent, i.e., 106-108 ohm cm2; the resistance can be lowered to values of 103 ohm cm2 by gramicidin, an antibiotic that modifies the conductance only when the membranes are of biomolecular thickness. In contrast to the resistance, there is a significant difference between the capacity of bilayers made from mono-layers and that of hydrocarbon-containing bilayers made by phase transition; the average values are 0.9 and 0.45 μF cm-2, respectively. The value of 0.9 μF cm-2 approximates that of biological membranes. Assuming a dielectric constant of 2.1 for the hydrocarbon region, the dielectric thickness, as calculated from a capacity of 0.9 μF cm-2, is 22 Å. This value is 6-10 Å smaller than the actual thickness of the hydrocarbon region of bilayers and cell membranes, as determined by x-ray diffraction. The difference may be due to a limited penetration of water into the hydrocarbon region near the ester groups that would lower the electrical resistance of this region and reduce the dielectric thickness. Asymmetric membranes have been formed by adjoining two lipid monolayers of different chemical composition. Images PMID:4509315

  11. Iteration scheme for implicit calculations of kinetic and equilibrium chemical reactions in fluid dynamics

    International Nuclear Information System (INIS)

    Ramshaw, J.D.; Chang, C.H.

    1995-01-01

    An iteration scheme for the implicit treatment of equilibrium chemical reactions in partial equilibrium flow has previously been described. Here we generalize this scheme to kinetic reactions as well as equilibrium reactions. This extends the applicability of the scheme to problems with kinetic reactions that are fast in regions of the flow field but slow in others. The resulting scheme thereby provides a single unified framework for the implicit treatment of an arbitrary number of coupled equilibrium and kinetic reactions in chemically reacting fluid flow. 10 refs., 2 figs

  12. Growth dynamics and composition of tubular structures in a reaction-precipitation system

    Science.gov (United States)

    Pagano, Jason John

    Self-organization in reaction precipitation systems occurs in many physical, chemical, biological, and geological systems. In particular, chemical reactions provide a wealth of examples for this intriguing process. Permanent tubular structures arise from the interplay of chemical and transport phenomena such as diffusion and fluid flow. These astonishing tubular structures are prevalent throughout nature. Examples include black smokers at hydrothermal vents, silica tubes in setting cement, soda-straw stalactites in caves, and biological structures such as the outer skeleton of certain algae. In this work, the aim is to establish and understand a laboratory scale model by examining the, seemingly simple, precipitation reaction between sodium silicate and copper sulfate as well as zinc sulfate. The tubular precipitation structures in so-called silica gardens are known to many scientists and non-scientists alike. However, little is known regarding their growth dynamics and chemical composition. We devised an injection technique which provides control over parameters that are not accessible in the classic silica garden system. For the example of cupric sulfate injection into waterglass solution, we identify three distinct growth regimes (jetting, popping, and budding) and study their concentration dependent transitions. Here we describe the composition and morphology of the tube material using techniques such as electron microscopy and vibrational spectroscopy. Specifically, we find that the tube wall consists of metal hydroxide that is stabilized by a thin, exterior silica layer. After synthesis the tubes can be further modified by using chemical and/or physical means. A second study aims to understand tubule formation under "reverse" conditions. More specifically, waterglass is being injected into lighter cupric sulfate solution. In these experiments, single, downward growing precipitation tubes are created. Four distinct growth regimes are observed and their

  13. Dynamical structure analysis of crystalline-state reaction and elucidation of chemical reactivity in crystalline environment

    International Nuclear Information System (INIS)

    Ohashi, Yuji

    2010-01-01

    It was found that a chiral alkyl group bonded to the cobalt atom in a cobalt complex crystal was racemized with retention of the single crystal form on exposure to visible light. Such reactions, which are called crystalline-state reactions, have been found in a variety of cobalt complex crystals. The concept of reaction cavity was introduced to explain the reaction rate quantitatively and the chirality of the photo-product. The new diffractometers and detectors were made for rapid data collection. The reaction mechanism was also elucidated using neutron diffraction analysis. The unstable reaction intermediates were analyzed using cryo-trapping method. The excited-state structures were obtained at the equilibrium state between ground and excited states. (author)

  14. Matrix photochemistry of small molecules: Influencing reaction dynamics on electronically excited hypersurfaces

    Energy Technology Data Exchange (ETDEWEB)

    Laursen, S.L.

    1990-01-01

    Investigations of chemical reactions on electronically excited reaction surfaces are presented. The role of excited-surface multiplicity is of particular interest, as are chemical reactivity and energy transfer in systems in which photochemistry is initiated through a metal atom sensitizer.'' Two approaches are employed: A heavy-atom matrix affords access to forbidden triplet reaction surfaces, eliminating the need for a potentially reactive sensitizer. Later, the role of the metal atom in the photosensitization process is examined directly.

  15. Matrix photochemistry of small molecules: Influencing reaction dynamics on electronically excited hypersurfaces

    International Nuclear Information System (INIS)

    Laursen, S.L.

    1990-01-01

    Investigations of chemical reactions on electronically excited reaction surfaces are presented. The role of excited-surface multiplicity is of particular interest, as are chemical reactivity and energy transfer in systems in which photochemistry is initiated through a metal atom ''sensitizer.'' Two approaches are employed: A heavy-atom matrix affords access to forbidden triplet reaction surfaces, eliminating the need for a potentially reactive sensitizer. Later, the role of the metal atom in the photosensitization process is examined directly

  16. Fast and stable redox reactions of MnO2/CNT hybrid electrodes for dynamically stretchable pseudocapacitors

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-01

    Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid electrodes. The extremely small relaxation time constant of less than 0.15 s indicates a fast redox reaction at the MnO2/CNT hybrid electrodes, securing a stable electrochemical performance for the dynamically stretchable pseudocapacitors. This finding and the fundamental understanding gained from the pseudo-capacitive behavior coupled with mechanical deformation under a dynamic stretching mode would provide guidance to further improve their overall performance including a higher power density than LIBs, a higher energy density than EDLCs, and a long-life cycling stability. Most importantly, these results will potentially accelerate the applications of stretchable pseudocapacitors for flexible and biomedical electronics.Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid

  17. Dynamic separation of Szilard-Chalmers reaction products applied to the trioxalatochromium ion adsorbed on anionic exchange resin

    International Nuclear Information System (INIS)

    Silva, J.B.S.

    1979-01-01

    A method of dynamic elution of recoiled 51 Cr +3 , formed by the Szilard-Chalmers reaction during the irradiation of trioxalatochromium ion adsorbed on anionic exchange resin is presented. The influence of some factors on the separation yield of chromium-51, such as: composition, concentration and flow rate of eluent, mesh size of the resin and irradiation time are studied. The results are compardd with those obtained by the static method, in which the recoiled atom is separated from the target after irradiation. Because of the high separation yield of chromium-51, the method of dynamic separation is proposed for routine production of this elemnt, with high specific activities. (author) [pt

  18. Mode specific dynamics of the H2 + CH3 → H + CH4 reaction studied using quasi-classical trajectory and eight-dimensional quantum dynamics methods

    International Nuclear Information System (INIS)

    Wang, Yan; Li, Jun; Guo, Hua; Chen, Liuyang; Yang, Minghui; Lu, Yunpeng

    2015-01-01

    An eight-dimensional quantum dynamical model is proposed and applied to the title reaction. The reaction probabilities and integral cross sections have been determined for both the ground and excited vibrational states of the two reactants. The results indicate that the H 2 stretching and CH 3 umbrella modes, along with the translational energy, strongly promote the reactivity, while the CH 3 symmetric stretching mode has a negligible effect. The observed mode specificity is confirmed by full-dimensional quasi-classical trajectory calculations. The mode specificity can be interpreted by the recently proposed sudden vector projection model, which attributes the enhancement effects of the reactant modes to their strong couplings with the reaction coordinate at the transition state

  19. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum-classical approximation. II. Proton transfer reaction in non-polar solvent

    Science.gov (United States)

    Kojima, H.; Yamada, A.; Okazaki, S.

    2015-05-01

    The intramolecular proton transfer reaction of malonaldehyde in neon solvent has been investigated by mixed quantum-classical molecular dynamics (QCMD) calculations and fully classical molecular dynamics (FCMD) calculations. Comparing these calculated results with those for malonaldehyde in water reported in Part I [A. Yamada, H. Kojima, and S. Okazaki, J. Chem. Phys. 141, 084509 (2014)], the solvent dependence of the reaction rate, the reaction mechanism involved, and the quantum effect therein have been investigated. With FCMD, the reaction rate in weakly interacting neon is lower than that in strongly interacting water. However, with QCMD, the order of the reaction rates is reversed. To investigate the mechanisms in detail, the reactions were categorized into three mechanisms: tunneling, thermal activation, and barrier vanishing. Then, the quantum and solvent effects were analyzed from the viewpoint of the reaction mechanism focusing on the shape of potential energy curve and its fluctuations. The higher reaction rate that was found for neon in QCMD compared with that found for water solvent arises from the tunneling reactions because of the nearly symmetric double-well shape of the potential curve in neon. The thermal activation and barrier vanishing reactions were also accelerated by the zero-point energy. The number of reactions based on these two mechanisms in water was greater than that in neon in both QCMD and FCMD because these reactions are dominated by the strength of solute-solvent interactions.

  20. Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

    Science.gov (United States)

    Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2014-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  1. Dynamics of activity free radical oxidation reactions in students with cerebral palsy results over the course of the educational process

    Directory of Open Access Journals (Sweden)

    Makarova E.V.

    2012-12-01

    Full Text Available The dynamics of changes activity of reactions is studied freely radical oxidize for students with the consequences of child's cerebral paralysis. 20 students took part in an experiment. Found that the course of study they have more active free radical oxidation reactions and decreases the activity of antiradical protection. Given the use of additional physical activity in aerobic training indicators intracellular antioxidant defense system increased, decreased content of reaction products of lipid peroxidation. However, increased rates of maximum oxygen consumption and increased tolerance of students with cerebral palsy to the consequences of physical activity. It is set that the pathological changes of metabolism for students ground the necessity of application of the differentiated physical loadings. The optimum forms of physical rehabilitation of the aerobic training is the dosed walking, medical swimming, dosed after distance, sometimes and by the corner of getting up pedestrian ascents. Loading is increased due to a volume, but not intensity of exercises.

  2. Quantum Dynamics Study of the Isotopic Effect on Capture Reactions: HD, D2 + CH3

    Science.gov (United States)

    Wang, Dunyou; Kwak, Dochan (Technical Monitor)

    2002-01-01

    Time-dependent wave-packet-propagation calculations are reported for the isotopic reactions, HD + CH3 and D2 + CH3, in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probabilities for different initial rotational-vibrational states are presented in this study. This study shows that excitations of the HD(D2) enhances the reactivities; whereas the excitations of the CH3 umbrella mode have the opposite effects. This is consistent with the reaction of H2 + CH3. The comparison of these three isotopic reactions also shows the isotopic effects in the initial-state-selected reaction probabilities. The cumulative reaction probabilities (CRP) are obtained by summing over initial-state-selected reaction probabilities. The energy-shift approximation to account for the contribution of degrees of freedom missing in the six dimensionality calculation is employed to obtain approximate full-dimensional CRPs. The rate constant comparison shows H2 + CH3 reaction has the biggest reactivity, then HD + CH3, and D2 + CH3 has the smallest.

  3. Direct Dynamics Simulation of the Thermal 3CH2 + 3O2 Reaction. Rate Constant and Product Branching Ratios.

    Science.gov (United States)

    Lakshmanan, Sandhiya; Pratihar, Subha; Machado, Francisco Bolivar Correto; Hase, William Louis

    2018-04-26

    The reaction of 3CH2 with 3O2 is of fundamental importance in combustion and the reaction is complex as a result of multiple extremely exothermic product channels. In the present study, direct dynamics simulations were performed to study the reaction on both the singlet and triplet potential energy surfaces (PESs). The simulations were performed at the UM06/6-311++G(d,p) level of theory. Trajectories were calculated at a temperature of 300 K and all reactive trajectories proceeded through the carbonyl oxide Criegee intermediate, CH2OO, on both the singlet and triplet PESs. The triplet surface leads to only one product channel, H2CO + O(3P), while the singlet surface leads to 8 product channels with their relative importance as: CO + H2O > CO + OH + H ~ H2CO + O(1D) > HCO + OH ~ CO2 + H2 ~ CO + H2 + O(1D) > CO2 + H + H > HCO + O(1D) + H. Reaction on the singlet PES is barrierless, consistent with experiment and the total rate constant on the singlet surface is 0.93 ± 0.22 x 10-12 cm3molecule-1s-1 in comparison to the recommended experimental rate constant of 3.3 x 10-12 cm3molecule-1s-1. The simulation product yields for the singlet PES are compared with experiment and the most significant differences are for H, CO2, and H2O. Reaction on the triplet surface is also barrierless, inconsistent with experiment. A discussion is given of the need for future calculations to address the: (1) barrier on the triplet PES for 3CH2 + 3O2 → 3CH2OO; (2) temperature dependence of the 3CH2 + 3O2 reaction rate constant and product branching ratios; and (3) possible non-RRKM dynamics of the 1CH2OO Criegee intermediate.

  4. Quantum mechanical calculations of reactive scattering cross sections in bimolecular encounters

    Science.gov (United States)

    Pirkle, J. C., Jr.

    1967-01-01

    Study applies the nonequilibrium collision theory of reaction rates to the estimation of rate constants for simple reactions. The complications in the quantum mechanical description of chemical reactions and the care needed in approximating the exact wave function for the collision are shown.

  5. NATO Advanced Research Workshop on The Theory of Chemical Reaction Dynamics

    CERN Document Server

    1986-01-01

    The calculation of cross sections and rate constants for chemical reactions in the gas phase has long been a major problem in theoretical chemistry. The need for reliable and applicable theories in this field is evident when one considers the significant recent advances that have been made in developing experimental techniques, such as lasers and molecular beams, to probe the microscopic details of chemical reactions. For example, it is now becoming possible to measure cross sections for chemical reactions state selected in the vibrational­ rotational states of both reactants and products. Furthermore, in areas such as atmospheric, combustion and interstellar chemistry, there is an urgent need for reliable reaction rate constant data over a range of temperatures, and this information is often difficult to obtain in experiments. The classical trajectory method can be applied routinely to simple reactions, but this approach neglects important quantum mechanical effects such as tunnelling and resonances. For al...

  6. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Zero Point Energy Conservation in Mu + H2 → MuH + H.

    Science.gov (United States)

    Pérez de Tudela, Ricardo; Aoiz, F J; Suleimanov, Yury V; Manolopoulos, David E

    2012-02-16

    A fundamental issue in the field of reaction dynamics is the inclusion of the quantum mechanical (QM) effects such as zero point energy (ZPE) and tunneling in molecular dynamics simulations, and in particular in the calculation of chemical reaction rates. In this work we study the chemical reaction between a muonium atom and a hydrogen molecule. The recently developed ring polymer molecular dynamics (RPMD) technique is used, and the results are compared with those of other methods. For this reaction, the thermal rate coefficients calculated with RPMD are found to be in excellent agreement with the results of an accurate QM calculation. The very minor discrepancies are within the convergence error even at very low temperatures. This exceptionally good agreement can be attributed to the dominant role of ZPE in the reaction, which is accounted for extremely well by RPMD. Tunneling only plays a minor role in the reaction.

  7. Reaction of atomic bromine with acetylene and loss rate of atmospheric acetylene due to reaction with OH, Cl, O, and Br

    Science.gov (United States)

    Payne, W. A.; Nava, D. F.; Brunning, J.; Stief, L. J.

    1986-01-01

    The first-order, diffusion, and bimolecular rate constants for the reaction Br + C2H2 yields C2H3Br are evaluated. The rate constants are measured at 210, 248, 298, and 393 K and at pressures between 15-100 torr Ar using flash photolysis combined with time-resolved detection of atomic bromine via Br resonance radiation. It is observed that the reaction is not affected by pressure or temperature and the bimolecular constant = (4.0 + or - 0.8) x 10 to the -15th cu cm/sec with an error of two standard deviations. The C2H2 + Br reaction rates are compared with reactions of C2H2 with Cl, OH, NH2, and H. The loss rates for atmospheric C2H2 for reactions with OH, Cl, O, and Br are calculated as a function of altitude.

  8. Concluding remarks presented at the Symposium on heavy ion reaction dynamics on the tandem energy region

    International Nuclear Information System (INIS)

    Betts, R.R.

    1988-01-01

    This paper discusses the divisions between different heavy ion reaction processes. Fusion, deep inelastic, quasi-elastic and elastic interactions are discussed in terms of coupled channel calculations. 20 refs., 8 figs

  9. Dynamic loadings of sodium-water reactions in LMFBR and fusion power designs

    Energy Technology Data Exchange (ETDEWEB)

    Chan, C. K.

    1977-07-01

    In liquid metal fast breeder reactor and lithium cooled fusion reactor, a sodium loop is being proposed to transfer heat from the primary coolant loop to the steam turbine cycle. Although by careful design and quality assurance programs, the probability for steam generator tube failure can be minimized, failure will still occur. The direct contact of sodium and water would cause a chemical reaction where hydrogen and sodium compounds are produced. This paper presents an evaluation of the potential hazards as a result of such a reaction. An analytical method is developed to investigate the extent of the reaction zone and the propagation of the pressure wave in the sodium system. In the calculation, the chemical reaction is assumed to be instantaneous, governed by the equation 2Na(l)+H/sub 2/O(l)..-->..Na/sub 2/O(l)+H/sub 2/(g)+31.4 K cal/gm. mole. Both the temperature and pressure rise in the reaction zone can be established from the energy balance and the equation of state for the gaseous product. As a consequence of the energy released, the chemical products suddenly expand with a high velocity. The expansion also generates a shock wave in both the water and the sodium systems. Results indicate that the reaction zone can expand in a rate of 1500 ft/sec and a shock wave with initial strength of 2300 atmospheres propagates with a speed of 8000 ft/sec into the sodium system. The propagating characteristics of the shock wave are obtained by solving the basic fluid equations. The shock wave decays rapidly, in the neighborhood of milliseconds, as soon as the reaction zone stops to expand. The decrease in the reaction zone pressure allows more water to react with the sodium and a second pulse is generated.

  10. Dynamic loadings of sodium-water reactions in LMFBR and fusion power designs

    International Nuclear Information System (INIS)

    Chan, C.K.

    1977-01-01

    In liquid metal fast breeder reactor and lithium cooled fusion reactor, a sodium loop is being proposed to transfer heat from the primary coolant loop to the steam turbine cycle. Although by careful design and quality assurance programs, the probability for steam generator tube failure can be minimized, failure will still occur. The direct contact of sodium and water would cause a chemical reaction where hydrogen and sodium compounds are produced. This paper presents an evaluation of the potential hazards as a result of such a reaction. An analytical method is developed to investigate the extent of the reaction zone and the propagation of the pressure wave in the sodium system. In the calculation, the chemical reaction is assumed to be instantaneous, governed by the equation 2Na(l)+H 2 O(l)→Na 2 O(l)+H 2 (g)+31.4 K cal/gm. mole. Both the temperature and pressure rise in the reaction zone can be established from the energy balance and the equation of state for the gaseous product. As a consequence of the energy released, the chemical products suddenly expand with a high velocity. The expansion also generates a shock wave in both the water and the sodium systems. Results indicate that the reaction zone can expand in a rate of 1500 ft/sec and a shock wave with initial strength of 2300 atmospheres propagates with a speed of 8000 ft/sec into the sodium system. The propagating characteristics of the shock wave are obtained by solving the basic fluid equations. The shock wave decays rapidly, in the neighborhood of milliseconds, as soon as the reaction zone stops to expand. The decrease in the reaction zone pressure allows more water to react with the sodium and a second pulse is generated

  11. New meson-nucleus dynamics from studies of (π,eta) and (π,2π) reactions

    International Nuclear Information System (INIS)

    Liu, L.C.

    1985-01-01

    The production of eta particles by pion collisions with nucleons, the reaction with the lowest genuine two-body reaction threshold, is discussed. For simple kinematic reasons, the threshold for nuclear pionic eta production reactions is much lower than 661 MeV. Using an off-shell model for the eta production amplitudes, theoretical cross sections are given for the reaction 3 He(π - ,eta) 3 H(g.s.) at 620 and 720 MeV/c. Pion-induced single pion production is then treated. Because the basic cross sections for this reaction becomes comparable to the pion-nucleon elastic scattering cross section at pion kinetic energies of about 600 MeV and exceeds the elastic scattering cross section at 1 GeV, it is believed that the (π,2π) reaction in complex nuclei represents a powerful tool to study nuclei at pion energies above the resonance region. Theoretical cross section ratios are given for 40 Ca at three different pion energies accessible at LAMPF. Also, the corresponding cross-section ratios are presented on a free proton. 14 refs., 7 figs

  12. Probing the role of Skyrme interactions on the fission dynamics of the {sup 6}Li + {sup 238}U reaction

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Ishita; Kumar, Raj; Sharma, Manoj K. [Thapar University, School of Physics and Materials Science, Patiala (India)

    2017-06-15

    The performance of selected five Skyrme forces (out of a set of 240), tested by Dutra et al., is analyzed in view of fusion-fission dynamics. These forces are assumed to perform better for neutron-rich systems, so the choice of the reaction is accordingly made by opting for a neutron-rich target in {sup 6}Li + {sup 238}U reaction. This reaction is diagnosed further in reference to fusion hindrance within the dynamical approach of the cluster-decay model (DCM). In order to reduce the computational time, three Skyrme forces are figured out with the criteria that these forces cover the barrier characteristics of the remaining two forces as well. The fission cross-sections are successfully addressed at low energies for the {sup 6}Li + {sup 238}U reaction. However, at relatively higher energies, the excitation functions show theoretical suppression with respect to experimental data, which may be associated with the possible existence of incomplete fusion (ICF). For ICF, we have considered that the {sup 6}Li broke into {sup 4}He + {sup 2}H, as mentioned in the experimental work. The calculations of ICF are carried out for the {sup 4}He + {sup 238}U reaction with the selected Skyrme forces at E{sub c.m.} = 26.20 and 27.51 MeV. These forces address the data nicely for the compound nucleus (CN) as well as ICF processes. Here, the NRAPR force seems to require lesser barrier modification as compared to the other forces, therefore it can be used as an alternate choice for calculating the interaction potential. Additionally, the prediction of cross-sections at lower energies has been done with DCM using the NRAPR force. The l-dependent % barrier modification of the Skyrme forces undertaken is also worked out in reference to fusion hindrance at below barrier energies. (orig.)

  13. [Study of Reaction Dynamics between Bovine Serum Albumin and Folic Acid by Stopped-Flow/Fluorescence].

    Science.gov (United States)

    Ye, San-xian; Luo, Yun-jing; Qiao, Shu-liang; Li, Li; Liu, Cai-hong; Shi, Jian-long; An, Xue-jing

    2016-01-01

    As a kind of coenzyme of one-carbon enzymes in vivo, folic acid belongs to B vitamins, which can interact with other vitamins and has great significance for converting among amino acids, dividing growth of cells and protein synthesis reactions. Half-life, concentration and reaction rate constant of drugs are important parameters in pharmacokinetic study. In this paper, by utilizing fluorescence spectrophotometer and stopped-flow spectrum analyzer, reaction kinetic parameters between bovine serum albumin(BSA) and folic acid in a bionic system have been investigated, which provide references for parameters of drug metabolism related to folic acid. By using Stern-Volmer equation dealing with fluorescence quenching experiments data, we concluded that under 25, 30, and 37 degrees C, the static quenching constants of folic acid to intrinsic fluorescence from bovine serum albumin were 2.455 x 10(10), 4.900 x 10(10) and 6.427 x 10(10) L x mol(-1) x s(-1) respectively; The results of kinetic reaction rate have shown that the reaction rate of BSA and folic acid are greater than 100 mol x L(-1) x s(-1) at different temperatures, pH and buffering media, illustrating that the quenching mechanism between BSA and folic acid is to form composite static quenching process. Reaction concentration of bovine serum albumin and its initial concentration were equal to the secondary reaction formula, and the correlation coefficient was 0.998 7, while the half-life (t1/2) was 0.059 s at physiological temperature. With the increase of folic acid concentration, the apparent rate constant of this reaction had a linear increasing trend, the BSA fluorescence quenching rate constant catalyzed by folic acid was 3.174 x 10(5) mol x L(-1) x s(-1). Furthermore, with different buffer, the apparent rate constant and reaction rate constant of BSA interacting with folic acid were detected to explore the influence on the reaction under physiological medium, which is of great significance to determine the

  14. Study on fusion potential barrier in heavy ion reactions based on the dynamical model

    International Nuclear Information System (INIS)

    Tian Junlong; Wu Xizhen; Li Zhuxia; Wang Ning; Liu Fuhu

    2004-01-01

    Based on an improved quantum molecular dynamics model the static and dynamic potential in the entrance channel of synthesis of superheavy nuclei are studied. The dependence of the static potential (and driving potential) on mass-asymmetry is obtained. From this study authors find out that the mass-symmetric system seems to be difficult to fuse and the fusing system with the largest driving potential could be the optimal choice of the projectile-target combination. By comparing the static potential barrier with the dynamic one authors find that the latter one is lower than former one obviously, and that the dynamical potential barrier is entrance energy dependent. The maximum and minimum of dynamic potential barriers approach to the diabatic (sudden approximation) and the adiabatic static potential barriers, respectively

  15. Dynamics of embedded curves by doubly-nonlocal reaction-diffusion systems

    Science.gov (United States)

    von Brecht, James H.; Blair, Ryan

    2017-11-01

    We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically motivated energetic models in terms of more classical, combinatorial measures of complexity for embedded curves. This line of investigation culminates in a family of complexity bounds that relate a rather broad class of models to a generalized, or weighted, variant of the crossing number. Our dynamic results include global well-posedness of the associated partial differential equations, regularity of equilibria for these flows as well as a more detailed investigation of dynamics near such equilibria. Finally, we explore a few global dynamical properties of these models numerically.

  16. Reaction Dynamics of CH{sub 3} + HBr → CH{sub 4} + Br at 150-1000 K

    Energy Technology Data Exchange (ETDEWEB)

    Ree, Jongbaik [Chonnam National Univ., Gwangju (Korea, Republic of); Kim, Yoo Hang [Inha Univ., Incheon (Korea, Republic of); Shin, Hyung Kyu [Univ. of Nevado, Nevado (United States)

    2013-08-15

    The kinetics of the radical-polar molecule reaction CH{sub 3} + HBr → CH{sub 4} + Br has been studied at temperatures between 150 and 1000 K using classical dynamics procedures. Potential energy surfaces constructed using analytical forms of inter- and intramolecular interaction energies show a shallow well and barrier in the entrance channel, which affect the collision dynamics at low temperatures. Different collision models are used to distinguish the reaction occurring at low- and high-temperature regions. The reaction proceeds rapidly via a complex-mode mechanism below room temperature showing strong negative temperature dependence, where the effects of molecular attraction, H-atom tunneling and recrossing of collision complexes are found to be important. The temperature dependence of the rate constant between 400 and 1000 K is positive, the values increasing in accordance with the increase of the mean speed of collision. The rate constant varies from 7.6 Χ 10{sup -12} at 150 K to 3.7 Χ 10{sup -12} at 1000 K via a minimum value of 2.5 Χ 10{sup -12} cm{sup 3} molecule{sup -1} s{sup -1} at 400 K.

  17. Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes

    International Nuclear Information System (INIS)

    Tateyama, Yoshitaka; Blumberger, Jochen; Sprik, Michiel; Tavernelli, Ivano

    2005-01-01

    The thermochemistry of the RuO 4 2- +MnO 4 - →RuO 4 - +MnO 4 2- redox reaction in aqueous solution is studied by separate density-functional-based ab initio molecular-dynamics simulations of the component half reactions RuO 4 2- →RuO 4 - +e - and MnO 4 2- →MnO 4 - +e - . We compare the results of a recently developed grand-canonical method for the computation of oxidation free energies to the predictions by the energy-gap relations of the Marcus theory that can be assumed to apply to these reactions. The calculated redox potentials are in good agreement. The subtraction of the half-reaction free energies gives an estimate of the free energy of the full reaction. The result obtained from the grand-canonical method is -0.4 eV, while the application of the Marcus theory gives -0.3 eV. These should be compared to the experimental value of 0.0 eV. Size effects, in response to increasing the number of water molecules in the periodic model system from 30 to 48, are found to be small (≅0.1 eV). The link to the Marcus theory also has enabled us to compute reorganization free energies for oxidation. For both the MnO 4 2- and RuO 4 2- redox reactions we find the same reorganization free energy of 0.8 eV (1.0 eV in the larger system). The results for the free energies and further analysis of solvation and electronic structure confirm that these two tetrahedral oxoanions show very similar behavior in solution in spite of the central transition-metal atoms occupying a different row and column in the periodic table

  18. A hetero retro Diels-Alder reaction in aqueous solution : A dramatic water-induced increase of the equilibrium constant and inhibition of cycloreversion

    NARCIS (Netherlands)

    Wijnen, J.W; Engberts, J.B.F.N.

    The adduct of the Diels-Alder reaction of nitrosobenzene with cyclopentadiene is not stable in solution. The equilibrium constant for the reaction depends strongly on the medium and water induces a spectacular shift to the adduct. Comparison with the bimolecular addition of nitrosobenzene to

  19. Do high school chemistry examinations inhibit deeper level understanding of dynamic reversible chemical reactions?

    Science.gov (United States)

    Wheeldon, R.; Atkinson, R.; Dawes, A.; Levinson, R.

    2012-07-01

    Background and purpose : Chemistry examinations can favour the deployment of algorithmic procedures like Le Chatelier's Principle (LCP) rather than reasoning using chemical principles. This study investigated the explanatory resources which high school students use to answer equilibrium problems and whether the marks given for examination answers require students to use approaches beyond direct application of LCP. Sample : The questionnaire was administered to 162 students studying their first year of advanced chemistry (age 16/17) in three high achieving London high schools. Design and methods : The students' explanations of reversible chemical systems were inductively coded to identify the explanatory approaches used and interviews with 13 students were used to check for consistency. AS level examination questions on reversible reactions were analysed to identify the types of explanations sought and the students' performance in these examinations was compared to questionnaire answers. Results : 19% of students used a holistic explanatory approach: when the rates of forward and reverse reactions are correctly described, recognising their simultaneous and mutually dependent nature. 36% used a mirrored reactions approach when the connected nature of the forward and reverse reactions is identified, but not their mutual dependency. 42% failed to recognize the interdependence of forward and reverse reactions (reactions not connected approach). Only 4% of marks for AS examination questions on reversible chemical systems asked for responses which went beyond either direct application of LCP or recall of equilibrium knowledge. 37% of students attained an A grade in their AS national examinations. Conclusions : Examinations favour the application of LCP making it possible to obtain the highest grade with little understanding of reversible chemical systems beyond a direct application of this algorithm. Therefore students' understanding may be attenuated so that they are

  20. Dual-level direct dynamics studies for the hydrogen abstraction reaction of 1,1-difluoroethane with O( 3P)

    Science.gov (United States)

    Liu, Jing-yao; Li, Ze-sheng; Dai, Zhen-wen; Zhang, Gang; Sun, Chia-chung

    2004-01-01

    We present dual-level direct dynamics calculations for the CH 3CHF 2 + O( 3P) hydrogen abstraction reaction in a wide temperature range, based on canonical variational transition-state theory including small curvature tunneling corrections. For this reaction, three distinct transition states, one for α-abstraction and two for β-abstraction, have been located. The potential energy surface information is obtained at the MP2(full)/6-311G(d,p) level of theory, and higher-level single-point calculations for the stationary points are preformed at several levels, namely QCISD(T)/6-311+G(3df,3pd), G2, and G3 using the MP2 geometries, as well as at the G3//MP4SDQ/6-311G(d,p) level. The energy profiles are further refined with the interpolated single-point energies method at the G3//MP2(full)/6-311G(d,p) level. The total rate constants match the experimental data reasonable well in the measured temperature range 1110-1340 K. It is shown that at low temperature α-abstraction may be the major reaction channel, while β-abstraction will have more contribution to the whole reaction rate as the temperature increases.

  1. Modeling heat dissipation at the nanoscale: an embedding approach for chemical reaction dynamics on metal surfaces.

    Science.gov (United States)

    Meyer, Jörg; Reuter, Karsten

    2014-04-25

    We present an embedding technique for metallic systems that makes it possible to model energy dissipation into substrate phonons during surface chemical reactions from first principles. The separation of chemical and elastic contributions to the interaction potential provides a quantitative description of both electronic and phononic band structure. Application to the dissociation of O2 at Pd(100) predicts translationally "hot" oxygen adsorbates as a consequence of the released adsorption energy (ca. 2.6 eV). This finding questions the instant thermalization of reaction enthalpies generally assumed in models of heterogeneous catalysis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Evaluation of driver reactions for effective use of dynamic message signs in Richmond, Virginia.

    Science.gov (United States)

    2010-02-01

    Dynamic message signs (DMS) are used in conjunction with other media to communicate traffic conditions, general information, and recommended diversion strategies to motorists. Previous studies using loop detector data to estimate diversion rates attr...

  3. Dynamic transition in the structure of an energetic crystal during chemical reactions at shock front prior to detonation.

    Science.gov (United States)

    Nomura, Ken-Ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya; van Duin, Adri C T; Goddard, William A

    2007-10-05

    Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front.

  4. Communication: Mode specific quantum dynamics of the F + CHD{sub 3} → HF + CD{sub 3} reaction

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Ji; Song, Hongwei; Yang, Minghui, E-mail: yangmh@wipm.ac.cn, E-mail: juliana@unq.edu.ar, E-mail: uwe.manthe@uni-bielefeld.de [Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Palma, Juliana, E-mail: yangmh@wipm.ac.cn, E-mail: juliana@unq.edu.ar, E-mail: uwe.manthe@uni-bielefeld.de [Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Sáenz Peña 352, Bernal B1876BXD (Argentina); Manthe, Uwe, E-mail: yangmh@wipm.ac.cn, E-mail: juliana@unq.edu.ar, E-mail: uwe.manthe@uni-bielefeld.de [Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld (Germany); Guo, Hua [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2016-05-07

    The mode specific reactivity of the F + CHD{sub 3} → HF + CD{sub 3} reaction is investigated using an eight-dimensional quantum dynamical model on a recently developed ab initio based full-dimensional potential energy surface. Our results indicate prominent resonance structures at low collision energies and absence of an energy threshold in reaction probabilities. It was also found that excitation of the C–D stretching or CD{sub 3} umbrella mode has a relatively small impact on reactivity. On the other hand, the excitation of the C–H vibration (v{sub 1}) in CHD{sub 3} is shown to significantly increase the reactivity, which, like several recent quasi-classical trajectory studies, is at odds with the available experimental data. Possible sources of the disagreement are discussed.

  5. [Microcalorimetric determination of thermochemical parameters of the phosphofructokinase reaction].

    Science.gov (United States)

    Böhme, H J; Schellenberger, W; Hofmann, E

    1975-01-01

    A calorimetric procedure for determining deltaH, deltaG, deltaS and Keq of a bimolecular reaction with two or more products is described. By using this method the thermodynamic parameters of the phosphofructokinase reaction are determined. At pH 7.0 and 25 degrees C a reaction enthalpy of-6.96kcal/mole was found after correction for the neutralization enthalpy of the buffer and of the enthalpy difference of the magnesium complexes of ATP and ADP, respectively. The free energy of the phosphofructokinase reaction has been found under these conditions to be -3.96kcal/mole.

  6. Complete and incomplete fusion dynamics of {sup 6,7}Li + {sup 159}Tb reactions near the Coulomb barrier

    Energy Technology Data Exchange (ETDEWEB)

    Gautam, Manjeet Singh [Thapar University, School of Physics and Materials Science, Patiala (India); Indus Degree College, Department of Physics, Kinana, Jind, Haryana (India); Grover, Neha; Sharma, Manoj K. [Thapar University, School of Physics and Materials Science, Patiala (India)

    2017-01-15

    The complete fusion (CF) and incomplete fusion (ICF) cross-sections are estimated for {sup 6,} {sup 7}Li + {sup 159}Tb reactions using the energy-dependent Woods-Saxon potential model (EDWSP model) and dynamical cluster-decay model (DCM). The CF data of the {sup 6}Li + {sup 159}Tb({sup 7}Li + {sup 159}Tb) reaction at above barrier energies is suppressed with reference to expectations of the EDWSP model by 25% (20%) which is smaller than the reported data by ∝ 9% (6%). This suppression is correlated with the projectile breakup effect. The projectiles {sup 6,7}Li are loosely bound systems, which may break up into charged fragments prior to reaching the fusion barrier and subsequently one of the fragment is captured by the target leading to the suppression of fusion data at above barrier energies. The sum of CF and ICF, which is termed as total fusion cross-section (TF), removes the discrepancies between theoretical predictions and the above barrier complete fusion data and hence is adequately explained via the EDWSP model over a wide range of energy spread across the Coulomb barrier. In addition to fusion, the decay mechanism of {sup 6}Li + {sup 159}Tb reaction is studied within the framework of the dynamical cluster-decay model (DCM). The breakup of the projectile ({sup 6}Li) in the entrance channel indicates the presence of ICF, which is investigated further using the collective clusterization approach of DCM. The present theoretical analysis suggests that a larger barrier modification is needed to address the fusion data of chosen reactions in the below barrier energy region. (orig.)

  7. Reaction dynamics of {sup 34-38}Mg projectile with carbon target using Glauber model

    Energy Technology Data Exchange (ETDEWEB)

    Shama, Mahesh K., E-mail: maheshphy82@gmail.com [School of Physics and Material Sciences, Thapar University Patiala-147004 (India); Department of Applied Sciences, Chandigarh Engineering College, Landran Mohali-140307 (India); Panda, R. N. [Department of Physics, ITER, Shiksha O Anusandhan University, Bhubaneswar-751030 (India); Sharma, Manoj K. [School of Physics and Material Sciences, Thapar University Patiala-147004 (India); Patra, S. K. [Institute of Physics, Sachivalaya marg Bhubneswar-751005 (India)

    2015-08-28

    We have studied nuclear reaction cross-sections for {sup 34-38}Mg isotopes as projectile with {sup 12}C target at projectile energy 240AMeV using Glauber model with the conjunction of densities from relativistic mean filed formalism. We found good agreement with the available experimental data. The halo status of {sup 37}Mg is also investigated.

  8. Effects of reagent translational and vibrational energy on the dynamics of endothermic reactions

    International Nuclear Information System (INIS)

    Krajnovich, D.; Zhang, Z.; Huisken, F.; Shen, Y.R.; Lee, Y.T.

    1981-07-01

    The endothermic reactions Br + CH 3 I → CH 3 + IBr (ΔH 0 0 = 13 kcal/mole) and Br + CF 3 I → CF 3 + IBr (ΔH 0 0 = 11 kcal/mole) have been studied by the crossed molecular beams method. Detailed center-of-mass contour maps of the IBr product flux as a function of recoil velocity and scattering angle are derived. For both systems it is found that the IBr product is sharply backward scattered with respect to the incident Br dirction, and that most of the available energy goes into product translation. Vibrational enhancement of the Br + CF 3 I reaction was investigated by using the infrared multiphoton absorption process to prepare highly vibrationally excited CF 3 I. At a collision energy of 31 kcal/mole (several times the barrier height), reagent vibrational energy appears to be less effective than an equivalent amount of (additional) translational energy in promoting reaction. More forward scattered IBr is produced in reactions of Br with vibrationally hot CF 3 I

  9. Ambulatory measurement of ground reaction force and estimation of ankle and foot dynamics

    NARCIS (Netherlands)

    Schepers, H. Martin; Koopman, Hubertus F.J.M.; Baten, Christian T.M.; Veltink, Petrus H.

    INTRODUCTION Traditionally, human body movement analysis is done in so-called ‘gait laboratories’. In these laboratories, body movement is measured by a camera system using optical markers, the ground reaction force by a force plate fixed in the floor, and the muscle activity by EMG. From the body

  10. Effects of reagent translational and vibrational energy on the dynamics of endothermic reactions

    Energy Technology Data Exchange (ETDEWEB)

    Krajnovich, D.; Zhang, Z.; Huisken, F.; Shen, Y.R.; Lee, Y.T.

    1981-07-01

    The endothermic reactions Br + CH/sub 3/I ..-->.. CH/sub 3/ + IBr (..delta..H/sub 0//sup 0/ = 13 kcal/mole) and Br + CF/sub 3/I ..-->.. CF/sub 3/ + IBr (..delta..H/sub 0//sup 0/ = 11 kcal/mole) have been studied by the crossed molecular beams method. Detailed center-of-mass contour maps of the IBr product flux as a function of recoil velocity and scattering angle are derived. For both systems it is found that the IBr product is sharply backward scattered with respect to the incident Br dirction, and that most of the available energy goes into product translation. Vibrational enhancement of the Br + CF/sub 3/I reaction was investigated by using the infrared multiphoton absorption process to prepare highly vibrationally excited CF/sub 3/I. At a collision energy of 31 kcal/mole (several times the barrier height), reagent vibrational energy appears to be less effective than an equivalent amount of (additional) translational energy in promoting reaction. More forward scattered IBr is produced in reactions of Br with vibrationally hot CF/sub 3/I.

  11. State-specific reactions and autoionization dynamics of Ar2+ produced by synchrotron radiation

    Czech Academy of Sciences Publication Activity Database

    Franceschi, P.; Thissen, R.; Dutuit, O.; Alcaraz, Ch.; Soldi-Lose, H.; Bassi, D.; Ascenzi, D.; Tosi, P.; Žabka, Ján; Herman, Zdeněk; Coreno, M.; De Simone, M.

    2009-01-01

    Roč. 280, 1-3 (2009), s. 119-127 ISSN 1387-3806 R&D Projects: GA AV ČR IAA400400702 Institutional research plan: CEZ:AV0Z40400503 Keywords : argon * dications * photoionization * ion molecule reaction Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.117, year: 2009

  12. Initial Dynamics of The Norrish Type I Reaction in Acetone: Probing Wave Packet Motion

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Y.; Sølling, Theis I.; Møller, Klaus Braagaard

    2011-01-01

    The Norrish Type I reaction in the S1 (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels...

  13. Photo induced multiple fragmentation of atoms and molecules: Dynamics of Coulombic many-particle systems studied with the COLTRIMS reaction microscope

    International Nuclear Information System (INIS)

    Czasch, A.; Schmidt, L.Ph.H.; Jahnke, T.; Weber, Th.; Jagutzki, O.; Schoessler, S.; Schoeffler, M.S.; Doerner, R.; Schmidt-Boecking, H.

    2005-01-01

    Many-particle dynamics in atomic and molecular physics has been investigated by using the COLTRIMS reaction microscope. The COLTRIMS technique visualizes photon and ion induced many-particle fragmentation processes in the eV and milli-eV regime. It reveals the complete momentum pattern in atomic and molecular many-particle reactions comparable to the bubble chamber in nuclear physics

  14. Pulsed fusion space propulsion: Computational Magneto-Hydro Dynamics of a multi-coil parabolic reaction chamber

    Science.gov (United States)

    Romanelli, Gherardo; Mignone, Andrea; Cervone, Angelo

    2017-10-01

    Pulsed fusion propulsion might finally revolutionise manned space exploration by providing an affordable and relatively fast access to interplanetary destinations. However, such systems are still in an early development phase and one of the key areas requiring further investigations is the operation of the magnetic nozzle, the device meant to exploit the fusion energy and generate thrust. One of the last pulsed fusion magnetic nozzle design is the so called multi-coil parabolic reaction chamber: the reaction is thereby ignited at the focus of an open parabolic chamber, enclosed by a series of coaxial superconducting coils that apply a magnetic field. The field, beside confining the reaction and preventing any contact between hot fusion plasma and chamber structure, is also meant to reflect the explosion and push plasma out of the rocket. Reflection is attained thanks to electric currents induced in conductive skin layers that cover each of the coils, the change of plasma axial momentum generates thrust in reaction. This working principle has yet to be extensively verified and computational Magneto-Hydro Dynamics (MHD) is a viable option to achieve that. This work is one of the first detailed ideal-MHD analysis of a multi-coil parabolic reaction chamber of this kind and has been completed employing PLUTO, a freely distributed computational code developed at the Physics Department of the University of Turin. The results are thus a preliminary verification of the chamber's performance. Nonetheless, plasma leakage through the chamber structure has been highlighted. Therefore, further investigations are required to validate the chamber design. Implementing a more accurate physical model (e.g. Hall-MHD or relativistic-MHD) is thus mandatory, and PLUTO shows the capabilities to achieve that.

  15. Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics

    International Nuclear Information System (INIS)

    Windus, Alastair; Jensen, Henrik J

    2008-01-01

    We consider a reaction-diffusion model incorporating the reactions A→φ, A→2A and 2A→3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.

  16. Reaction dynamics studies for the system 7Be + 208Pb at Coulomb barrier energies

    Directory of Open Access Journals (Sweden)

    Mazzocco M.

    2017-01-01

    Full Text Available The scattering process of the Radioactive Ion Beam 7Be from a 208Pb target was measured at three near-barrier energies. The quasi-elastic angular distributions were analyzed within the framework of the optical model to extract the reaction cross sections. The results are compared with those obtained for the reactions induced by the mirror projectile 7Li and by the lightest particle-stable lithium isotope 6Li on the same target. The angular distributions for the production of the two 7Be constituent clusters, namely 3He and 4He, were also measured. In agreement with what observed for the interaction of 7Be with lighter targets, the production of the heavier helium isotope resulted to be much more abundant than that of its lighter counterpart.

  17. Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Windus, Alastair; Jensen, Henrik J [The Institute for Mathematical Sciences, 53 Prince' s Gate, South Kensington, London SW7 2PG (United Kingdom)], E-mail: h.jensen@imperial.ac.uk

    2008-11-15

    We consider a reaction-diffusion model incorporating the reactions A{yields}{phi}, A{yields}2A and 2A{yields}3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.

  18. Reaction dynamics studies for the system 7Be + 208Pb at Coulomb barrier energies

    Science.gov (United States)

    Mazzocco, M.; Boiano, A.; Boiano, C.; La Commara, M.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Strano, E.; Torresi, D.; Acosta, L.; Di Meo, P.; Fernandez-Garcia, J. P.; Glodariu, T.; Grebosz, J.; Guglielmetti, A.; Marquinez-Duran, G.; Martel, I.; Nicoletto, M.; Pakou, A.; Sánchez-Benítez, A. M.; Sava, T.; Sgouros, O.; Signorini, C.; Soramel, F.; Soukeras, V.; Stroe, L.

    2017-11-01

    The scattering process of the Radioactive Ion Beam 7Be from a 208Pb target was measured at three near-barrier energies. The quasi-elastic angular distributions were analyzed within the framework of the optical model to extract the reaction cross sections. The results are compared with those obtained for the reactions induced by the mirror projectile 7Li and by the lightest particle-stable lithium isotope 6Li on the same target. The angular distributions for the production of the two 7Be constituent clusters, namely 3He and 4He, were also measured. In agreement with what observed for the interaction of 7Be with lighter targets, the production of the heavier helium isotope resulted to be much more abundant than that of its lighter counterpart.

  19. Spin distribution studies: a sensitive probe for in-complete fusion reaction dynamics

    International Nuclear Information System (INIS)

    Singh, Pushpendra P.; Singh, B.P.; Unnati; Sharma, Bhavna; Sharma, Manoj Kumar; Singh, D.; Afzal Ansari, M.; Prasad, R.; Rakesh Kumar; Golda, K.S.; Muralithar, S.; Singh, R.P.; Bhowmik, R.K.; Bhardwaj, H.D.

    2006-01-01

    With the view to get the conclusive information on critical angular momentum involvement for various degrees of incomplete fusion, an in-beam particle-gamma coincidence experiment has been performed in 16 O + 169 Tm system at ≅ 5.6 MeV/nucleon. Spin distributions for different reaction products have been measured by studying the relative population of different levels in a rotational band

  20. Characterization of CD46 and β1 integrin dynamics during sperm acrosome reaction

    Czech Academy of Sciences Publication Activity Database

    Frolíková, Michaela; Šebková, Nataša; Děd, Lukáš; Dvořáková-Hortová, Kateřina

    2016-01-01

    Roč. 6, Sep 26 (2016), s. 1-15 ISSN 2045-2322 R&D Projects: GA ČR GA14-05547S; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : CD46 * β1 integrin * acrosome reaction * actin * SIM * latrunculin A Subject RIV: EC - Immunology Impact factor: 4.259, year: 2016

  1. Study of the nucleon-induced preequilibrium reactions by the quantum molecular dynamics

    International Nuclear Information System (INIS)

    Chiba, Satoshi; Chadwick, M.B.; Niita, Koji; Maruyama, Toshiki; Maruyama, Tomoyuki; Iwamoto, Akira

    1996-01-01

    The preequilibrium (nucleon-in, nucleon-out) angular distributions have been analyzed in the energy region around 100 to 200 MeV in terms of the Quantum Molecular Dynamics (QMD) theory. The step-wise contribution to the angular distribution, the effects of momentum distribution and surface refraction/reflection to the quasifree scattering have been studied. (author)

  2. Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

    Czech Academy of Sciences Publication Activity Database

    Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

    2016-01-01

    Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

  3. State-to-state quantum dynamics of the F + HCl (vi = 0, ji = 0) → HF(vf, jf) + Cl reaction on the ground state potential energy surface.

    Science.gov (United States)

    Li, Anyang; Guo, Hua; Sun, Zhigang; Kłos, Jacek; Alexander, Millard H

    2013-10-07

    The state-to-state reaction dynamics of the title reaction is investigated on the ground electronic state potential energy surface using two quantum dynamical methods. The results obtained using the Chebyshev real wave packet method are in excellent agreement with those obtained using the time-independent method, except at low translational energies. It is shown that this exothermic hydrogen abstraction reaction is direct, resulting in a strong back-scattered bias in the product angular distribution. The HF product is highly excited internally. Agreement with available experimental data is only qualitative. We discuss several possible causes of disagreement with experiment.

  4. Dynamics of {sup 58}Ni + {sup 54}Fe → {sup 112}Xe* reaction across the Coulomb barrier

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Manpreet; Sharma, Manoj K. [Thapar University, School of Physics and Materials Science, Patiala (India)

    2014-03-15

    The dynamical cluster-decay model (DCM) has been applied to study the decay of the {sup 112}Xe* compound nucleus formed in the massive heavy-ion reaction {sup 58}Ni + {sup 54}Fe at energies across the Coulomb barrier with E{sub c.m.} ∼ 85-110 MeV. The calculations are done for spherical fragmentation as well as by including deformation and orientation degrees of freedom of the decaying fragments. DCM-based cross sections give a nice description of the experimental fusion excitation function σ{sub ER}, within one parameter fitting, the neck length parameter (ΔR), whose value remains within the range of nuclear proximity interaction. The barrier height corresponding to the neck length parameter brings into the picture the barrier modification which enables us to address the data particularly at below barrier energies. The role of excitation energy (or temperature), deformations, orientations, angular momentum and diffuseness parameter is investigated to understand the dynamics of the {sup 58}Ni + {sup 54}Fe reaction. Finally the N/Z dependence of the fragmentation structure of different compound systems formed via {sup 58}Ni beam (projectile) is explored. (orig.)

  5. Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal

    International Nuclear Information System (INIS)

    Zhao, Bin; Guo, Hua; Sun, Zhigang

    2015-01-01

    Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H 2 O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H 2 O → H 2 + OH reaction. The strong enhancement of reactivity by the H 2 O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal

  6. Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal.

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-06-28

    Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H2O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H2O → H2 + OH reaction. The strong enhancement of reactivity by the H2O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal.

  7. Theoretical studies of the reaction dynamics of the matrix-isolated F2+cis-d2 -ethylene system

    Science.gov (United States)

    Raff, Lionel M.

    1991-12-01

    The molecular dynamics of the F2+cis-d2 -ethylene addition reaction and the subsequent decomposition dynamics of the vibrationally excited 1,2-difluoroethane-d2 product isolated in Ar or Xe matrices at 12 K are investigated using trajectory methods that incorporate nonstatistical sampling to enhance the reaction probabilities. The matrix is represented by a face-centered-cubic crystal containing 125 unit cells with 666 lattice atoms in a cubic (5×5×5) arrangement. Both interstitial and substitutional sites for the F2/cis-d2 -ethylene pair are examined. Transport effects of the bulk are simulated using the velocity reset method introduced by Riley, Coltrin, and Diestler [J. Chem. Phys. 88, 5934 (1988)]. The potential-energy hypersurface for the system is written as the separable sum of a lattice potential, a lattice-substrate interaction, and a gas-phase potential for 1,2-difluoroethane-d2. The first two of these have pairwise form, while the 1,2-difluoroethane-d2 potential is identical to that employed previously to study the unimolecular reaction dynamics of matrix-isolated 1,2-difluoroethane-d4 [J. Chem. Phys. 93, 3160 (1990)]. The major F2+cis-d2 -ethylene reaction mechanism involves a four-center, concerted αβ addition across the C=C double bond. A small contribution from an atomic addition mechanism that initially forms fluoroethyl and fluorine radicals is observed in a xenon matrix, but not in argon. Subsequent to the formation of 1,2-difluoroethane-d2, the observed dynamic processes are vibrational relaxation to the lattice phonon modes, orientational exchange, and HF or DF elimination reactions. Vibrational relaxation is found to be very similar to that observed previously for 1,2-difluoroethane-d4. The process is well described by a first-order rate law with rate coefficients in the range 0.046-0.069 ps-1. The distribution of rate coefficients, as well as the averages, are nearly identical for Ar and Xe lattices. Very little difference is found between

  8. Proton transfer and unimolecular decay in the low-energy-reaction dynamics of H3O+ with acetone

    International Nuclear Information System (INIS)

    Creasy, W.R.; Farrar, J.M.

    1983-01-01

    The title reaction has been studied at collision energies of 0.83 and 2.41 eV. Direct reaction dynamics have been observed at both energies and an increasingly high fraction of the total energy appears in product translation as the collision energy increases. This result is consistent with the concept of induced repulsive energy release, which becomes more effective as trajectories sample the corner of the potential energy surface. At the higher collision energy, the protonated acetone cation undergoes two unimolecular decay channels: C-C bond cleavage to CH 3 CO + and CH 4 , and C-O bond cleavagto C 3 H 5 + (presumably to allyl cation) and H 2 O. The CH 3 CO + channel, endothermic relative to ground state protonated acetone cations by 0.74 eV, appears to liberate 0.4 eV in relative product translation while the C 3 H 5 + channel, endothermic by 2.17 eV, liberates only 0.07 eV in relative translation. These results are discussed in terms of the location on the reaction coordinate and magnitudes of potential energy barriers to 1,3-hydrogen atoms shifts which must precede the bond cleavage processes

  9. Dynamic behavior of the bray-liebhafsky oscillatory reaction controlled by sulfuric acid and temperature

    Science.gov (United States)

    Pejić, N.; Vujković, M.; Maksimović, J.; Ivanović, A.; Anić, S.; Čupić, Ž.; Kolar-Anić, Lj.

    2011-12-01

    The non-periodic, periodic and chaotic regimes in the Bray-Liebhafsky (BL) oscillatory reaction observed in a continuously fed well stirred tank reactor (CSTR) under isothermal conditions at various inflow concentrations of the sulfuric acid were experimentally studied. In each series (at any fixed temperature), termination of oscillatory behavior via saddle loop infinite period bifurcation (SNIPER) as well as some kind of the Andronov-Hopf bifurcation is presented. In addition, it was found that an increase of temperature, in different series of experiments resulted in the shift of bifurcation point towards higher values of sulfuric acid concentration.

  10. A classical approach in simple nuclear fusion reaction 1H2+1H3 using two-dimension granular molecular dynamics model

    International Nuclear Information System (INIS)

    Viridi, S.; Kurniadi, R.; Waris, A.; Perkasa, Y. S.

    2012-01-01

    Molecular dynamics in 2-D accompanied by granular model provides an opportunity to investigate binding between nuclei particles and its properties that arises during collision in a fusion reaction. A fully classical approach is used to observe the influence of initial angle of nucleus orientation to the product yielded by the reaction. As an example, a simplest fusion reaction between 1 H 2 and 1 H 3 is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary 2 He 4 nucleus.

  11. Exogenous reference gene normalization for real-time reverse transcription-polymerase chain reaction analysis under dynamic endogenous transcription.

    Science.gov (United States)

    Johnston, Stephen; Gallaher, Zachary; Czaja, Krzysztof

    2012-05-15

    Quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is widely used to investigate transcriptional changes following experimental manipulations to the nervous system. Despite the widespread utilization of qPCR, the interpretation of results is marred by the lack of a suitable reference gene due to the dynamic nature of endogenous transcription. To address this inherent deficiency, we investigated the use of an exogenous spike-in mRNA, luciferase, as an internal reference gene for the 2(-∆∆Ct) normalization method. To induce dynamic transcription, we systemically administered capsaicin, a neurotoxin selective for C-type sensory neurons expressing the TRPV-1 receptor, to adult male Sprague-Dawley rats. We later isolated nodose ganglia for qPCR analysis with the reference being either exogenous luciferase mRNA or the commonly used endogenous reference β-III tubulin. The exogenous luciferase mRNA reference clearly demonstrated the dynamic expression of the endogenous reference. Furthermore, variability of the endogenous reference would lead to misinterpretation of other genes of interest. In conclusion, traditional reference genes are often unstable under physiologically normal situations, and certainly unstable following the damage to the nervous system. The use of exogenous spike-in reference provides a consistent and easily implemented alternative for the analysis of qPCR data.

  12. Quantum chemistry and dynamics of the abstraction reaction of H atoms from formaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    Siaï, A. [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Oueslati, I. [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Observatoire de Paris-Meudon, Sorbonne Universités, UPMC Univ Paris 06, UMR8112 du CNRS, LERMA, 5 Place Jules Janssen, 92195 Meudon cedex (France); Académie Militaire, Fondouk Jedid, 8012 Nabeul (Tunisia); Kerkeni, Boutheïna, E-mail: Boutheina.kerkeni@obspm.fr [Faculté des Sciences de Tunis, Département de Physique, (LPMC), Université de Tunis El Manar, 2092 Tunis (Tunisia); Observatoire de Paris-Meudon, Sorbonne Universités, UPMC Univ Paris 06, UMR8112 du CNRS, LERMA, 5 Place Jules Janssen, 92195 Meudon cedex (France); Institut Supérieur des Arts Multimédia de la Manouba, Université de la Manouba, 2010 la Manouba (Tunisia)

    2016-08-02

    This work reports a reduced dimensionality rate constant calculation of the H-abstraction reaction from formaldehyde. Quantum scattering calculations are performed treating explicitly the bonds being broken and formed. Geometry optimisations and frequency calculations are done at the MP2/cc-pVTZ level while energies are calculated with the CCSD(T) method. An analytical potential energy surface was developed from a relatively small number of grid points. When compared to semi-classical approaches, the quantum scattering calculations show that quantum tunnelling yields large contributions at low temperatures. At 200 K, we note a difference of about 5 orders of magnitude between transition state theory (TST) and quantum rate constants. Our predicted results show that the quantum and the CVT/SCT rate constants are in reasonable agreement with the available experiment at high temperatures, but that the last one gives better agreement to experimental results at low temperatures.

  13. Enabling nucleophilic substitution reactions of activated alkyl fluorides through hydrogen bonding.

    Science.gov (United States)

    Champagne, Pier Alexandre; Pomarole, Julien; Thérien, Marie-Ève; Benhassine, Yasmine; Beaulieu, Samuel; Legault, Claude Y; Paquin, Jean-François

    2013-05-03

    It was discovered that the presence of water as a cosolvent enables the reaction of activated alkyl fluorides for bimolecular nucleophilic substitution reactions. DFT calculations show that activation proceeds through stabilization of the transition structure by a stronger F···H2O interaction and diminishing C-F bond elongation, and not simple transition state electrostatic stabilization. Overall, the findings put forward a distinct strategy for C-F bond activation through H-bonding.

  14. Dynamics of the reaction of the N+ ion with hydrogen isotopes and helium

    International Nuclear Information System (INIS)

    Ruska, W.E.W.

    1976-01-01

    Molecular beam techniques were used to study the reactive and non-reactive scattering of the nitrogen positive ion from hydrogen isotopes and helium, at energies above the stability limit for spectator stripping. Reactive scattering was observed from H 2 and HD targets. Non-reactive scattering was observed from H 2 and D 2 targets, and from He at one energy. A correlation diagram for the system is presented and compared with the available a priori calculations. Two surfaces are expected to lead to reaction. One is a 3 A 2 - 3 PI surface, the other, a 3 B 1 - 3 Σ - surface. Collinear approaches are expected to be most reactive on the 3 B 1 - 3 Σ - surface; noncollinear, on the 3 A 1 - 3 PI surface. Theoretical models are presented in which an incident hard sphere A, representing the projectile ion, strikes one of a pair of hard spheres B-C representing the B hydrogen molecule. After an impulsive A-B collision, an impulsive B-C collision may take place. The relative energy of A to B is then examined, and a reactive event is considered to have occurred if the energy is less than the dissociation energy for the A-B molecule. This model is treated both in the collinear case and in three dimensions. A graphical technique for the collinear case is summarized and applied to reaction on the 3 B 1 - 3 Σ - surface. An integral equation for the three-dimensional case is developed. A synthesis of two treatments, representing the behavior of the system on both reactive surfaces, and considering the charge-exchange channel, correctly predicts the observed product distribution. Predictions are also presented for the as yet unobserved case of reactive scattering from a D 2 target

  15. Spectroscopy and dynamics of chemical reactions in van der Waals complexes

    International Nuclear Information System (INIS)

    Soorkia, Satchin

    2008-09-01

    Transition metal elements have d valence electrons and are characterized by a great variety of electronic configurations responsible for their specific reactivity. The elements of the second row in particular have 4d and 5s atomic orbitals of similar size and energy which can be both involved in chemical processes. We have been interested in the reactivity of a transition metal element, zirconium, combined with a simple organic functionalized molecule in a van der Waals complex formed in a supersonic molecular beam in the model reaction Zr + CH 3 F. In this context, one of the chemicals reactions that we are interested in leads to the formation of ZrF. The electronic spectroscopy of ZrF in the spectral domain 400 - 470 nm is extremely rich and surprising for a diatomic molecule. With this study, we have been able to identify the ground state of ZrF (X 2 Δ) by simulating the observed rotational structures and obtain essential information on the electronic structure. These experimental results are in agreement with ab initio calculations. The excited states of the complex Zr...F-CH 3 have been studied with a depopulation method. The spectral domain 615 - 700 nm is particularly interesting because it reveals a group of diffuse bands red-shifted and broadened with respect to the transition a 3 F → z 3 F in the metal. This transition is forbidden from the ground state a 3 F 2 of zirconium but allowed from the a 3 F 4 state. Complexation of the metal atom with a CH 3 F molecule allows coupling of these two states to occur which ensures the optical transition from the ground state of the complex. (author)

  16. Ion imaging study of reaction dynamics in the N{sup +}+ CH{sub 4} system

    Energy Technology Data Exchange (ETDEWEB)

    Pei, Linsen; Farrar, James M. [Department of Chemistry, University of Rochester, Rochester, New York 14627 (United States)

    2012-10-21

    The velocity map ion imaging method is applied to the ion-molecule reactions of N{sup +} with CH{sub 4}. The velocity space images are collected at collision energies of 0.5 and 1.8 eV, providing both product kinetic energy and angular distributions for the reaction products CH{sub 4}{sup +}, CH{sub 3}{sup +}, and HCNH{sup +}. The charge transfer process is energy resonant and occurs by long-range electron transfer that results in minimal deflection of the products. The formation of the most abundant product, CH{sub 3}{sup +}, proceeds by dissociative charge transfer rather than hydride transfer, as reported in earlier publications. The formation of HCNH{sup +} by C-N bond formation appears to proceed by two different routes. The triplet state intermediates CH{sub 3}NH{sup +} and CH{sub 2}NH{sub 2}{sup +} that are formed as N{sup +}({sup 3}P) approaches CH{sub 4} may undergo sequential loss of two hydrogen atoms to form ground state HCNH{sup +} products on a spin-allowed pathway. However, the kinetic energy distributions for formation of HCNH{sup +} extend past the thermochemical limit to form HCNH{sup +}+ 2H, implying that HCNH{sup +} may also be formed in concert with molecular hydrogen, and requiring that intersystem crossing to the singlet manifold must occur in a significant ({approx}25%) fraction of reactive collisions. We also report GAUSSIAN G2 calculations of the energies and structures of important singlet and triplet [CNH{sub 4}{sup +}] complexes that serve as precursors to product formation.

  17. On experimental and theoretical studies of dynamics and particle production in p-nucleus and heavy ion reactions

    Energy Technology Data Exchange (ETDEWEB)

    Fokin, A.B

    1998-11-01

    Several experiments and theoretical models of intermediate energy heavy ion collision physics are presented in this thesis. Statistical and dynamical aspects of nuclear collisions are widely discussed these days, particularly in connection with the multifragmentation phenomenon and the possible link to a liquid-gas phase transition in the spinodal region of nuclear matter phase diagram. Experimental techniques which allow us to measure various parameters of hot and dense (equilibrated) regions (emission sources) formed in a heavy ion collision are well established nowadays. In recent CHIC (Celsius Heavy Ion Collaboration) experiments the properties of such sources were measured using slowly ramping mode of the CELSIUS storage ring. In this thesis the entropy and chaos production in nuclear collisions is discussed in connection with the t/d/p ratios. Subthreshold pion production explores collective effects in heavy ion collisions and brings additional information about the equation of state of nuclear matter. Continuous pion production excitation functions were measured in the beam energy region from far below the nucleon-nucleon threshold up to the delta dominant region. Mass and angular dependencies of pion production are discussed. A version of the molecular dynamics model which includes pion production in direct nucleon-nucleon collisions was developed and experimental data were analysed in the scope of this model. Properties of the emission sources formed in heavy ion collisions at energies below 50A MeV were studied in the experiments of fragmentation type performed by CHIC. Temperatures of these sources were extracted from fragment energy spectra and from `isotopic effect`. A version of the quantum molecular dynamics model, where the Pauli potential is introduced into the Hamiltonian, was combined with the statistical multifragmentation model and used to explore dynamical and statistical properties of the reaction development. The artificial neural networks

  18. On experimental and theoretical studies of dynamics and particle production in p-nucleus and heavy ion reactions

    International Nuclear Information System (INIS)

    Fokin, A.B.

    1998-11-01

    Several experiments and theoretical models of intermediate energy heavy ion collision physics are presented in this thesis. Statistical and dynamical aspects of nuclear collisions are widely discussed these days, particularly in connection with the multifragmentation phenomenon and the possible link to a liquid-gas phase transition in the spinodal region of nuclear matter phase diagram. Experimental techniques which allow us to measure various parameters of hot and dense (equilibrated) regions (emission sources) formed in a heavy ion collision are well established nowadays. In recent CHIC (Celsius Heavy Ion Collaboration) experiments the properties of such sources were measured using slowly ramping mode of the CELSIUS storage ring. In this thesis the entropy and chaos production in nuclear collisions is discussed in connection with the t/d/p ratios. Subthreshold pion production explores collective effects in heavy ion collisions and brings additional information about the equation of state of nuclear matter. Continuous pion production excitation functions were measured in the beam energy region from far below the nucleon-nucleon threshold up to the delta dominant region. Mass and angular dependencies of pion production are discussed. A version of the molecular dynamics model which includes pion production in direct nucleon-nucleon collisions was developed and experimental data were analysed in the scope of this model. Properties of the emission sources formed in heavy ion collisions at energies below 50A MeV were studied in the experiments of fragmentation type performed by CHIC. Temperatures of these sources were extracted from fragment energy spectra and from 'isotopic effect'. A version of the quantum molecular dynamics model, where the Pauli potential is introduced into the Hamiltonian, was combined with the statistical multifragmentation model and used to explore dynamical and statistical properties of the reaction development. The artificial neural networks

  19. Dynamics of the reaction of the N/sup +/ ion with hydrogen isotopes and helium

    Energy Technology Data Exchange (ETDEWEB)

    Ruska, W.E.W.

    1976-06-28

    Molecular beam techniques were used to study the reactive and non-reactive scattering of the nitrogen positive ion from hydrogen isotopes and helium, at energies above the stability limit for spectator stripping. Reactive scattering was observed from H/sub 2/ and HD targets. Non-reactive scattering was observed from H/sub 2/ and D/sub 2/ targets, and from He at one energy. A correlation diagram for the system is presented and compared with the available a priori calculations. Two surfaces are expected to lead to reaction. One is a /sup 3/A/sub 2/ - /sup 3/PI surface, the other, a /sup 3/B/sub 1/ - /sup 3/..sigma../sup -/ surface. Collinear approaches are expected to be most reactive on the /sup 3/B/sub 1/ - /sup 3/..sigma../sup -/ surface; noncollinear, on the /sup 3/A/sub 1/ - /sup 3/PI surface. Theoretical models are presented in which an incident hard sphere A, representing the projectile ion, strikes one of a pair of hard spheres B-C representing the B hydrogen molecule. After an impulsive A-B collision, an impulsive B-C collision may take place. The relative energy of A to B is then examined, and a reactive event is considered to have occurred if the energy is less than the dissociation energy for the A-B molecule. This model is treated both in the collinear case and in three dimensions. A graphical technique for the collinear case is summarized and applied to reaction on the /sup 3/B/sub 1/ - /sup 3/..sigma../sup -/ surface. An integral equation for the three-dimensional case is developed. A synthesis of two treatments, representing the behavior of the system on both reactive surfaces, and considering the charge-exchange channel, correctly predicts the observed product distribution. Predictions are also presented for the as yet unobserved case of reactive scattering from a D/sub 2/ target.

  20. Oxygen plasma etching of graphene: A first-principles dynamical inspection of the reaction mechanisms and related activation barriers

    Science.gov (United States)

    Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi; Dept. of Applied Physics Team; Institute of Physics and Chemistry of Strasbourg (IPCMS) Collaboration; Department Of Materials Engineering Science Collaboration

    2013-03-01

    Oxygen plasma etching is a crucial step in the fabrication of electronic circuits and has recently received a renovated interest in view of the realization of carbon-based nanodevices. In an attempt at unraveling the atomic-scale details and to provide guidelines for the control of the etching processes mechanisms, we inspected the possible reaction pathways via reactive first principles simulations. These processes involve breaking and formation of several chemical bonds and are characterized by different free-energy barriers. Free-energy sampling techniques (metadynamics and blue moon), used to enhance the standard Car-Parrinello molecular dynamics, provide us a detailed microscopic picture of the etching of graphene surfaces and a comprehensive scenario of the activation barriers involved in the various steps. MEXT, Japan - contract N. 22104005

  1. Water Bridging Dynamics of Polymerase Chain Reaction in the Gauge Theory Paradigm of Quantum Fields

    Directory of Open Access Journals (Sweden)

    L. Montagnier

    2017-05-01

    Full Text Available We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent results showing that London dispersion forces between delocalized electrons of base pairs of DNA are responsible for the formation of dipole modes that can be recognized by Taq polymerase. We describe the dynamic origin of the high efficiency and precise targeting of Taq activity in PCR. The spatiotemporal distribution of interaction couplings, frequencies, amplitudes, and phase modulations comprise a pattern of fields which constitutes the electromagnetic image of DNA in the surrounding water, which is what the polymerase enzyme actually recognizes in the DNA water environment. The experimental realization of PCR amplification, achieved through replacement of the DNA template by the treatment of pure water with electromagnetic signals recorded from viral and bacterial DNA solutions, is found consistent with the gauge theory paradigm of quantum fields.

  2. Heinrich event 1: an example of dynamical ice-sheet reaction to oceanic changes

    Directory of Open Access Journals (Sweden)

    J. Álvarez-Solas

    2011-11-01

    Full Text Available Heinrich events, identified as enhanced ice-rafted detritus (IRD in North Atlantic deep sea sediments (Heinrich, 1988; Hemming, 2004 have classically been attributed to Laurentide ice-sheet (LIS instabilities (MacAyeal, 1993; Calov et al., 2002; Hulbe et al., 2004 and assumed to lead to important disruptions of the Atlantic meridional overturning circulation (AMOC and North Atlantic deep water (NADW formation. However, recent paleoclimate data have revealed that most of these events probably occurred after the AMOC had already slowed down or/and NADW largely collapsed, within about a thousand years (Hall et al., 2006; Hemming, 2004; Jonkers et al., 2010; Roche et al., 2004, implying that the initial AMOC reduction could not have been caused by the Heinrich events themselves.

    Here we propose an alternative driving mechanism, specifically for Heinrich event 1 (H1; 18 to 15 ka BP, by which North Atlantic ocean circulation changes are found to have strong impacts on LIS dynamics. By combining simulations with a coupled climate model and a three-dimensional ice sheet model, our study illustrates how reduced NADW and AMOC weakening lead to a subsurface warming in the Nordic and Labrador Seas resulting in rapid melting of the Hudson Strait and Labrador ice shelves. Lack of buttressing by the ice shelves implies a substantial ice-stream acceleration, enhanced ice-discharge and sea level rise, with peak values 500–1500 yr after the initial AMOC reduction. Our scenario modifies the previous paradigm of H1 by solving the paradox of its occurrence during a cold surface period, and highlights the importance of taking into account the effects of oceanic circulation on ice-sheets dynamics in order to elucidate the triggering mechanism of Heinrich events.

  3. Quantum dynamics of the Eley-Rideal hydrogen formation reaction on graphite at typical interstellar cloud conditions.

    Science.gov (United States)

    Casolo, Simone; Martinazzo, Rocco; Bonfanti, Matteo; Tantardini, Gian Franco

    2009-12-31

    Eley-Rideal formation of hydrogen molecules on graphite, as well as competing collision induced processes, are investigated quantum dynamically at typical interstellar cloud conditions, focusing in particular on gas-phase temperatures below 100 K, where much of the chemistry of the so-called diffuse clouds takes place on the surface of bare carbonaceous dust grains. Collisions of gas-phase hydrogen atoms with both chemisorbed and physisorbed species are considered using available potential energy surfaces (Sha et al., J. Chem. Phys.2002 116, 7158), and state-to-state, energy-resolved cross sections are computed for a number of initial vibrational states of the hydrogen atoms bound to the surface. Results show that (i) product molecules are internally hot in both cases, with vibrational distributions sharply peaked around few (one or two) vibrational levels, and (ii) cross sections for chemisorbed species are 2-3x smaller than those for physisorbed ones. In particular, we find that H(2) formation cross sections out of chemically bound species decrease steadily when the temperature drops below approximately 1000 K, and this is likely due to a quantum reflection phenomenon. This suggests that such Eley-Rideal reaction is all but efficient in the relevant gas-phase temperature range, even when gas-phase H atoms happen to chemisorb barrierless to the surface as observed, e.g., for forming so-called para dimers. Comparison with results from classical trajectory calculations highlights the need of a quantum description of the dynamics in the astrophysically relevant energy range, whereas preliminary results of an extensive first-principles investigation of the reaction energetics reveal the importance of the adopted substrate model.

  4. Spirals in a reaction-diffusion system: Dependence of wave dynamics on excitability

    Science.gov (United States)

    Mahanta, Dhriti; Das, Nirmali Prabha; Dutta, Sumana

    2018-02-01

    A detailed study of the effects of excitability of the Belousov-Zhabotinsky (BZ) reaction on spiral wave properties has been carried out. Using the Oregonator model, we explore the various regimes of wave activity, from sustained oscillations to wave damping, as the system undergoes a Hopf bifurcation, that is achieved by varying the excitability parameter, ɛ . We also discover a short range of parameter values where random oscillations are observed. With an increase in the value of ɛ , the frequency of the wave decreases exponentially, as the dimension of the spiral core expands. These numerical results are confirmed by carrying out experiments in thin layers of the BZ system, where the excitability is changed by varying the concentrations of the reactant species. Effect of reactant concentrations on wave properties like time period and wavelength are also explored in detail. Drifting and meandering spirals are found in the parameter space under investigation, with the excitability affecting the tip trajectory in a way predicted by the numerical studies. This study acts as a quantitative evidence of the relationship between the excitability parameter, ɛ , and the substrate concentrations.

  5. Spirals in a reaction-diffusion system: Dependence of wave dynamics on excitability.

    Science.gov (United States)

    Mahanta, Dhriti; Das, Nirmali Prabha; Dutta, Sumana

    2018-02-01

    A detailed study of the effects of excitability of the Belousov-Zhabotinsky (BZ) reaction on spiral wave properties has been carried out. Using the Oregonator model, we explore the various regimes of wave activity, from sustained oscillations to wave damping, as the system undergoes a Hopf bifurcation, that is achieved by varying the excitability parameter, ε. We also discover a short range of parameter values where random oscillations are observed. With an increase in the value of ε, the frequency of the wave decreases exponentially, as the dimension of the spiral core expands. These numerical results are confirmed by carrying out experiments in thin layers of the BZ system, where the excitability is changed by varying the concentrations of the reactant species. Effect of reactant concentrations on wave properties like time period and wavelength are also explored in detail. Drifting and meandering spirals are found in the parameter space under investigation, with the excitability affecting the tip trajectory in a way predicted by the numerical studies. This study acts as a quantitative evidence of the relationship between the excitability parameter, ε, and the substrate concentrations.

  6. Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

    Science.gov (United States)

    Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

    2010-05-25

    Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

  7. 4D Biofabrication of Branching Multicellular Structures: A Morphogenesis Simulation Based on Turing’s Reaction-Diffusion Dynamics

    Science.gov (United States)

    Zhu, Xiaolu; Yang, Hao

    2017-12-01

    The recently emerged four-dimensional (4D) biofabrication technique aims to create dynamic three-dimensional (3D) biological structures that can transform their shapes or functionalities with time when an external stimulus is imposed or when cell postprinting self-assembly occurs. The evolution of 3D pattern of branching geometry via self-assembly of cells is critical for 4D biofabrication of artificial organs or tissues with branched geometry. However, it is still unclear that how the formation and evolution of these branching pattern are biologically encoded. We study the 4D fabrication of lung branching structures utilizing a simulation model on the reaction-diffusion mechanism, which is established using partial differential equations of four variables, describing the reaction and diffusion process of morphogens with time during the development process of lung branching. The simulation results present the forming process of 3D branching pattern, and also interpret the behaviors of side branching and tip splitting as the stalk growing, through 3D visualization of numerical simulation.

  8. Study of incomplete fusion reaction dynamics in 13C +165 Ho system and its dependence on various entrance channel parameters

    Science.gov (United States)

    Tali, Suhail A.; Kumar, Harish; Ansari, M. Afzal; Ali, Asif; Singh, D.; Ali, Rahbar; Giri, Pankaj K.; Linda, Sneha B.; Parashari, Siddharth; Kumar, R.; Singh, R. P.; Muralithar, S.

    2018-02-01

    The excitation functions for the evaporation residues populated in the interaction of 13C +165 Ho system have been measured at projectile energies ≈ 4-7 MeV/nucleon. Stacked foil activation technique followed by off-line γ-ray spectroscopy have been employed in the present work. The experimentally measured cross-sections are analyzed in the frame work of statistical model code PACE4, which takes into account only the complete fusion reaction cross-sections. The evaporation residues populated via xn and pxn channels were found to be in good agreement with the PACE4 predictions, while a significant enhancement in the measured cross-sections over PACE4 predictions is observed in case of α-emitting channels, which may be attributed to the incomplete fusion process. For the better understanding of incomplete fusion dynamics, the incomplete fusion fraction has also been deduced and its sensitivity with various entrance channel parameters like: projectile energy, mass-asymmetry, projectile structure in terms of Qα-value and Coulomb effect has been studied in the present work. The incomplete fusion fraction is found to increase with increasing the projectile energy and a strong projectile structure dependent mass-asymmetry systematic is also observed. The incomplete fusion fraction is also found to be small for more negative Qα-value projectile (13C) induced reactions as compared to less negative Qα-value projectiles (12C, 16O and 20Ne) induced reactions with the same target nucleus 165Ho. An interesting trend is obtained on further investigation of incomplete fusion dependence on Coulomb effect (ZPZT).

  9. Chiral dynamics and the reactions pp→dK+ anti K0 and pp→dπ+η

    International Nuclear Information System (INIS)

    Oset, E.; Oller, J.A.; Meissner, U.G.

    2001-01-01

    We perform a study of the final-state interactions of the K + anti K 0 and the anti K 0 d systems in the reactions pp→dK + anti K 0 and pp→dπ + η. Since the two-meson system couples strongly to the a 0 (980) resonance, these reactions are expected to be an additional source of information about the controversial scalar sector. We also show that these reactions present peculiar features which can shed additional light on the much debated meson-baryon scalar sector with strangeness -1. We deduce the general structure of the amplitudes close to the dK + anti K 0 threshold, allowing for primary K + anti K 0 as well as π + η production with the two mesons in relative S- or P-wave. The interactions of the mesons are accounted for by using chiral unitary techniques, which generate dynamically the a 0 (980) resonance, and the anti K 0 d interaction is also taken into account. General formulae are derived that allow to incorporate the final-state interactions in these systems for any model of the production mechanism. We illustrate this approach by considering two specific production mechanisms based on three flavor meson-baryon chiral perturbation theory. It is demonstrated that in this scenario the anti K 0 d interactions are very important and can change the cross-section by as much as one order of magnitude. The amount of π + η versus K + anti K 0 production is shown to depend critically on the primary mixture of the two mechanisms, with large interference effects due to final-state interactions. These effects are also shown to occur in the event distributions of invariant masses which are drastically modified by the final-state interactions of the two-meson or the anti Kd system. (orig.)

  10. Non-parametric correlative uncertainty quantification and sensitivity analysis: Application to a Langmuir bimolecular adsorption model

    Science.gov (United States)

    Feng, Jinchao; Lansford, Joshua; Mironenko, Alexander; Pourkargar, Davood Babaei; Vlachos, Dionisios G.; Katsoulakis, Markos A.

    2018-03-01

    We propose non-parametric methods for both local and global sensitivity analysis of chemical reaction models with correlated parameter dependencies. The developed mathematical and statistical tools are applied to a benchmark Langmuir competitive adsorption model on a close packed platinum surface, whose parameters, estimated from quantum-scale computations, are correlated and are limited in size (small data). The proposed mathematical methodology employs gradient-based methods to compute sensitivity indices. We observe that ranking influential parameters depends critically on whether or not correlations between parameters are taken into account. The impact of uncertainty in the correlation and the necessity of the proposed non-parametric perspective are demonstrated.

  11. Non-parametric correlative uncertainty quantification and sensitivity analysis: Application to a Langmuir bimolecular adsorption model

    Directory of Open Access Journals (Sweden)

    Jinchao Feng

    2018-03-01

    Full Text Available We propose non-parametric methods for both local and global sensitivity analysis of chemical reaction models with correlated parameter dependencies. The developed mathematical and statistical tools are applied to a benchmark Langmuir competitive adsorption model on a close packed platinum surface, whose parameters, estimated from quantum-scale computations, are correlated and are limited in size (small data. The proposed mathematical methodology employs gradient-based methods to compute sensitivity indices. We observe that ranking influential parameters depends critically on whether or not correlations between parameters are taken into account. The impact of uncertainty in the correlation and the necessity of the proposed non-parametric perspective are demonstrated.

  12. Effects of ion-neutral chemical reactions on dynamics of lightning-induced electric field

    International Nuclear Information System (INIS)

    Hiraki, Yasutaka

    2009-01-01

    Secondary lightning phenomena in the upper atmosphere called sprites attract interest from the viewpoint of atomic-molecular and plasma physics. Lightning-induced electric field accelerates the ionospheric electrons up to tens of electron-volts, inducing electrical breakdown as well as strong optical emissions, through electron impact ionization of molecules. A large-scale structure of sprites is constructed by collective dynamics of filamentary streamer discharges in a rarified gas, which in turn is controlled by the distribution of the background electric field. In this paper, we firstly reanalyze the relationship between quasi-static field formation and local ion chemistry with first-order perturbation techniques. Secondly, we investigate with a full ion chemical model the effects of electron attachment to oxygen molecules on its density in moderate cases of undervoltage lightning electric fields rather than the cases of intense ionization in streamers. We estimate the minimum values that are provided by the chemical balance with electron detachment from negative ions. We also investigate the recovery timescale of the electron density and find that the scale (≥1 s) is occasionally much larger than the interval of each lightning stroke (∼10 ms). We suggest that the subsequent sprite event as well as the field formation could be well affected by the ghost of the primary event. We discuss further the negative ion chemistry triggered by electron attachment in the nighttime mesosphere.

  13. Study of the intermediate-energy nucleon-nucleus reactions in terms of the quantum molecular dynamics

    International Nuclear Information System (INIS)

    Chiba, Satoshi; Niita, Koji; Maruyama, Toshiki; Fukahori, Tokio; Takada, Hiroshi; Iwamoto, Akira

    1995-01-01

    The double-differential (p,xp') and (p,xn) reaction cross sections of 58 Ni and 90 Zr in the energy range from 120 to 200 MeV have been studied in terms of the Quantum Molecular Dynamics. It was found that the present calculation could give a quantitative explanation of experimentally observed values of both channels simultaneously without adjusting any parameter, showing the usefulness of the QMD approach to study the pre-equilibrium process in this energy region. Comparisons were also made with prediction of other theories such as Antisymmetrized Molecular Dynamics (AMD) and semiclassical distorted wave theory. Effect of the anti-symmetrization, which is in AMD but not in QMD, was found surprisingly small, being the result of QMD even slightly better. At the same time, it was found that the present calculation does not give the quasi-free peak of the 1-step cross sections similar to the semiclassical model, due probably to different treatment of the refraction and acceleration effects caused by the mean field. (author)

  14. Picosecond dynamics of reactions in the liquid phase: studies of iodine photodissociation and development of new laser techniques

    International Nuclear Information System (INIS)

    Berg, M.A.

    1985-09-01

    Iodine photodissociation and recombination was studied as a model for processes common to chemical reaction in the liquid phase. Picosecond transient absorption measurements from 1000 to 295 nm were used to monitor the dynamics in a variety of solvents. Most of the atoms which undergo geminate recombination were found to do so in less than or equal to 15 ps, in agreement with the results of existing molecular dynamics simulations. Vibrational relaxation times vary from approx.15 ps near the middle of the ground state well to approx.150 ps for complete relaxation to v = 0. The prediction of strong resonant vibrational energy transfer to chlorinated methane solvents was not supported, but some evidence for this mechanism was found for alkane solvents. Current theory is unable to explain the large variation (65 to 2700 ps) of the excited A'-state lifetime in various solvents. The 10-Hz amplified, synchronously-pumped dye laser which was used in these studies is described and characterized. SERS (Stimulated Electronic Raman Scattering) and difference frequency mixing were used in the generation of the infrared and far-infrared, respectively. 54 refs., 38 figs., 3 tabs

  15. Role of rotational energy and deformations in the dynamics of {sup 6}Li+{sup 90}Zr reaction

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Gurvinder; Grover, Neha; Sandhu, Kirandeep; Sharma, Manoj K., E-mail: msharma@thapar.edu

    2014-07-15

    In reference to recent experimental data, the dynamical cluster-decay model (DCM) has been applied to study the neutron evaporation residue (ER) cross sections of intermediate mass nucleus {sup 96}Tc{sup ⁎} spread over a wide range of incident energy across the Coulomb barrier. In order to analyze the effect of rotational energy in the dynamics of {sup 6}Li+{sup 90}Zr reaction, the cross sections have been calculated using the sticking (I{sub S}) and the non-sticking (I{sub NS}) limits of moment of inertia with inclusion of quadrupole (β{sub 2}) deformation within optimum orientation approach. The effect of either of the two approaches on the angular momentum, and hence the rotational energy associated with it, is assessed through the fragment mass distribution, preformation factor and the barrier penetrability. Also, the role of deformations is studied through a comparative analysis of decay path for spherical and β{sub 2} deformed fragmentation. The calculated evaporation residue cross sections show excellent agreement with the reported data at all incident energies for both spherical and β{sub 2}-deformed approach. Finally, the incomplete fusion (ICF) process observed due to loosely bound projectile {sup 6}Li is addressed within the framework of DCM.

  16. Effect of an organoclay on the reaction-induced phase-separation in a dynamically asymmetric epoxy/PCL system

    Directory of Open Access Journals (Sweden)

    J. Rotrekl

    2013-12-01

    Full Text Available The addition of layered silicates can significantly affect the phase behaviour of both immiscible thermoplastic blends and partially miscible thermoset systems that undergo reaction-induced phase separation (RIPS during curing. This study focuses on the phase behaviour of polycaprolactone (PCL/epoxy in the presence of organically modified montmorillonite (oMMT. Due to the high dynamic asymmetry caused by the differences in the molecular weights and viscosities of the PCL and the uncured epoxy, the critical point is localised at low PCL concentrations, as indicated by the pseudophase diagram. The addition of oMMT to the system led to the marked shift of the critical point towards higher concentrations of PCL, with an increase in the oMMT content occurring as a consequence of the preferential localisation of the clay in the epoxy phase, making this phase more dynamically slow. Significant changes in morphology, including phase inversion of the PCL/epoxy systems caused by the presence of oMMT, were recorded for PCL concentrations ranging from 10 to 30%.

  17. Monitoring dynamic reactions of red blood cells to UHF electromagnetic waves radiation using a novel micro-imaging technology.

    Science.gov (United States)

    Ruan, Ping; Yong, Junguang; Shen, Hongtao; Zheng, Xianrong

    2012-12-01

    Multiple state-of-the-art techniques, such as multi-dimensional micro-imaging, fast multi-channel micro-spetrophotometry, and dynamic micro-imaging analysis, were used to dynamically investigate various effects of cell under the 900 MHz electromagnetic radiation. Cell changes in shape, size, and parameters of Hb absorption spectrum under different power density electromagnetic waves radiation were presented in this article. Experimental results indicated that the isolated human red blood cells (RBCs) do not have obviously real-time responses to the ultra-low density (15 μW/cm(2), 31 μW/cm(2)) electromagnetic wave radiation when the radiation time is not more than 30 min; however, the cells do have significant reactions in shape, size, and the like, to the electromagnetic waves radiation with power densities of 1 mW/cm(2) and 5 mW/cm(2). The data also reveal the possible influences and statistical relationships among living human cell functions, radiation amount, and exposure time with high-frequency electromagnetic waves. The results of this study may be significant on protection of human being and other living organisms against possible radiation affections of the high-frequency electromagnetic waves.

  18. Spin dynamics and zero-field splitting constants of the triplet exciplex generated by photoinduced electron transfer reaction between erythrosin B and duroquinone

    OpenAIRE

    Tachikawa, Takashi; Kobori, Yasuhiro; Akiyama, Kimio; Katsuki, Akio; Steiner, Ulrich; Tero-Kubota, Shozo

    2002-01-01

    The spin dynamics of the duroquinone anion radical generated by photoinduced electron transfer reactions from triplet erythrosin B to duroquinone has been studied by using transient absorption and pulsed FT-EPR spectroscopy. Triplet exciplex formation as the reaction intermediate is verified by the observation of spin orbit coupling induced electron spin polarization. The kinetic parameters for exciplex formation and the intrinsic enhancement factors of electron spin polarization are determin...

  19. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

    2018-04-01

    A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

  20. Direct dynamics trajectory study of the reaction of formaldehyde cation with D2: vibrational and zero-point energy effects on quasiclassical trajectories.

    Science.gov (United States)

    Liu, Jianbo; Song, Kihyung; Hase, William L; Anderson, Scott L

    2005-12-22

    Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.

  1. Dynamically biased statistical model for the ortho/para conversion in the H2 + H3+ → H3+ + H2 reaction

    OpenAIRE

    Gómez-Carrasco, Susana; González-Sánchez, Lola; Aguado, Alfredo; Sanz-Sanz, Cristina; Zanchet, Alexandre; Roncero, Octavio

    2012-01-01

    In this work we present a dynamically biased statistical model to describe the evolution of the title reaction from statistical to a more direct mechanism, using quasi-classical trajectories (QCT). The method is based on the one previously proposed by Park and Light [J. Chem. Phys. 126, 044305 (2007)10.1063/1.2430711]. A recent global potential energy surface is used here to calculate the capture probabilities, instead of the long-range ion-induced dipole interactions. The dynamical constrain...

  2. Bimolecular Complementation to Visualize Filovirus VP40-Host Complexes in Live Mammalian Cells: Toward the Identification of Budding Inhibitors

    Directory of Open Access Journals (Sweden)

    Yuliang Liu

    2011-01-01

    Full Text Available Virus-host interactions play key roles in promoting efficient egress of many RNA viruses, including Ebola virus (EBOV or “e” and Marburg virus (MARV or “m”. Late- (L- domains conserved in viral matrix proteins recruit specific host proteins, such as Tsg101 and Nedd4, to facilitate the budding process. These interactions serve as attractive targets for the development of broad-spectrum budding inhibitors. A major gap still exists in our understanding of the mechanism of filovirus budding due to the difficulty in detecting virus-host complexes and mapping their trafficking patterns in the natural environment of the cell. To address this gap, we used a bimolecular complementation (BiMC approach to detect, localize, and follow the trafficking patterns of eVP40-Tsg101 complexes in live mammalian cells. In addition, we used the BiMC approach along with a VLP budding assay to test small molecule inhibitors identified by in silico screening for their ability to block eVP40 PTAP-mediated interactions with Tsg101 and subsequent budding of eVP40 VLPs. We demonstrated the potential broad spectrum activity of a lead candidate inhibitor by demonstrating its ability to block PTAP-dependent binding of HIV-1 Gag to Tsg101 and subsequent egress of HIV-1 Gag VLPs.

  3. Asymmetrical distorted structure, dynamics, and reactions of the silacyclohexane and related radical cations: ESR and ab-initio MO study

    International Nuclear Information System (INIS)

    Komaguchi, Kenji; Shiotani, Masaru; Ishikawa, Mitsuo

    1995-01-01

    The σ-type radical cations generated by one electron oxidation of the saturated hydrocarbon have been attracted much attention because of their fundamental importance as primary reactant species in radiation chemistry. Our studies on σ-type radical cations were recently extended to the silacyclohexane (cSiC5), silacyclopentane (cSiC4), and silacyclobutane (cSiC3) radical cations. Their electronic structure, dynamics, and reactions were investigated by means of low temperature matrix isolation ESR technique combined with ionizing radiation (γ-rays from 60 Co). In the preceding paper, the 1-methylsilacyclohexane (1-Me-cSiC5) radical cation has been found to take an asymmetrically distorted C 1 structure with one of two Si-C bonds elongated in which the unpaired electron mainly resides ( 2 A in C 1 ). This conclusion was based on the 4.2 K ESR spectra of radical cations of selectively deuteriated and/or methylsubstituted silacyclohexanes, i.e., cSiC5-2,2,6,6-d 4 + , 1-Me-cSiC5 + , 1-Me-cSiC5-2,2-d 2 + , 1-Me-cSiC5-2,2,6,6-d 4 + , 1,1-Me 2 -cSiC5 + , and 4,4-Me 2 -cSiC5 + , in a frozen CF 3 -cC 6 F 11 matrix. Here we report further experimental and theoretical results on 1-methylsilacyclohexane radical cation, especially on the ab initio MO results and matrix effects on the structural distortion, as well as thermal reactions of the radical cations. The results will make it clear that the distorted C 1 structure of the 1-Me-cSiC5 + is the intrinsic nature at the ground electronic state. (J.P.N.)

  4. Study of breakup and transfer of weakly bound nucleus 6Li to explore the low energy reaction dynamics

    Science.gov (United States)

    Zhang, G. L.; Zhang, G. X.; Hu, S. P.; Zhang, H. Q.; Gomes, P. R. S.; Lubian, J.; Guo, C. L.; Wu, X. G.; Yang, J. C.; Zheng, Y.; Li, C. B.; He, C. Y.; Zhong, J.; Li, G. S.; Yao, Y. J.; Guo, M. F.; Sun, H. B.; Valiente-Dobòn, J. J.; Goasduff, A.; Siciliano, M.; Galtarosa, F.; Francesco, R.; Testov, D.; Mengoni, D.; Bazzacco, D.; John, P. R.; Qu, W. W.; Wang, F.; Zheng, L.; Yu, L.; Chen, Q. M.; Luo, P. W.; Li, H. W.; Wu, Y. H.; Zhou, W. K.; Zhu, B. J.; Li, E. T.; Hao, X.

    2017-11-01

    Investigation of the breakup and transfer effect of weakly bound nuclei on the fusion process has been an interesting research topic in the past several years. However, owing to the low intensities of the presently available radioactive ion beam (RIB), it is difficult to clearly explore the reaction mechanisms of nuclear systems with unstable nuclei. In comparison with RIB, the beam intensities of stable weakly bound nuclei such as 6,7Li and 9Be, which have significant breakup probability, are orders of magnitude higher. Precise fusion measurements have already been performed with those stable weakly bound nuclei, and the effect of breakup of those nuclei on the fusion process has been extensively studied. Those nuclei indicated large production cross sections for particles other than the α + x breakup. The particles are originated from non-capture breakup (NCBU), incomplete fusion (ICF) and transfer processes. However, the conclusion of reaction dynamics was not clear and has the contradiction. In our previous experiments we have performed 6Li+96Zr and 154Sm at HI-13 Tandem accelerator of China Institute of Atomic Energy (CIAE) by using HPGe array. It is shown that there is a small complete fusion (CF) suppression on medium-mass target nucleus 96Zr different from about 35% suppression on heavier target nucleus 154Sm at near-barrier energies. It seems that the CF suppression factor depends on the charge of target nuclei. We also observed one neutron transfer process. However, the experimental data are scarce for medium-mass target nuclei. In order to have a proper understanding of the influence of breakup and transfer of weakly bound projectiles on the fusion process, we performed the 6Li+89Y experiment with incident energies of 22 MeV and 34 MeV on Galileo array in cooperation with Si-ball EUCLIDES at Legnaro National Laboratory (LNL) in Italy. Using particle-particle and particle-γ coincidences, the different reaction mechanisms can be clearly explored.

  5. Dynamically Adapted Mesh Construction for the Efficient Numerical Solution of a Singular Perturbed Reaction-diffusion-advection Equation

    Directory of Open Access Journals (Sweden)

    Dmitry V. Lukyanenko

    2017-01-01

    Full Text Available This  work develops  a theory  of the  asymptotic-numerical investigation of the  moving fronts  in reaction-diffusion-advection models.  By considering  the  numerical  solution  of the  singularly perturbed Burgers’s  equation  we discuss a method  of dynamically  adapted mesh  construction that is able to significantly  improve  the  numerical  solution  of this  type of equations.  For  the  construction we use a priori information that is based  on the  asymptotic analysis  of the  problem.  In  particular, we take  into account the information about  the speed of the transition layer, its width  and structure. Our algorithms  are able to reduce significantly complexity and enhance stability of the numerical  calculations in comparison  with classical approaches for solving this class of problems.  The numerical  experiment is presented to demonstrate the effectiveness of the proposed  method.The article  is published  in the authors’  wording. 

  6. Chemical reaction dynamics of Rydberg atoms with neutral molecules: A comparison of molecular-beam and classical trajectory results for the H(n)+D2→HD+D(n') reaction

    International Nuclear Information System (INIS)

    Song Hui; Dai Dongxu; Wu Guorong; Wang, C.-C.; Harich, Steven A.; Hayes, Michael Y.; Wang Xiuyan; Gerlich, Dieter; Yang Xueming; Skodje, Rex T.

    2005-01-01

    Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D 2 →HD+D(n) at low collision energies. It was discovered that the rotationally resolved product distribution was remarkably similar to a much more limited data set obtained at a single scattering angle for the ion-molecule reaction H + +D 2 →D + +HD. The equivalence of these two problems would be consistent with the Fermi-independent-collider model (electron acting as a spectator) and would provide an important new avenue for the study of ion-molecule reactions. In this work, we employ a classical trajectory calculation on the ion-molecule reaction to facilitate a more extensive comparison between the two systems. The trajectory simulations tend to confirm the equivalence of the ion+molecule dynamics to that for the Rydberg-atom+molecule system. The theory reproduces the close relationship of the two experimental observations made previously. However, some differences between the Rydberg-atom experiments and the trajectory simulations are seen when comparisons are made to a broader data set. In particular, the angular distribution of the differential cross section exhibits more asymmetry in the experiment than in the theory. The potential breakdown of the classical model is discussed. The role of the 'spectator' Rydberg electron is addressed and several crucial issues for future theoretical work are brought out

  7. Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

    Science.gov (United States)

    Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

    2016-07-14

    We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

  8. Improved thermodynamics of the dense solar plasma and molecular-dynamics simulations of the nuclear-reaction rates

    Science.gov (United States)

    Mao, Dan

    available, there is no alternative source. The official OPAL tables, however, have disadvantages. First, they are inflexible regarding the chemical mix, which is set once and for all by the producers of the tables. Our equation of state will allow the user to choose, in principle, an arbitrary mix. Second, the OPAL tables by their very nature are limited by the errors of interpolation within tables. The second equation of state model is a density expansion based on the Feynman-Kac path-integral formalism. By making use of the equivalence of quantum Hamiltonian matrix and the classical action of closed and open filaments (paths), an analytic formalism of equation of state. Although the character of density expansion limits its application, the formalism can still be valid in most region in the Sun. Our work provides the link between the abstract theoretical formalism that was developed in the 1990s and a numerically smooth realization that can be used in solar and stellar models. Since it is so far the most exact and systematic approach for an EOS, it provides another way to study the influence of different very fine physical effects, despite considerable limitations in its domain of applicability. In the nuclear-reaction part of the thesis, we have used a molecular-dynamics method to simulate the motion of protons in a hydrogen plasma (which is a good approximation for this purpose). Quantum tunneling explains why nuclear fusion can occur in the first place, considering the "low" temperature in the solar core. It is well known that this tunneling is enhanced (which leads to higher nuclear reaction rates) in the presence of Coulomb screening. In the 1950, Salpeter formulated a theory based on the static-screened Coulomb potential, as derived by Debye and H=FCckel in the 1920s. As expected, Salpeter obtained enhanced reaction rates. But from our simulation, we confirmed the results of a recent controversy about the existence of a dynamic effect. Since the bulk of fusion

  9. Optimization and application of ICPMS with dynamic reaction cell for precise determination of 44Ca/40Ca isotope ratios.

    Science.gov (United States)

    Boulyga, Sergei F; Klötzli, Urs; Stingeder, Gerhard; Prohaska, Thomas

    2007-10-15

    An inductively coupled plasma mass spectrometer with dynamic reaction cell (ICP-DRC-MS) was optimized for determining (44)Ca/(40)Ca isotope ratios in aqueous solutions with respect to (i) repeatability, (ii) robustness, and (iii) stability. Ammonia as reaction gas allowed both the removal of (40)Ar+ interference on (40)Ca+ and collisional damping of ion density fluctuations of an ion beam extracted from an ICP. The effect of laboratory conditions as well as ICP-DRC-MS parameters such a nebulizer gas flow rate, rf power, lens potential, dwell time, or DRC parameters on precision and mass bias was studied. Precision (calculated using the "unbiased" or "n - 1" method) of a single isotope ratio measurement of a 60 ng g(-1) calcium solution (analysis time of 6 min) is routinely achievable in the range of 0.03-0.05%, which corresponded to the standard error of the mean value (n = 6) of 0.012-0.020%. These experimentally observed RSDs were close to theoretical precision values given by counting statistics. Accuracy of measured isotope ratios was assessed by comparative measurements of the same samples by ICP-DRC-MS and thermal ionization mass spectrometry (TIMS) by using isotope dilution with a (43)Ca-(48)Ca double spike. The analysis time in both cases was 1 h per analysis (10 blocks, each 6 min). The delta(44)Ca values measured by TIMS and ICP-DRC-MS with double-spike calibration in two samples (Ca ICP standard solution and digested NIST 1486 bone meal) coincided within the obtained precision. Although the applied isotope dilution with (43)Ca-(48)Ca double-spike compensates for time-dependent deviations of mass bias and allows achieving accurate results, this approach makes it necessary to measure an additional isotope pair, reducing the overall analysis time per isotope or increasing the total analysis time. Further development of external calibration by using a bracketing method would allow a wider use of ICP-DRC-MS for routine calcium isotopic measurements, but it

  10. Laser ablation inductively coupled plasma dynamic reaction cell mass spectrometry for the multi-element analysis of polymers

    Science.gov (United States)

    Resano, M.; García-Ruiz, E.; Vanhaecke, F.

    2005-11-01

    In this work, the potential of laser ablation-inductively coupled plasma-mass spectrometry for the fast analysis of polymers has been explored. Different real-life samples (polyethylene shopping bags, an acrylonitrile butadiene styrene material and various plastic bricks) as well as several reference materials (VDA 001 to 004, Cd in polyethylene) have been selected for the study. Two polyethylene reference materials (ERM-EC 680 and 681), for which a reference or indicative value for the most relevant metals is available, have proved their suitability as standards for calibration. Special attention has been paid to the difficulties expected for the determination of Cr at the μg g - 1 level in this kind of materials, due to the interference of ArC + ions on the most abundant isotopes of Cr. The use of ammonia as a reaction gas in a dynamic reaction cell is shown to alleviate this problem, resulting in a limit of detection of 0.15 μg g - 1 for this element, while limiting only modestly the possibilities of the technique for simultaneous multi-element analysis. In this regard, As is the analyte most seriously affected by the use of ammonia, and its determination has to be carried out in vented mode, at the expense of measuring time. In all cases studied, accurate results could be obtained for elements ranging in content from the sub-μg g - 1 level to tens of thousands of μg g - 1 . However, the use of an element of known concentration as internal standard may be needed for materials with a matrix significantly different from that of the standard (polyethylene in this work). Precision ranged between 5% and 10% RSD for elements found at the 10 μg g - 1 level or higher, while this value could deteriorate to 20% for analytes found at the sub-μg g - 1 level. Overall, the technique evaluated presents many advantages for the fast and accurate multi-element analysis of these materials, avoiding laborious digestion procedures and minimizing the risk of analyte losses due

  11. Direct characterization of phase transformations and morphologies in moving reaction zones in Al/Ni nanolaminates using dynamic transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.S., E-mail: judy.kim@materials.ox.ac.uk [Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 (United States); Chemical Engineering and Materials Science/Molecular and Cellular Biology, University of California-Davis, 1 Shields Avenue, Davis, CA 95616 (United States); LaGrange, T.; Reed, B.W. [Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 (United States); Knepper, R.; Weihs, T.P. [Department of Materials Science and Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 (United States); Browning, N.D. [Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 (United States); Chemical Engineering and Materials Science/Molecular and Cellular Biology, University of California-Davis, 1 Shields Avenue, Davis, CA 95616 (United States); Campbell, G.H. [Condensed Matter and Materials Division, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550 (United States)

    2011-05-15

    Highlights: > Fast phase transformations are examined in Al/Ni reactive nanolaminates. > Results visible only by dynamic transmission electron microscopy at ns resolution. > NiAl forms under 15 ns after reaction front in all three stoichiometries studied. > DTEM imaging reveals a transient cellular morphology in nonequiatomic films. - Abstract: Phase transformations and transient morphologies are examined as exothermic formation reactions self-propagate across Al/Ni nanolaminate films. The rapid evolution of these phases and sub-micrometer morphological features requires nanoscale temporal and spatial resolution that is not available with traditional in situ electron microscopy. This work uses dynamic transmission electron microscopy to identify intermetallic products and phase morphologies, as exothermic formation reactions self-propagate in nanolaminate films grown with 3:2, 2:3 and 1:1 Al/Ni atomic ratios. Single-shot diffraction patterns with 15 ns temporal resolution reveal that the NiAl intermetallic forms within {approx}15 ns of the reaction front's arrival in all three types of films and is the only intermetallic phase to form, as the reactions self-propagate and quench very rapidly. Time-resolved imaging reveals a transient cellular morphology in the Al-rich and Ni-rich foils, but not in the equiatomic films. The cellular features in the Al-rich and Ni-rich films are attributed to a cooling trajectory through a two-phase field of liquid + NiAl.

  12. WE-FG-202-01: Early Prediction of Radiotherapy Induced Skin Reactions Using Dynamic Infrared Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Biswal, N [Rutgers Cancer Institute of New Jersey, New Brunswick, NJ (United States); Cifter, G [Boston, MA (United States); Sun, J [Argonne National Laboratory, Lemont, IL (United States); Sen, N; Wang, D; Diaz, A; Griem, K [Rush University Medical Center, Chicago, IL (United States); Chu, J [Rush University Medical Center, Oak Brook, IL (United States)

    2016-06-15

    Purpose: To predict radiotherapy induced skin reactions using dynamic infrared imaging. Methods: Thermal images were captured by our homebuilt system consisting of two flash lamps and an infrared (IR) camera. The surface temperature of the skin was first raised by ∼ 6 oC from ∼1 ms flashes. The camera then captured a series of IR images for 10 seconds. For each image, a baseline skin temperature was recorded for 0.5sec before heat impulse. The temporal temperature gradients were calculated between a reference point (immediately after the flash) and at a time point 9sec after that. Thermal effusivity, an intrinsic thermal property of a material, was calculated from the surface temperature decay of skin. We present experimental data in five patients undergoing radiation therapy, of which 2 were Head & Neck, 1 was Sarcoma and 2 were Breast cancer patients. The prescribed doses were 45 – 60 Gy in 25 – 30 fractions. Each patient was imaged before treatment and after every fifth fraction until end of the treatment course. An area on the skin, outside the radiation field, was imaged as control region. During imaging, each patient’s irradiated skins were scored based on RTOG skin morbidity scoring criteria. Results: Temperature gradient, which is the temperature recovery rate, depends on the thermal properties of underlying tissue. It was observed that, the skin temperature and temporal temperature gradient increases with delivered radiation dose and skin RTOG score. The treatment does not change effusivity of superficial skin layer, however there was a significant difference in effusivity between treated and control areas at depth of ∼ 1.5 – 1.8 mm, increases with dose. Conclusion: The higher temporal temperature gradient and effusivity from irradiated areas suggest that there is more fluid under the irradiated skin, which causes faster temperature recovery. The mentioned effects may be predictors of Moist Desquamation.

  13. A combined crossed molecular beam and theoretical investigation of the reaction of the meta-tolyl radical with vinylacetylene--toward the formation of methylnaphthalenes.

    Science.gov (United States)

    Yang, Tao; Muzangwa, Lloyd; Kaiser, Ralf I; Jamal, Adeel; Morokuma, Keiji

    2015-09-07

    Crossed molecular beam experiments and electronic structure calculations on the reaction of the meta-tolyl radical with vinylacetylene were conducted to probe the formation of methyl-substituted naphthalene isomers. We present the compelling evidence that under single collision conditions 1- and 2-methylnaphthalene can be formed without an entrance barrier via indirect scattering dynamics through a bimolecular collision of two non-PAH reactants: the meta-tolyl radical and vinylacetylene. The electronic structure calculations, conducted at the UCCSD(T)-F12b/cc-pVDZ//UM06-2x/cc-pVTZ + ZPE(UM06-2x/cc-pVTZ) level of theory, reveal that this reaction is initiated by the barrierless addition of the meta-tolyl radical to the terminal vinyl carbon (C1) of vinylacetylene, via a van-der-Waals complex implying that this mechanism can play a key role in forming methyl-substituted PAHs in low temperature extreme environments such as the low temperature interstellar medium and hydrocarbon-rich atmospheres of planets and their moons in the outer solar system. The reaction mechanism, proposed from the C11H11 potential energy surface, involves a sequence of isomerizations involving hydrogen transfer and ring closure, followed by hydrogen dissociation, which eventually leads to 1- and 2-methylnaphthalene in an overall exoergic process.

  14. Laser sources and techniques for spectroscopy and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Kung, A.H. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    This program focuses on the development of novel laser and spectroscopic techniques in the IR, UV, and VUV regions for studying combustion related molecular dynamics at the microscopic level. Laser spectroscopic techniques have proven to be extremely powerful in the investigation of molecular processes which require very high sensitivity and selectivity. The authors approach is to use quantum electronic and non-linear optical techniques to extend the spectral coverage and to enhance the optical power of ultrahigh resolution laser sources so as to obtain and analyze photoionization, fluorescence, and photoelectron spectra of jet-cooled free radicals and of reaction products resulting from unimolecular and bimolecular dissociations. New spectroscopic techniques are developed with these sources for the detection of optically thin and often short-lived species. Recent activities center on regenerative amplification of high resolution solid-state lasers, development of tunable high power mid-IR lasers and short-pulse UV/VUV tunable lasers, and development of a multipurpose high-order suppressor crossed molecular beam apparatus for use with synchrotron radiation sources. This program also provides scientific and technical support within the Chemical Sciences Division to the development of LBL`s Combustion Dynamics Initiative.

  15. Cooper pair formation dynamics in Bi2Sr2CaCu2O8+δ

    International Nuclear Information System (INIS)

    Kaindl, R.A.; Carnahan, M.A.; Orenstein, J.; Chemla, D.S.; Oh, S.; Eckstein, J.N.

    2003-01-01

    We utilize ultrafast terahertz pulses to monitor the carrier dynamics in the high-TC superconductor Bi2Sr2CaCu2O8+delta. The temperature, density and time dependence distinctly exposes a bimolecular recombination process of quasiparticles which underlies formation of Cooper pairs

  16. Dynamics of Chemical and Charge Transfer Reactions of Molecular Dications: IV. Proton Transfer and Reactions of Dication Isomers in the CHCl2+ +D2 System

    Czech Academy of Sciences Publication Activity Database

    Roithová, Jana; Žabka, Ján; Hrušák, Jan; Thissen, R.; Herman, Zdeněk

    2003-01-01

    Roč. 107, - (2003), s. 7347-7354 ISSN 1089-5639 R&D Projects: GA ČR GA203/00/0632; GA AV ČR KJB4040302 Grant - others:Barrande(FR) 2002-013-1 Institutional research plan: CEZ:AV0Z4040901 Keywords : dynamics of chemical * molecular dications * proton transfer Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.792, year: 2003

  17. Heavy ion transfer reactions

    Indian Academy of Sciences (India)

    array (CLARA), extensive investigations of nuclear structure and reaction dynamics have been carried out. In the present paper aspects of these studies will be presented, focussing more closely on the reaction mechanism, in particular on the ...

  18. Dynamic pathways to mediate reactions buried in thermal fluctuations. I. Time-dependent normal form theory for multidimensional Langevin equation.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2009-12-14

    We present a novel theory which enables us to explore the mechanism of reaction selectivity and robust functions in complex systems persisting under thermal fluctuation. The theory constructs a nonlinear coordinate transformation so that the equation of motion for the new reaction coordinate is independent of the other nonreactive coordinates in the presence of thermal fluctuation. In this article we suppose that reacting systems subject to thermal noise are described by a multidimensional Langevin equation without a priori assumption for the form of potential. The reaction coordinate is composed not only of all the coordinates and velocities associated with the system (solute) but also of the random force exerted by the environment (solvent) with friction constants. The sign of the reaction coordinate at any instantaneous moment in the region of a saddle determines the fate of the reaction, i.e., whether the reaction will proceed through to the products or go back to the reactants. By assuming the statistical properties of the random force, one can know a priori a well-defined boundary of the reaction which separates the full position-velocity space in the saddle region into mainly reactive and mainly nonreactive regions even under thermal fluctuation. The analytical expression of the reaction coordinate provides the firm foundation on the mechanism of how and why reaction proceeds in thermal fluctuating environments.

  19. Crossed-beam reaction of carbon atoms with hydrocarbon molecules. IV. Chemical dynamics of methylpropargyl radical formation, C4H5, from reaction of C(3Pj) with propylene, C3H6 (X1A)

    International Nuclear Information System (INIS)

    Kaiser, R.I.; Stranges, D.; Bevsek, H.M.; Lee, Y.T.; Suits, A.G.

    1997-01-01

    The reaction between ground state carbon atoms and propylene, C 3 H 6 , was studied at average collision energies of 23.3 and 45.0 kJmol -1 using the crossed molecular beam technique. Product angular distributions and time-of-flight spectra of C 4 H 5 at m/e=53 were recorded. Forward-convolution fitting of the data yields a maximum energy release as well as angular distributions consistent with the formation of methylpropargyl radicals. Reaction dynamics inferred from the experimental results suggest that the reaction proceeds on the lowest 3 A surface via an initial addition of the carbon atom to the π-orbital to form a triplet methylcyclopropylidene collision complex followed by ring opening to triplet 1,2-butadiene. Within 0.3 endash 0.6 ps, 1,2-butadiene decomposes through carbon endash hydrogen bond rupture to atomic hydrogen and methylpropargyl radicals. The explicit identification of C 4 H 5 under single collision conditions represents a further example of a carbon endash hydrogen exchange in reactions of ground state carbon with unsaturated hydrocarbons. This versatile machine represents an alternative pathway to build up unsaturated hydrocarbon chains in combustion processes, chemical vapor deposition, and in the interstellar medium. copyright 1997 American Institute of Physics

  20. Effect of CH stretching excitation on the reaction dynamics of F + CHD{sub 3} → DF + CHD{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiayue; Zhang, Dong; Chen, Zhen; Jiang, Bo [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, Liaoning 116023 (China); Blauert, Florian [Dynamics at Surfaces, Faculty of Chemistry, Georg-August-Universität Göttingen, 37077 Göttingen (Germany); Dai, Dongxu; Wu, Guorong, E-mail: wugr@dicp.ac.cn, E-mail: xmyang@dicp.ac.cn; Zhang, Donghui; Yang, Xueming, E-mail: wugr@dicp.ac.cn, E-mail: xmyang@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, Liaoning 116023 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-07-28

    The vibrationally excited reaction of F + CHD{sub 3}(ν{sub 1} = 1) → DF + CHD{sub 2} at a collision energy of 9.0 kcal/mol is investigated using the crossed-beams and time-sliced velocity map imaging techniques. Detailed and quantitative information of the CH stretching excitation effects on the reactivity and dynamics of the title reaction is extracted with the help of an accurate determination of the fraction of the excited CHD{sub 3} reagent in the crossed-beam region. It is found that all vibrational states of the CHD{sub 2} products observed in the ground-state reaction, which mainly involve the excitation of the umbrella mode of the CHD{sub 2} products, are severely suppressed by the CH stretching excitation. However, there are four additional vibrational states of the CHD{sub 2} products appearing in the excited-state reaction which are not presented in the ground-state reaction. These vibrational states either have the CH stretching excitation retained or involve one quantum excitation in the CH stretching and the excitation of the umbrella mode. Including all observed vibrational states, the overall cross section of the excited-state reaction is estimated to be 66.6% of that of the ground-state one. Experimental results also show that when the energy of CH stretching excitation is released during the reaction, it is deposited almost exclusively as the rovibrational energy of the DF products, with little portion in the translational degree of freedom. For vibrational states of the CHD{sub 2} products observed in both ground- and excited-state reactions, the CH stretching excitation greatly suppresses the forward scattered products, causing a noticeable change in the product angular distributions.

  1. Microscopic approach of molecular dynamics. Applications to reactions near the barrier; Approches microscopiques de la dynamique nucleaire. Applications aux reactions autour de la barriere

    Energy Technology Data Exchange (ETDEWEB)

    Simenel, C.; Avez, B. [CEA Saclay, Dept. d' Astrophysique, de Physique des Particules de Physique Nucleaire et de l' Instrumentation Associee (DSM/DAPNIA/SPhN), 91- Gif sur Yvette (France); Lacroix, D. [GANIL, 14 - Caen (France)

    2007-07-01

    This lecture introduces several microscopic approaches to nuclear dynamics. Our goal is to provide a good description of low energy heavy ions collisions. We study both the formalism and the practical application of the time-dependent Hartree-Fock (TDHF) theory. The TDHF approach gives a mean field dynamics of the system under the assumption of independent particles. As an example, we study the fusion of both spherical and deformed nuclei with TDHF. We also show that nucleon transfer may occur between nuclei below the barrier. These studies allow us to specify the field of applications of TDHF in one hand, and, in the other hand, its intrinsic limitations, as for instance the fact that there is no fusion by tunnel effect with TDHF. It is then important to get rid of the independent particle assumption. We finally present some approaches to go beyond TDHF, including for instance pairing and/or collision term between nucleons, though only few realistic applications have been performed so far. (authors)

  2. The dynamics of the H(+) + D(2) reaction: a comparison of quantum mechanical wavepacket, quasi-classical and statistical-quasi-classical results.

    Science.gov (United States)

    Jambrina, P G; Aoiz, F J; Bulut, N; Smith, Sean C; Balint-Kurti, G G; Hankel, M

    2010-02-07

    A detailed study of the proton exchange reaction H(+) + D(2)(v = 0, j = 0) --> HD + D(+) on its ground 1(1)A' potential energy surface has been carried out using 'exact' close-coupled quantum mechanical wavepacket (WP-EQM), quasi-classical trajectory (QCT), and statistical quasi-classical trajectory (SQCT) calculations for a range of collision energies starting from the reaction threshold to 1.3 eV. The WP-EQM calculations include all total angular momenta up to J(max) = 50, and therefore the various dynamical observables are converged up to 0.6 eV. It has been found that it is necessary to include all Coriolis couplings to obtain reliable converged results. Reaction probabilities obtained using the different methods are thoroughly compared as a function of the total energy for a series of J values. Comparisons are also made of total reaction cross sections as function of the collision energy, and rate constants. In addition, opacity functions, integral cross sections (ICS) and differential cross sections (DCS) are presented at 102 meV, 201.3 meV and 524.6 meV collision energy. The agreement between the three sets of results is only qualitative. The QCT calculations fail to describe the overall reactivity and most of the dynamical observables correctly. At low collision energies, the QCT method is plagued by the lack of conservation of zero point energy, whilst at higher collision energies and/or total angular momenta, the appearance of an effective repulsive potential associated with the centrifugal motion "over" the well causes a substantial decrease of the reactivity. In turn, the statistical models overestimate the reactivity over the whole range of collision energies as compared with the WP-EQM method. Specifically, at sufficiently high collision energies the reaction cannot be deemed to be statistical and important dynamical effects seem to be present. In general the WP-EQM results lie in between those obtained using the QCT and SQCT methods. One of the main

  3. Magnetic Dipole and Gamow-Teller Modes in Neutrino-Nucleus Reactions: Impact on Supernova Dynamics and Nucleosynthesis

    International Nuclear Information System (INIS)

    Neumann-Cosel, P. von; Byelikov, A.; Richter, A.; Shevchenko, A.; Adachi, T.; Fujita, Y.; Shimbara, Y.; Fujita, H.; Heger, A.; Kolbe, E.; Langanke, K.; Martinez-Pinedo, G.

    2006-01-01

    Some aspects of the importance of neutrino-induced reactions on nuclei within supernova physics are discussed. It is argued that important constraints on the experimentally unknown cross sections can be obtained from experimental studies of the nuclear response in selected cases. Examples are neutral-current induced reactions on fp-shell nuclei extracted from high-resolution inelastic electron scattering data providing the M1 strength distributions and the production of the exotic heavy, odd-odd nuclei 138La and 180Ta through charged-current reactions dominated by Gamow-Teller transitions. The Gamow-Teller strength can deduced from the (3He,t) charge-exchange reaction at zero degree

  4. Calculation of rate coefficients of some proton-transfer ion-molecule reactions in weakly ionized gases

    International Nuclear Information System (INIS)

    Stiller, W.

    1985-01-01

    A classical collision theory is used to describe thermal bimolecular rate coefficeints for reaction between positive and negative ions and polar molecules in a carrier gas. Special attention is paid to ion-molecule reaction in which proton transfer occurs. These reactions play an important role in terrestrial plasma devices, in ionosphere, in planetary atmospheres and in interstellar matter. The equilibrium rate coefficients of the reactions are calculated based on a microscopic reactive cross section derived from a long distance polar molecule-ion potential. The results are compared with experimental values of afterglow measurements. (D.Gy.)

  5. Modelling of gas-liquid reactors - stability and dynamic behaviour of gas-liquid mass transfer accompanied by irreversible reaction

    NARCIS (Netherlands)

    Elk, E.P. van; Borman, P.C.; Kuipers, J.A.M.; Versteeg, G.F.

    1999-01-01

    The dynamic behaviour and stability of single-phase reacting systems has been investigated thoroughly in the past and design rules for stable operation are available from literature. The dynamic behaviour of gas-liquid processes is considerably more complex and has received relatively little

  6. Modelling of gas-liquid reactors - stability and dynamic behaviour of gas-liquid mass transfer accompanied by irreversible reaction

    NARCIS (Netherlands)

    Elk, van E.P.; Borman, P.C.; Kuipers, J.A.M.; Versteeg, G.F.

    1999-01-01

    The dynamic behaviour and stability of single-phase reacting systems has been investigated thoroughly in the past and design rules for stable operation are available from literature. The dynamic behaviour of gas–liquid processes is considerably more complex and has received relatively little

  7. Impact of the in-medium nucleon-nucleon cross section on early-reaction-phase dynamics below 100 MeV/u

    International Nuclear Information System (INIS)

    Basrak, Z.; Zoric, M.; Eudes, P.; Sebille, F.

    2009-01-01

    It has been shown theoretically [1] and confirmed experimentally [2] that heavy ion reactions (HIR) at intermediate energies, especially for central collisions, are strongly dominated by the mid-rapidity emission, a component which is emitted early during the dynamical reaction phase. This prompt and copious dynamical emission is proportional to the impact parameter 6 and evacuates a large amount of available system energy [1,3]. Since this emission occurs in the early compact phase of HIR, it is crucial to study details of the early transformation of the initial relative motion of the entrance reaction channel into other forms of energy in particular to its main components, heat E th and compression E compr . We have carried out such a study within the framework of the semi-classical Landau-Vlasov model with the momentum-dependent Gogny interaction D1-G1 [4]. In this model, σ NN is the free nucleon-nucleon cross section with its usual energy and isospin dependence. For the sake of simplicity, σ NN is assumed to be isotropic and density independent, an approximation which is fully justified in HIR below 100 MeV/u. In an earlier work the free nucleon-nucleon cross section was considered [5]. Here, we investigate the in-medium effects, i.e. how the change of σ NN influences the early energy transformation and the early particle emission. The change is taken into account by multiplying σ NN by a corrective constant factor F. In other words, we examine how the E th and E compr evolve with the reaction time and how the dynamical emission behaves and both as a function of the factor F. We investigate two systems: 3 6A r + 6 8N i and 6 8N i + 6 8N i reactions at 52, 74, and 95 MeV/u (52, 74, and 90 MeV/u for the latter reaction) at all impact parameters from central to peripheral collisions. The results of the simulations show that the time evolution of heat E th and compression E compr during the early dynamical reaction phase present maxima at all incident energies

  8. Atom-radical reaction dynamics of O(3P)+C3H5→C3H4+OH: Nascent rovibrational state distributions of product OH

    Science.gov (United States)

    Park, Jong-Ho; Lee, Hohjai; Kwon, Han-Cheol; Kim, Hee-Kyung; Choi, Young-Sang; Choi, Jong-Ho

    2002-08-01

    The reaction dynamics of ground-state atomic oxygen [O(3P)] with allyl radicals (C3H5) has been investigated by applying a combination of crossed beams and laser induced fluorescence techniques. The reactants O(3P) and C3H5 were produced by the photodissociation of NO2 and the supersonic flash pyrolysis of precursor allyl iodide, respectively. A new exothermic channel of O(3P)+C3H5→C3H4+OH was observed and the nascent internal state distributions of the product OH (X 2Π:υ″=0,1) showed substantial bimodal internal excitations of the low- and high-N″ components without Λ-doublet and spin-orbit propensities in the ground and first excited vibrational states. With the aid of the CBS-QB3 level of ab initio theory and Rice-Ramsperger-Kassel-Marcus calculations, it is predicted that on the lowest doublet potential energy surface the major reaction channel of O(3P) with C3H5 is the formation of acrolein (CH2CHCHO)+H, which is consistent with the previous bulk kinetic experiments performed by Gutman et al. [J. Phys. Chem. 94, 3652 (1990)]. The counterpart C3H4 of the probed OH product in the title reaction is calculated to be allene after taking into account the factors of reaction enthalpy, barrier height and the number of intermediates involved along the reaction pathway. On the basis of population analyses and comparison with prior calculations, the statistical picture is not suitable to describe the reactive atom-radical scattering processes, and the dynamics of the title reaction is believed to proceed through two competing dynamical pathways. The major low N″-components with significant vibrational excitation may be described by the direct abstraction process, while the minor but extraordinarily hot rotational distribution of high N″-components implies that some fraction of reactants is sampled to proceed through the indirect short-lived addition-complex forming process.

  9. Pericyclic reactions in an aqueous molecular flask.

    Science.gov (United States)

    Murase, Takashi; Fujita, Makoto

    2010-10-01

    A self-assembled molecular flask with a nanometer-sized restricted cavity offers a new reaction environment that is quite different from the bulk solution. The self-assembled cage accommodates a pair of hydrophobic molecules to perform unusual Diels-Alder reactions and [2+2] photoadditions of otherwise unreactive aromatic molecules. In this cage, for example, the Diels-Alder reaction of naphthalene proceeds smoothly under mild conditions, and aceanthrylene shows reactivity for both [2+2] and [2+4] cycloadditions via the identical ternary host-guest complex. The observed greatly enhanced reactivity stems from the increased local concentration and pre-organization of the substrate pair within the cage, which reduces the entropic cost and switches the reaction profile from a bimolecular to a pseudo-intramolecular reaction pathway. The reinforced orientation and arrangement of substrate pairs specify regio- and stereo-selectivities of the subsequent reactions in the cavity. Chiral auxiliaries outside the cage create the inner chiral environment and induce asymmetric reactions inside the cage (up to 50% ee). © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  10. The Atmospheric Oxidation of Volatile Organic Compounds Through Hydrogen Shift Reactions

    DEFF Research Database (Denmark)

    Knap, Hasse Christian

    a radical is denoted as a H-shift reaction. Quantum chemical calculations were carried out to investigate the potential energy surface of the H-shift reactions and the subsequent decomposition pathways. The transition state theory including the Eckart quantum tunneling correction have been used to calculate...... the reaction rate constants of the H-shift reactions. The autoxidation of volatile organic compounds is an important oxidation mechanism that produces secondary organic aerosols (SOA) and recycles hydroxyl (OH) radicals. The autoxidation cycle produces a second generation peroxy radical (OOQOOH) through...... a series of H-shift reactions and O2 attachments. I have investigated the H-shift reactions in two OOQOOH radicals (hydroperoxy peroxy radicals and hydroperoxy acyl peroxy radicals). The H-shift reaction rate constants have been compared with the bimolecular reaction rate constants of the peroxy radicals...

  11. Special aspects of hemo-dynamic and reaction of erythrocytes in blood to standard physical load of different qualification female volleyball players

    Directory of Open Access Journals (Sweden)

    S. L. Popel’

    2017-10-01

    Full Text Available Purpose: to study the aspects of organism’s cardio-hemo-dynamic and blood erythrocytes reaction of female volleyball players to standard physical load. Material: with functional methods we studied cardio-hemo-dynamic and with the help of scanning electronic microscopy - erythrocytes’ structure in 18 female volleyball players of different qualification (age - 22.0±0.60 years. Results: it was found that maximal physical load causes substantial changes in cardio-hemo-dynamic, which depend on female volleyball players’ qualification. These changes have intrinsic to them type of blood circulation system reacting, which is manifested in the following: appropriate changes of some indicators; natural changes of periphery blood erythrocytes. In the article possible mechanisms of realization of female volleyball players’ organism’s typological features, depending on blood circulation type and erythrocytes’ conformation, are discussed. Conclusions: In relaxed state all female volleyball players have non-uniform cardio-hemo-dynamic of blood circulation. With hyper-dynamic blood circulation type, higher indicators of strike and minute blood volume were observed. With hypo-kinetic blood circulation type the opposite picture was observed: indicators of strike and minute blood volume, heart index, load on cardio-vascular system in different periods of day were low.

  12. Experimental and theoretical studies of the O(3P) + C2H4 reaction dynamics: Collision energy dependence of branching ratios and extent of intersystem crossing

    Science.gov (United States)

    Fu, Bina; Han, Yong-Chang; Bowman, Joel M.; Leonori, Francesca; Balucani, Nadia; Angelucci, Luca; Occhiogrosso, Angela; Petrucci, Raffaele; Casavecchia, Piergiorgio

    2012-12-01

    The reaction of O(3P) with C2H4, of importance in combustion and atmospheric chemistry, stands out as paradigm reaction involving not only the indicated triplet state potential energy surface (PES) but also an interleaved singlet PES that is coupled to the triplet surface. This reaction poses great challenges for theory and experiment, owing to the ruggedness and high dimensionality of these potentials, as well as the long lifetimes of the collision complexes. Crossed molecular beam (CMB) scattering experiments with soft electron ionization detection are used to disentangle the dynamics of this polyatomic multichannel reaction at a collision energy Ec of 8.4 kcal/mol. Five different primary products have been identified and characterized, which correspond to the five exothermic competing channels leading to H + CH2CHO, H + CH3CO, CH3 + HCO, CH2 + H2CO, and H2 + CH2CO. These experiments extend our previous CMB work at higher collision energy (Ec ˜ 13 kcal/mol) and when the results are combined with the literature branching ratios from kinetics experiments at room temperature (Ec ˜ 1 kcal/mol), permit to explore the variation of the branching ratios over a wide range of collision energies. In a synergistic fashion, full-dimensional, QCT surface hopping calculations of the O(3P) + C2H4 reaction using ab initio PESs for the singlet and triplet states and their coupling, are reported at collision energies corresponding to the CMB and the kinetics ones. Both theory and experiment find almost an equal contribution from the triplet and singlet surfaces to the reaction, as seen from the collision energy dependence of branching ratios of product channels and extent of intersystem crossing (ISC). Further detailed comparisons at the level of angular distributions and translational energy distributions are made between theory and experiment for the three primary radical channel products, H + CH2CHO, CH3 + HCO, and CH2 + H2CO. The very good agreement between theory and

  13. Unraveling the role of entropy in tuning unimolecular vs . bimolecular reaction rates: The case of olefin polymerization catalyzed by transition metals

    KAUST Repository

    Falivene, Laura; Barone, Vincenzo; Talarico, Giovanni

    2018-01-01

    by different ligand frameworks, metal, and growing polymeric chain for which experimental data are available have been selected in order to validate the main approaches to entropy calculation. Applying the “standard” protocol results in a strong disagreement

  14. Trajectory calculation of a trapped particle in electro-dynamic balance for study of chemical reaction of aerosol particles

    International Nuclear Information System (INIS)

    Okuma, Miho; Itou, Takahiro; Harano, Azuchi; Takarada, Takayuki; James, Davis E

    2013-01-01

    Electrodynamic balance (EDB) is a powerful tool for investigating the chemical reactions between a fine particle and gaseous species. But the EDB device alone is inadequate to match the rapid weight change of a fine particle caused by chemical reactions, because it takes a few seconds to set a fine particle at null point. The particle trajectory calculation for the trapped particle added to the EDB is thus a very useful tool for the measurement of the transient response of a particle weight change with no need to adjust the applied DC voltage to set the null point. The purpose of this study is to develop the trajectory calculation method to track the particle oscillation pattern in the EDB and examine the possibility for kinetic studies on the reaction of a single aerosol particle with gaseous species. The results demonstrated the feasibility of applying particle trajectory calculation to realize the research purpose.

  15. A Ring Polymer Molecular Dynamics Approach to Study the Transition between Statistical and Direct Mechanisms in the H2 + H3+ → H3+ + H2 Reaction.

    Science.gov (United States)

    Suleimanov, Yury V; Aguado, Alfredo; Gómez-Carrasco, Susana; Roncero, Octavio

    2018-05-03

    Because of its fundamental importance in astrochemistry, the H 2 + H 3 + → H 3 + + H 2 reaction has been studied experimentally in a wide temperature range. Theoretical studies of the title reaction significantly lag primarily because of the challenges associated with the proper treatment of the zero-point energy (ZPE). As a result, all previous theoretical estimates for the ratio between a direct proton-hop and indirect exchange (via the H 5 + complex) channels deviate from the experiment, in particular, at lower temperatures where the quantum effects dominate. In this work, the ring polymer molecular dynamics (RPMD) method is applied to study this reaction, providing very good agreement with the experiment. RPMD is immune to the shortcomings associated with the ZPE leakage and is able to describe the transition from direct to indirect mechanisms below room temperature. We argue that RPMD represents a useful tool for further studies of numerous ZPE-sensitive chemical reactions that are of high interest in astrochemistry.

  16. The dynamics of immunologic reactions in rats affected by repeated external γ-irradiation and internal irradiation with radionuclides

    International Nuclear Information System (INIS)

    Shubik, V.M.; Livshits, R.E.

    1975-01-01

    Nonspecific factors of immunity and formation of autoantibodies in rats exposed to comparable doses of repeated external γ-irradiation and of internal irradiation with Cs 137 , Sr 90 and I 131 chronically administered to animals have been studied comparatively. No essential variations have been found in changes induced in the immunologic reactions by chronic external and even internal γ-irradiation. Certain peculiarities have been revealed in the character of changes in the immunologic reactions depending on biophysical properties of the radionuclides used in the experiments

  17. Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

    Science.gov (United States)

    Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

    2018-05-01

    Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

  18. Experimental effects of dynamics and thermodynamics in nuclear reactions on the symmetry energy as seen by the CHIMERA 4 π detector

    Energy Technology Data Exchange (ETDEWEB)

    De Filippo, E.; Pagano, A. [INFN, Catania (Italy)

    2014-02-15

    Heavy-ion collisions have been widely used in the last decade to constrain the parameterizations of the symmetry energy term of the nuclear equation of state (EOS) for asymmetric nuclear matter as a function of baryonic density. In the Fermi energy domain one is faced with variations of the density within a narrow range of values around the saturation density ρ{sub 0}=0.16 fm{sup -3} down towards sub-saturation densities. The experimental observables which are sensitive to the symmetry energy are constructed starting from the detected light particles, clusters and heavy fragments that, in heavy-ion collisions, are generally produced by different emission mechanisms at different stages and time scales of the reaction. In this review the effects of dynamics and thermodynamics on the symmetry energy in nuclear reactions are discussed and characterized using an overview of the data taken so far with the CHIMERA multi detector array. (orig.)

  19. Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

    Science.gov (United States)

    Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

    2011-05-14

    We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

  20. What's new in the proton transfer reaction from pyranine to water? A femtosecond study of the proton transfer dynamics

    International Nuclear Information System (INIS)

    Prayer, C.; Gustavsson, T.; Tran-Thi, T.-H.

    1996-01-01

    The proton transfer from excited pyranine to water is studied by the femtosecond fluorescence upconversion technique. It is shown for the first time that the proton transfer reaction in water proceeds by three successive steps: the solvent cage relaxation, the specific solute-solvent hydrogen-bond formation and finally the ion pair dissociation/diffusion

  1. A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait.

    Science.gov (United States)

    Hamner, Samuel R; Seth, Ajay; Steele, Katherine M; Delp, Scott L

    2013-06-21

    Recent advances in computational technology have dramatically increased the use of muscle-driven simulation to study accelerations produced by muscles during gait. Accelerations computed from muscle-driven simulations are sensitive to the model used to represent contact between the foot and ground. A foot-ground contact model must be able to calculate ground reaction forces and moments that are consistent with experimentally measured ground reaction forces and moments. We show here that a rolling constraint can model foot-ground contact and reproduce measured ground reaction forces and moments in an induced acceleration analysis of muscle-driven simulations of walking, running, and crouch gait. We also illustrate that a point constraint and a weld constraint used to model foot-ground contact in previous studies produce inaccurate reaction moments and lead to contradictory interpretations of muscle function. To enable others to use and test these different constraint types (i.e., rolling, point, and weld constraints) we have included them as part of an induced acceleration analysis in OpenSim, a freely-available biomechanics simulation package. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Probing the Energy Transfer Dynamics of Photosynthetic Reaction Center Complexes Through Hole-Burning and Single-Complex Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Kerry Joseph [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Photosynthesis is the process by which light energy is used to drive reactions that generate sugars to supply energy for cellular processes. It is one of the most important fundamental biological reactions and occurs in both prokaryotic (e.g. bacteria) and eukaryotic (e.g. plants and algae) organisms. Photosynthesis is also remarkably intricate, requiring the coordination of many different steps and reactions in order to successfully transform absorbed solar energy into a biochemical usable form of energy. However, the net reaction for all photosynthetic organisms can be reduced to the following, deceptively general, equation developed by Van Niel[1] H2 - D + Aimplieshv A - H2 + D where H2-D is the electron donor, e.g. H2O, H2S. A is the electron acceptor, e.g. CO2, and A-H2 is the synthesized sugar. Amazingly, this simple net equation is responsible for creating the oxidizing atmosphere of Earth and the recycling of CO2, both of which are necessary for the sustainment of the global ecosystem.

  3. Intersystem crossing and dynamics in O(3P) + C2H4 multichannel reaction: Experiment validates theory

    Science.gov (United States)

    Fu, Bina; Han, Yong-Chang; Bowman, Joel M.; Angelucci, Luca; Balucani, Nadia; Leonori, Francesca; Casavecchia, Piergiorgio

    2012-01-01

    The O(3P) + C2H4 reaction, of importance in combustion and atmospheric chemistry, stands out as a paradigm reaction involving triplet- and singlet-state potential energy surfaces (PESs) interconnected by intersystem crossing (ISC). This reaction poses challenges for theory and experiments owing to the ruggedness and high dimensionality of these potentials, as well as the long lifetimes of the collision complexes. Primary products from five competing channels (H + CH2CHO, H + CH3CO, H2 + CH2CO, CH3 + HCO, CH2 + CH2O) and branching ratios (BRs) are determined in crossed molecular beam experiments with soft electron-ionization mass-spectrometric detection at a collision energy of 8.4 kcal/mol. As some of the observed products can only be formed via ISC from triplet to singlet PESs, from the product BRs the extent of ISC is inferred. A new full-dimensional PES for the triplet state as well as spin-orbit coupling to the singlet PES are reported, and roughly half a million surface hopping trajectories are run on the coupled singlet-triplet PESs to compare with the experimental BRs and differential cross-sections. Both theory and experiment find almost equal contributions from the two PESs to the reaction, posing the question of how important is it to consider the ISC as one of the nonadiabatic effects for this and similar systems involved in combustion chemistry. Detailed comparisons at the level of angular and translational energy distributions between theory and experiment are presented for the two primary channel products, CH3 + HCO and H + CH2CHO. The agreement between experimental and theoretical functions is excellent, implying that theory has reached the capability of describing complex multichannel nonadiabatic reactions. PMID:22665777

  4. Exploring the dynamics of hydrogen atom release from the radical-radical reaction of O(3P) with C3H5

    International Nuclear Information System (INIS)

    Joo, Sun-Kyu; Kwon, Lee-Kyoung; Lee, Hohjai; Choi, Jong-Ho

    2004-01-01

    The gas-phase radical-radical reaction dynamics of O( 3 P)+C 3 H 5 →H( 2 S)+C 3 H 4 O was studied at an average collision energy of 6.4 kcal/mol in a crossed beam configuration. The ground-state atomic oxygen [O( 3 P)] and allyl radicals (C 3 H 5 ) were generated by the photolysis of NO 2 and the supersonic flash pyrolysis of allyl iodide, respectively. Nascent hydrogen atom products were probed by the vacuum-ultraviolet-laser induced fluorescence spectroscopy in the Lyman-α region centered at 121.6 nm. With the aid of the CBS-QB3 level of ab initio theory, it has been found that the barrierless addition of O( 3 P) to C 3 H 5 forms the energy-rich addition complexes on the lowest doublet potential energy surface, which are predicted to undergo a subsequent direct decomposition step leading to the reaction products H+C 3 H 4 O. The major counterpart C 3 H 4 O of the probed hydrogen atom is calculated to be acrolein after taking into account the factors of barrier height, reaction enthalpy, and the number of intermediates involved along the reaction pathway. The nascent H-atom Doppler profile analysis shows that the average center-of-mass translational energy of the H+C 3 H 4 O products and the fraction of the total available energy released as the translational energy were determined to be 3.83 kcal/mol and 0.054, respectively. On the basis of comparison with statistical calculations, the reaction proceeds through the formation of short-lived addition complexes rather than statistical, long-lived intermediates, and the polyatomic acrolein product is significantly internally excited at the moment of the decomposition

  5. Exploring the dynamics of hydrogen atom release from the radical-radical reaction of O(3P) with C3H5

    Science.gov (United States)

    Joo, Sun-Kyu; Kwon, Lee-Kyoung; Lee, Hohjai; Choi, Jong-Ho

    2004-05-01

    The gas-phase radical-radical reaction dynamics of O(3P)+C3H5→H(2S)+C3H4O was studied at an average collision energy of 6.4 kcal/mol in a crossed beam configuration. The ground-state atomic oxygen [O(3P)] and allyl radicals (C3H5) were generated by the photolysis of NO2 and the supersonic flash pyrolysis of allyl iodide, respectively. Nascent hydrogen atom products were probed by the vacuum-ultraviolet-laser induced fluorescence spectroscopy in the Lyman-α region centered at 121.6 nm. With the aid of the CBS-QB3 level of ab initio theory, it has been found that the barrierless addition of O(3P) to C3H5 forms the energy-rich addition complexes on the lowest doublet potential energy surface, which are predicted to undergo a subsequent direct decomposition step leading to the reaction products H+C3H4O. The major counterpart C3H4O of the probed hydrogen atom is calculated to be acrolein after taking into account the factors of barrier height, reaction enthalpy, and the number of intermediates involved along the reaction pathway. The nascent H-atom Doppler profile analysis shows that the average center-of-mass translational energy of the H+C3H4O products and the fraction of the total available energy released as the translational energy were determined to be 3.83 kcal/mol and 0.054, respectively. On the basis of comparison with statistical calculations, the reaction proceeds through the formation of short-lived addition complexes rather than statistical, long-lived intermediates, and the polyatomic acrolein product is significantly internally excited at the moment of the decomposition.

  6. Direct Visualization of Barrier Crossing Dynamics in a Driven Optical Matter System.

    Science.gov (United States)

    Figliozzi, Patrick; Peterson, Curtis W; Rice, Stuart A; Scherer, Norbert F

    2018-04-25

    A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer ( e. g., an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles, i. e. passing events, in an optical ring trap. A two-step mechanism similar to a bimolecular exchange reaction or the Michaelis-Menten scheme is revealed by analysis that combines detailed knowledge of each trajectory, a statistically significant number of repetitions of the passing events, and the driving force dependence of the process. We find that while the total event rate increases with driving force, this increase is due to an increase in the rate of encounters. There is no drive force dependence on the rate of barrier crossing because the key motion for the process involves a random (thermal) radial fluctuation of one particle allowing the other to pass. This simple experiment can readily be extended to study more complex barrier crossing processes by replacing the spherical metal nanoparticles with anisotropic ones or by creating more intricate optical trapping potentials.

  7. In vitro and in vivo mapping of the Prunus necrotic ringspot virus coat protein C-terminal dimerization domain by bimolecular fluorescence complementation.

    Science.gov (United States)

    Aparicio, Frederic; Sánchez-Navarro, Jesús A; Pallás, Vicente

    2006-06-01

    Interactions between viral proteins are critical for virus viability. Bimolecular fluorescent complementation (BiFC) technique determines protein interactions in real-time under almost normal physiological conditions. The coat protein (CP) of Prunus necrotic ringspot virus is required for multiple functions in its replication cycle. In this study, the region involved in CP dimerization has been mapped by BiFC in both bacteria and plant tissue. Full-length and C-terminal deleted forms of the CP gene were fused in-frame to the N- and C-terminal fragments of the yellow fluorescent protein. The BiFC analysis showed that a domain located between residues 9 and 27 from the C-end plays a critical role in dimerization. The importance of this C-terminal region in dimer formation and the applicability of the BiFC technique to analyse viral protein interactions are discussed.

  8. Nonlinear Hamiltonian mechanics applied to molecular dynamics theory and computational methods for understanding molecular spectroscopy and chemical reactions

    CERN Document Server

    Farantos, Stavros C

    2014-01-01

    This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.

  9. Fusion dynamics of 2020Ne + 20882Pb reaction using static and energy dependent Woods-Saxon potential

    International Nuclear Information System (INIS)

    Gautam, Manjeet Singh; Kaur, Amandeep; Sharma, Manoj K.

    2015-01-01

    The present work compares the theoretical predictions based on static Woods-Saxon potential and the EDWSP model along with one dimensional Wong formula. For 20 20 Ne + 208 82 Pb reaction, the theoretical calculations obtained by using static Woods-Saxon potential are substantially smaller than that of experimental data at below barrier energies and explain the fusion data at above barrier energies only. On the other hand, the EDWSP model based calculations adequately describe the observed fusion enhancement of 20 20 Ne + 208 82 Pb reaction in whole range of energy spread across the Coulomb barrier. Furthermore, a wide range of the diffuseness parameter ranging from 0.96 fm to 0.85 fm is required to address the sub-barrier fusion data

  10. Numerical Analysis of the Interaction between Thermo-Fluid Dynamics and Auto-Ignition Reaction in Spark Ignition Engines

    Science.gov (United States)

    Saijyo, Katsuya; Nishiwaki, Kazuie; Yoshihara, Yoshinobu

    The CFD simulations were performed integrating the low-temperature oxidation reaction. Analyses were made with respect to the first auto-ignition location in the case of a premixed-charge compression auto-ignition in a laminar flow field and in the case of the auto-ignition in an end gas during an S. I. Engine combustion process. In the latter simulation, the spatially-filtered transport equations were solved to express fluctuating temperatures in a turbulent flow in consideration of strong non-linearity to temperature in the reaction equations. It is suggested that the first auto-ignition location does not always occur at higher-temperature locations and that the difference in the locations of the first auto-ignition depends on the time period during which the local end gas temperature passes through the region of shorter ignition delay, including the NTC region.

  11. Study of breakup and transfer of weakly bound nucleus 6Li to explore the low energy reaction dynamics

    Directory of Open Access Journals (Sweden)

    Zhang G. L.

    2017-01-01

    In order to have a proper understanding of the influence of breakup and transfer of weakly bound projectiles on the fusion process, we performed the 6Li+89Y experiment with incident energies of 22 MeV and 34 MeV on Galileo array in cooperation with Si-ball EUCLIDES at Legnaro National Laboratory (LNL in Italy. Using particle-particle and particle-γ coincidences, the different reaction mechanisms can be clearly explored.

  12. Isotope effects in gas-phase chemical reactions and photodissociation processes: Overview

    International Nuclear Information System (INIS)

    Kaye, J.A.

    1992-01-01

    The origins of isotope effects in equilibrium and non-equilibrium chemical processes are reviewed. In non-equilibrium processes, attention is given to isotope effects in simple bimolecular reactions, symmetry-related reactions, and photodissociation processes. Recent examples of isotope effects in these areas are reviewed. Some indication of other scientific areas for which measurements and/or calculations of isotope effects are used is also given. Examples presented focus on neutral molecule chemistry and in many cases complement examples considered in greater detail in the other chapters of this volume

  13. On the some reactions of mixed ethers of phosphorus acid with acrylonitrile and methyl iodide

    International Nuclear Information System (INIS)

    Gusev, Yu.K.; Chistokletov, V.N.; Petrov, A.A.

    1977-01-01

    The bimolecular mechanism has been confirmed of the redgrouping stage of Arbuzov's classical reactions for phosphites containing primary and secondary radicals in reactions of acrylonitrile and methyl iodide with some mixed ethers of phosphoric acid. It is suggested that dealcylation of the intermediate products formed on interaction of olefins activated by electron-acceptor groups with phosphites containing primary radicals occurs according to the Ssub(N)2-mechanism, secondary radicals, according to the mixed Ssub(N)2 and Ssub(N)1-mechanism,and radicals capable of forming stable carbonium ions, according to the Ssub(N)1-mechanism

  14. The dynamics of the reaction of 16O(1D)+D218O→16OD+18OD

    International Nuclear Information System (INIS)

    Guillory, W.A.; Gericke, K.H.; Comes, F.J.

    1983-01-01

    The detailed energy partitioning in the reaction of a metastable oxygen atom O( 1 D) with D 2 O proceeding to two OD molecules has been studied. In order to distinguish the product state distribution between the two chemically identical product molecules OD, the oxygen atom in the heavy water molecule was labeled isotopically. The use of spectroscopic methods allows a complete analysis of the products' state distribution including such fine details as the distribution of the different #betta# components and of the electron spin. The vibrational energy is almost exclusively channeled into the new ( 16 OD) bond, whereas the original ( 18 OD) bond is produced (>90%) in the ground vibrational state. Both OD radicals show a broad rotational excitation and the rotational energy is equally partitioned among the two bonds. The energy distribution over the rovibrational levels strongly reflects the influence of coincident product molecules emerging from this chemical reaction. The reaction is very direct and must proceed on a time scale which does not allow for efficient energy transfer into all the available phase space

  15. Reactive scattering of H2 from Cu(100): comparison of dynamics calculations based on the specific reaction parameter approach to density functional theory with experiment.

    Science.gov (United States)

    Sementa, L; Wijzenbroek, M; van Kolck, B J; Somers, M F; Al-Halabi, A; Busnengo, H F; Olsen, R A; Kroes, G J; Rutkowski, M; Thewes, C; Kleimeier, N F; Zacharias, H

    2013-01-28

    We present new experimental and theoretical results for reactive scattering of dihydrogen from Cu(100). In the new experiments, the associative desorption of H(2) is studied in a velocity resolved and final rovibrational state selected manner, using time-of-flight techniques in combination with resonance-enhanced multi-photon ionization laser detection. Average desorption energies and rotational quadrupole alignment parameters were obtained in this way for a number of (v = 0, 1) rotational states, v being the vibrational quantum number. Results of quantum dynamics calculations based on a potential energy surface computed with a specific reaction parameter (SRP) density functional, which was derived earlier for dihydrogen interacting with Cu(111), are compared with the results of the new experiments and with the results of previous molecular beam experiments on sticking of H(2) and on rovibrationally elastic and inelastic scattering of H(2) and D(2) from Cu(100). The calculations use the Born-Oppenheimer and static surface approximations. With the functional derived semi-empirically for dihydrogen + Cu(111), a chemically accurate description is obtained of the molecular beam experiments on sticking of H(2) on Cu(100), and a highly accurate description is obtained of rovibrationally elastic and inelastic scattering of D(2) from Cu(100) and of the orientational dependence of the reaction of (v = 1, j = 2 - 4) H(2) on Cu(100). This suggests that a SRP density functional derived for H(2) interacting with a specific low index face of a metal will yield accurate results for H(2) reactively scattering from another low index face of the same metal, and that it may also yield accurate results for H(2) interacting with a defected (e.g., stepped) surface of that same metal, in a system of catalytic interest. However, the description that was obtained of the average desorption energies, of rovibrationally elastic and inelastic scattering of H(2) from Cu(100), and of the

  16. Dynamic structural change of the self-assembled lanthanum complex induced by lithium triflate for direct catalytic asymmetric aldol-Tishchenko reaction.

    Science.gov (United States)

    Horiuchi, Yoshihiro; Gnanadesikan, Vijay; Ohshima, Takashi; Masu, Hyuma; Katagiri, Kosuke; Sei, Yoshihisa; Yamaguchi, Kentaro; Shibasaki, Masakatsu

    2005-09-05

    The development of a direct catalytic asymmetric aldol-Tishchenko reaction and the nature of its catalyst are described. An aldol-Tishchenko reaction of various propiophenone derivatives with aromatic aldehydes was promoted by [LaLi3(binol)3] (LLB), and reactivity and enantioselectivity were dramatically enhanced by the addition of lithium trifluoromethanesulfonate (LiOTf). First, we observed a dynamic structural change of LLB by the addition of LiOTf using 13C NMR spectroscopy, electronspray ionization mass spectrometry (ESI-MS), and cold-spray ionization mass spectrometry (CSI-MS). X-ray crystallography revealed that the structure of the newly generated self-assembled complex was a binuclear [La2Li4(binaphthoxide)5] complex 6. A reverse structural change of complex 6 to LLB by the addition of one equivalent of Li2(binol) was also confirmed by ESI-MS and experimental results. The drastic concentration effects on the direct catalytic asymmetric aldol-Tishchenko reaction suggested that the addition of LiOTf to LLB generated an active oligomeric catalyst species.

  17. Using high-frequency nitrogen and carbon measurements to decouple temporal dynamics of catchment and in-stream transport and reaction processes in a headwater stream

    Science.gov (United States)

    Blaen, P.; Riml, J.; Khamis, K.; Krause, S.

    2017-12-01

    Within river catchments across the world, headwater streams represent important sites of nutrient transformation and uptake due to their high rates of microbial community processing and relative abundance in the landscape. However, separating the combined influence of in-stream transport and reaction processes from the overall catchment response can be difficult due to spatio-temporal variability in nutrient and organic matter inputs, flow regimes, and reaction rates. Recent developments in optical sensor technologies enable high-frequency, in situ nutrient measurements, and thus provide opportunities for greater insights into in-stream processes. Here, we use in-stream observations of hourly nitrate (NO3-N), dissolved organic carbon (DOC) and dissolved oxygen (DO) measurements from paired in situ sensors that bound a 1 km headwater stream reach in a mixed-use catchment in central England. We employ a spectral approach to decompose (1) variances in solute loading from the surrounding landscape, and (2) variances in reach-scale in-stream nutrient transport and reaction processes. In addition, we estimate continuous rates of reach-scale NO3-N and DOC assimilation/dissimilation, ecosystem respiration and primary production. Comparison of these results over a range of hydrological conditions (baseflow, variable storm events) and timescales (event-based, diel, seasonal) facilitates new insights into the physical and biogeochemical processes that drive in-stream nutrient dynamics in headwater streams.

  18. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD{sub 3}CN treated with a parallel multi-state EVB model

    Energy Technology Data Exchange (ETDEWEB)

    Glowacki, David R., E-mail: drglowacki@gmail.com [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Department of Computer Science, University of Bristol, Bristol BS8 1UB (United Kingdom); PULSE Institute and Department of Chemistry, Stanford University, Stanford, California 94305 (United States); SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Orr-Ewing, Andrew J. [School of Chemistry, University of Bristol, Bristol BS8 1TS (United Kingdom); Harvey, Jeremy N. [Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Heverlee (Belgium)

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD{sub 3}CN → DF + CD{sub 2}CN reaction in CD{sub 3}CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD{sub 3}CN solvent, equilibrium power spectra of DF in CD{sub 3}CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol{sup −1} localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD{sub 3}CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational

  19. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.

    Science.gov (United States)

    Glowacki, David R; Orr-Ewing, Andrew J; Harvey, Jeremy N

    2015-07-28

    We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ∼23 kcal mol(-1) localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral

  20. Study of the dynamics of the MoO2-Mo2C system for catalytic partial oxidation reactions

    Science.gov (United States)

    Cuba Torres, Christian Martin

    On a global scale, the energy demand is largely supplied by the combustion of non-renewable fossil fuels. However, their rapid depletion coupled with environmental and sustainability concerns are the main drivers to seek for alternative energetic strategies. To this end, the sustainable generation of hydrogen from renewable resources such as biodiesel would represent an attractive alternative solution to fossil fuels. Furthermore, hydrogen's lower environmental impact and greater independence from foreign control make it a strong contender for solving this global problem. Among a wide variety of methods for hydrogen production, the catalytic partial oxidation offers numerous advantages for compact and mobile fuel processing systems. For this reaction, the present work explores the versatility of the Mo--O--C catalytic system under different synthesis methods and reforming conditions using methyl oleate as a surrogate biodiesel. MoO2 exhibits good catalytic activity and exhibits high coke-resistance even under reforming conditions where long-chain oxygenated compounds are prone to form coke. Moreover, the lattice oxygen present in MoO2 promotes the Mars-Van Krevelen mechanism. Also, it is introduced a novel beta-Mo2C synthesis by the in-situ formation method that does not utilize external H2 inputs. Herein, the MoO 2/Mo2C system maintains high catalytic activity for partial oxidation while the lattice oxygen serves as a carbon buffer for preventing coke formation. This unique feature allows for longer operation reforming times despite slightly lower catalytic activity compared to the catalysts prepared by the traditional temperature-programmed reaction method. Moreover, it is demonstrated by a pulse reaction technique that during the phase transformation of MoO2 to beta-Mo2C, the formation of Mo metal as an intermediate is not responsible for the sintering of the material wrongly assumed by the temperature-programmed method.

  1. Adsorption effect on the dynamic response of a biochemical reaction in a biofilm reactor for wastewater treatment

    Energy Technology Data Exchange (ETDEWEB)

    Tsuneda, S.; Inoue, Y.; Auresenia, J.; Hirata, A. [Department of Chemical Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555 (Japan)

    2003-09-01

    The dynamic behavior of a completely mixed, three-phase, fluidized bed biofilm reactor treating simulated domestic wastewater was studied with step changes in inlet concentration. It was found that the response curves showed second order characteristics, i.e., as the inlet concentration was increased, the outlet concentration also increased, reached a peak value and then decreased until it leveled to a new steady-state value corresponding to the new inlet concentration level. Nonlinear regression analysis was performed using Monod-type rate equations with and without an adsorption term. As a result, the theoretical curve of the kinetic model that incorporates the adsorption term has best fit to the actual response in most cases. Thus, it was concluded that the adsorption of a substrate onto the biofilm and carrier particles has a significant effect on the dynamic response in biofilm processes. (Abstract Copyright [2003], Wiley Periodicals, Inc.)

  2. Quasi-Classical Trajectory Dynamics Study of the Cl(2P) + C2H6 → HCl(v,j) + C2H5 Reaction. Comparison with Experiment.

    Science.gov (United States)

    Espinosa-Garcia, Joaquin; Martinez-Nuñez, Emilio; Rangel, Cipriano

    2018-03-15

    To understand and simulate the dynamics behavior of the title reaction, QCT calculations were performed on a recently developed global analytical potential energy surface, PES-2017. These calculations combine the classical description of the dynamics with pseudoquantization in the reactants and products to perform a theoretical/experimental comparison on the same footing. Thus, in the products a series of constraints are included to analyze the HCl(v = 0,j) product, which is experimentally detected. At collision energies of 5.5 and 6.7 kcal mol -1 the largest fraction of available energy is deposited as translation, 67%, while the ethyl radical shows significant internal energy, 27%, and so it does not act as a spectator of the reaction, thus reproducing recent experimental evidence. The HCl(v=0, j) rotational distribution is cold, peaking at j = 2, only one unit hotter than experiment, which represents an error of 0.12 kcal mol -1 . At a collision energy of 5.5 kcal mol -1 product translational distribution is slightly hotter than experiment, but at 6.7 kcal mol -1 agreement with recent experiments is practically quantitative, suggesting that the first experiments should be revised. In addition, we observe that the HCl(v=0, j) scattering distribution shifts from isotropic at low values of j to backward at high values of j, which is in agreement with experimental data. Finally, no evidence was found for the "chattering" mechanism suggested to explain the low translational energy of the HCl product in the backward scattering region. In sum, agreement with experiments of a series of sensible dynamic properties permits us to be optimistic on the quality and accuracy of the theoretical tools used in the present work, QCT and PES-2017.

  3. Matching the reaction-diffusion simulation to dynamic [18F]FMISO PET measurements in tumors: extension to a flow-limited oxygen-dependent model.

    Science.gov (United States)

    Shi, Kuangyu; Bayer, Christine; Gaertner, Florian C; Astner, Sabrina T; Wilkens, Jan J; Nüsslin, Fridtjof; Vaupel, Peter; Ziegler, Sibylle I

    2017-02-01

    Positron-emission tomography (PET) with hypoxia specific tracers provides a noninvasive method to assess the tumor oxygenation status. Reaction-diffusion models have advantages in revealing the quantitative relation between in vivo imaging and the tumor microenvironment. However, there is no quantitative comparison of the simulation results with the real PET measurements yet. The lack of experimental support hampers further applications of computational simulation models. This study aims to compare the simulation results with a preclinical [ 18 F]FMISO PET study and to optimize the reaction-diffusion model accordingly. Nude mice with xenografted human squamous cell carcinomas (CAL33) were investigated with a 2 h dynamic [ 18 F]FMISO PET followed by immunofluorescence staining using the hypoxia marker pimonidazole and the endothelium marker CD 31. A large data pool of tumor time-activity curves (TAC) was simulated for each mouse by feeding the arterial input function (AIF) extracted from experiments into the model with different configurations of the tumor microenvironment. A measured TAC was considered to match a simulated TAC when the difference metric was below a certain, noise-dependent threshold. As an extension to the well-established Kelly model, a flow-limited oxygen-dependent (FLOD) model was developed to improve the matching between measurements and simulations. The matching rate between the simulated TACs of the Kelly model and the mouse PET data ranged from 0 to 28.1% (on average 9.8%). By modifying the Kelly model to an FLOD model, the matching rate between the simulation and the PET measurements could be improved to 41.2-84.8% (on average 64.4%). Using a simulation data pool and a matching strategy, we were able to compare the simulated temporal course of dynamic PET with in vivo measurements. By modifying the Kelly model to a FLOD model, the computational simulation was able to approach the dynamic [ 18 F]FMISO measurements in the investigated

  4. Dynamic of bioelectric activity back hypothalamus changes in conditions of pyroxan application on the background of stress-reaction developmen

    Directory of Open Access Journals (Sweden)

    T. G. Chaus

    2005-04-01

    Full Text Available The dynamic of changes of capacity of electroencephalogram’s rhythms back hypothalamus at animals of control group and group in stress conditions in parallel with rats who on a background of stress development accepted pyroxan is analyzed. The submitted results have shown influence of a pharmacological preparation pyroxan on bioelectric activity of back hypothalamus in stress conditions that restoration of electric activity under action of this preparation was more shown at 3 weeks of its application.

  5. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    International Nuclear Information System (INIS)

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H 2 reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H 2 reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H 2 reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables

  6. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    Energy Technology Data Exchange (ETDEWEB)

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.

  7. Analysis of the dynamic response of a double rupture disc assembly to simulated sodium-water reaction pressure pulses

    International Nuclear Information System (INIS)

    Leonard, J.R.

    1980-03-01

    A series of double rupture disc experiments were conducted in 1979 to evaluate the dynamic response characteristics of this pressure relief apparatus. The tests were performed in a facility with water simulating sodium and rising pressure pulses representative of the pressure increase resulting from a water/steam leak from a steam generator into sodium in the intermediate heat transport system of a breeder reactor power plant. Maximum source pressures ranged in magnitude from 50 psi to 800 psi. Dynamic response characteristics of each of the two rupture discs were similar to those observed in larger scale sodium-water experiments conducted in the Series I and Series II Large Leak Test Program at the Energy Technology Engineering Center. The SRI double rupture disc dynamic behavior was found to be consistent and amendable to modelling in the TRANSWRAP II computer code. A series of correlations which represent rupture disc buckling parameters were developed for use in the TRANSWRAP II code. The semi-empirical modeling of the rupture discs in the TRANSWRAP II code showed very good agreement with the experimental results

  8. Numerical Simulation of Desulfurization Behavior in Gas-Stirred Systems Based on Computation Fluid Dynamics-Simultaneous Reaction Model (CFD-SRM) Coupled Model

    Science.gov (United States)

    Lou, Wentao; Zhu, Miaoyong

    2014-10-01

    A computation fluid dynamics-simultaneous reaction model (CFD-SRM) coupled model has been proposed to describe the desulfurization behavior in a gas-stirred ladle. For the desulfurization thermodynamics, different models were investigated to determine sulfide capacity and oxygen activity. For the desulfurization kinetic, the effect of bubbly plume flow, as well as oxygen absorption and oxidation reactions in slag eyes are considered. The thermodynamic and kinetic modification coefficients are proposed to fit the measured data, respectively. Finally, the effects of slag basicity and gas flow rate on the desulfurization efficiency are investigated. The results show that as the interfacial reactions (Al2O3)-(FeO)-(SiO2)-(MnO)-[S]-[O] simultaneous kinetic equilibrium is adopted to determine the oxygen activity, and the Young's model with the modification coefficient R th of 1.5 is adopted to determine slag sulfide capacity, the predicted sulfur distribution ratio LS agrees well with the measured data. With an increase of the gas blowing time, the predicted desulfurization rate gradually decreased, and when the modification parameter R k is 0.8, the predicted sulfur content changing with time in ladle agrees well with the measured data. If the oxygen absorption and oxidation reactions in slag eyes are not considered in this model, then the sulfur removal rate in the ladle would be overestimated, and this trend would become more obvious with an increase of the gas flow rate and decrease of the slag layer height. With the slag basicity increasing, the total desulfurization ratio increases; however, the total desulfurization ratio changes weakly as the slag basicity exceeds 7. With the increase of the gas flow rate, the desulfurization ratio first increases and then decreases. When the gas flow rate is 200 NL/min, the desulfurization ratio reaches a maximum value in an 80-ton gas-stirred ladle.

  9. Hydrogen incorporation and radiation induced dynamics in metal-oxide-silicon structures. A study using nuclear reaction analysis

    International Nuclear Information System (INIS)

    Briere, M.A.

    1993-07-01

    Resonant nuclear reaction analysis, using the 1 H( 15 N, αγ) 12 C reaction at 6.4 MeV, has been successfully applied to the investigation of hydrogen incorporation and radiation induced migration in metal-oxide-silicon structures. A preliminary study of the influence of processing parameters on the H content of thermal oxides, with and without gate material present, has been performed. It is found that the dominant source of hydrogen in Al gate devices and dry oxides is often contamination, likely in the form of adsorbed water vapor, formed upon exposure to room air after removal from the oxidation furnace. Concentrations of hydrogen in the bulk oxide as high as 3 10 20 cm -3 (Al gate), and as low as 1 10 18 cm -3 (poly Si-gate) have been observed. Hydrogen accumulation at the Si-SiO 2 interface has been reproducibly demonstrated for as-oxidized samples, as well as for oxides exposed to H 2 containing atmospheres during subsequent thermal processing. The migration of hydrogen, from the bulk oxide to the silicon-oxide interface during NRA, has been observed and intensively investigated. A direct correlation between the hydrogen content of the bulk oxide and the radiation generated oxide charges and interface states is presented. These data provide strong support for the important role of hydrogen in determining the radiation sensitivity of electronic devices. (orig.)

  10. Reaction-based small-molecule fluorescent probes for dynamic detection of ROS and transient redox changes in living cells and small animals.

    Science.gov (United States)

    Lü, Rui

    2017-09-01

    Dynamic detection of transient redox changes in living cells and animals has broad implications for human health and disease diagnosis, because intracellular redox homeostasis regulated by reactive oxygen species (ROS) plays important role in cell functions, normal physiological functions and some serious human diseases (e.g., cancer, Alzheimer's disease, diabetes, etc.) usually have close relationship with the intracellular redox status. Small-molecule ROS-responsive fluorescent probes can act as powerful tools for dynamic detection of ROS and redox changes in living cells and animals through fluorescence imaging techniques; and great advances have been achieved recently in the design and synthesis of small-molecule ROS-responsive fluorescent probes. This article highlights up-to-date achievements in designing and using the reaction-based small-molecule fluorescent probes (with high sensitivity and selectivity to ROS and redox cycles) in the dynamic detection of ROS and transient redox changes in living cells and animals through fluorescence imaging. Copyright © 2017. Published by Elsevier Ltd.

  11. An integrated ion trap and time-of-flight mass spectrometer for chemical and photo- reaction dynamics studies.

    Science.gov (United States)

    Schowalter, Steven J; Chen, Kuang; Rellergert, Wade G; Sullivan, Scott T; Hudson, Eric R

    2012-04-01

    We demonstrate the integration of a linear quadrupole trap with a simple time-of-flight mass spectrometer with medium-mass resolution (m/Δm ∼ 50) geared towards the demands of atomic, molecular, and chemical physics experiments. By utilizing a novel radial ion extraction scheme from the linear quadrupole trap into the mass analyzer, a device with large trap capacity and high optical access is realized without sacrificing mass resolution. This provides the ability to address trapped ions with laser light and facilitates interactions with neutral background gases prior to analyzing the trapped ions. Here, we describe the construction and implementation of the device as well as present representative ToF spectra. We conclude by demonstrating the flexibility of the device with proof-of-principle experiments that include the observation of molecular-ion photodissociation and the measurement of trapped-ion chemical reaction rates. © 2012 American Institute of Physics

  12. An integrated ion trap and time-of-flight mass spectrometer for chemical and photo- reaction dynamics studies

    International Nuclear Information System (INIS)

    Schowalter, Steven J.; Chen Kuang; Rellergert, Wade G.; Sullivan, Scott T.; Hudson, Eric R.

    2012-01-01

    We demonstrate the integration of a linear quadrupole trap with a simple time-of-flight mass spectrometer with medium-mass resolution (m/Δm∼ 50) geared towards the demands of atomic, molecular, and chemical physics experiments. By utilizing a novel radial ion extraction scheme from the linear quadrupole trap into the mass analyzer, a device with large trap capacity and high optical access is realized without sacrificing mass resolution. This provides the ability to address trapped ions with laser light and facilitates interactions with neutral background gases prior to analyzing the trapped ions. Here, we describe the construction and implementation of the device as well as present representative ToF spectra. We conclude by demonstrating the flexibility of the device with proof-of-principle experiments that include the observation of molecular-ion photodissociation and the measurement of trapped-ion chemical reaction rates.

  13. Global Controllability of Chemical Reactions

    OpenAIRE

    Drexler, Dániel András; Tóth, János

    2015-01-01

    Controllability of chemical reactions is an important problem in chemical engineering science. In control theory, analysis of the controllability of linear systems is well-founded, however the dynamics of chemical reactions is usually nonlinear. Global controllability properties of chemical reactions are analyzed here based on the Lie-algebra of the vector fields associated to elementary reactions. A chemical reaction is controllable almost everywhere if all the reaction rate coefficients can...

  14. Structure and Dynamics of Zr6O8 Metal-Organic Framework Node Surfaces Probed with Ethanol Dehydration as a Catalytic Test Reaction.

    Science.gov (United States)

    Yang, Dong; Ortuño, Manuel A; Bernales, Varinia; Cramer, Christopher J; Gagliardi, Laura; Gates, Bruce C

    2018-03-14

    Some metal-organic frameworks (MOFs) incorporate nodes that are metal oxide clusters such as Zr 6 O 8 . Vacancies on the node surfaces, accidental or by design, act as catalytic sites. Here, we report elucidation of the chemistry of Zr 6 O 8 nodes in the MOFs UiO-66 and UiO-67 having used infrared and nuclear magnetic resonance spectroscopies to determine the ligands on the node surfaces originating from the solvents and modifiers used in the syntheses and having elucidated the catalytic properties of the nodes for ethanol dehydration, which takes place selectively to make diethyl ether but not ethylene at 473-523 K. Density functional theory calculations show that the key to the selective catalysis is the breaking of node-linker bonds (or the accidental adjacency of open/defect sites) that allows catalytically fruitful bonding of the reactant ethanol to neighboring sites on the nodes, facilitating the bimolecular ether formation through an S N 2 mechanism.

  15. Browndye: A software package for Brownian dynamics

    Science.gov (United States)

    Huber, Gary A.; McCammon, J. Andrew

    2010-11-01

    A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems. Program summaryProgram title: Browndye Catalogue identifier: AEGT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: MIT license, included in distribution No. of lines in distributed program, including test data, etc.: 143 618 No. of bytes in distributed program, including test data, etc.: 1 067 861 Distribution format: tar.gz Programming language: C++, OCaml ( http://caml.inria.fr/) Computer: PC, Workstation, Cluster Operating system: Linux Has the code been vectorised or parallelized?: Yes. Runs on multiple processors with shared memory using pthreads RAM: Depends linearly on size of physical system Classification: 3 External routines: uses the output of APBS [1] ( http://www.poissonboltzmann.org/apbs/) as input. APBS must be obtained and installed separately. Expat 2.0.1, CLAPACK, ocaml-expat, Mersenne Twister. These are included in the Browndye distribution. Nature of problem: Exploration and determination of rate constants of bimolecular interactions involving large biological molecules. Solution method: Brownian dynamics with electrostatic, excluded volume, van der Waals, and desolvation forces. Running time: Depends linearly on size of physical system and quadratically on precision of results. The included example executes in a few minutes.

  16. Slow desensitization of imatinib-induced nonimmediate reactions and dynamic changes of drug-specific CD4+CD25+CD134+ lymphocytes.

    Science.gov (United States)

    Klaewsongkram, Jettanong; Thantiworasit, Pattarawat; Sodsai, Pimpayao; Buranapraditkun, Supranee; Mongkolpathumrat, Pungjai

    2016-11-01

    Imatinib is a tyrosine kinase inhibitor indicated for the treatment of gastrointestinal stromal tumors (GISTs) and certain neoplastic diseases; however, nonimmediate adverse reactions are common. To describe the process of imatinib slow desensitization in patients who experienced nonimmediate reactions to imatinib and the dynamic change in drug-specific CD4 + CD25 + CD134 + T-lymphocyte percentages. Five patients diagnosed as having GISTs and with a recent history of imatinib-induced nonimmediate reactions (maculopapular exanthema with eosinophilia, exfoliative dermatitis, palmar-plantar erythrodysesthesia, and drug rash with eosinophilia and systemic symptoms) were desensitized using a slow desensitization protocol. The reintroduced imatinib dosage was stepped up every week starting from 10 mg/d and increasing to 25, 50, 75, 100, 150, 200, and 300 mg/d until the target dose of 400 mg/d was achieved. Prednisolone of up to 30 mg/d was allowed if allergic reactions recurred. The percentages of CD4 + CD25 + CD134 + T cells present after incubating peripheral blood mononuclear cells with imatinib, at baseline and after successful desensitization, were analyzed using flow cytometric analysis. By using a slow desensitization technique, all patients were able to receive 400 mg/d of imatinib, and prednisolone was gradually tapered off. The percentages of imatinib-induced CD4 + CD25 + CD134 + T cells decreased from a mean (SD) of 11.3% (6.5%) and 13.4% (7.3%) at baseline to 3.2% (0.7%) and 3.0% (1.1%) after successful desensitization, when stimulating peripheral blood mononuclear cells with 1 and 2 μM of imatinib, respectively. Slow desensitization is a helpful procedure in treating patients with imatinib-induced nonimmediate reactions other than simple maculopapular exanthema. The reduced percentages of imatinib-induced CD4 + CD25 + CD134 + T cells in these patients may be associated with immune tolerance. Copyright © 2016 American College of Allergy, Asthma & Immunology

  17. Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski-Fixman approximation

    Science.gov (United States)

    Chaudhury, Srabanti; Cherayil, Binny J.

    2007-09-01

    Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder—modeled by the anomalous diffusion of a particle in a harmonic well—are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme β-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.

  18. Dynamical evolution of angular momentum in damped nuclear reactions. I. Accumulation of angular momentum by nucleon transfer

    International Nuclear Information System (INIS)

    Doessing, T.; Randrup, J.

    1984-01-01

    An important goal in the theory of nuclear dynamics is to understand the observed transport phenomena in terms of the basic microscopic processes in the system. For this purpose a model was developed in which the dissipative mechanism responsible for the transport process is the transfer of nucleons between the two reacting nuclides. Until now, most efforts to confront that theory with data have concentrated on the evolution of the charge and mass distribution with energy loss, and overall good agreement has been obtained for a variety of features. While this success lends strong support to the theory, it is important to broaden the contact with experiment by considering also other aspects of the data. Therefore the authors have undertaken a comprehensive study of the angular momentum variables which represent six additional observables (three for each fragment spin) and thus provide a rich testing ground for the theory

  19. Exploiting dynamic reaction cell inductively coupled plasma mass spectrometry (DRC-ICP-MS) for sequential determination of trace elements in blood using a dilute-and-shoot procedure

    International Nuclear Information System (INIS)

    Lemos Batista, Bruno; Lisboa Rodrigues, Jairo; Andrade Nunes, Juliana; Oliveira Souza, Vanessa Cristina de; Barbosa, Fernando

    2009-01-01

    Inductively coupled plasma mass spectrometry with quadrupole (q-ICP-MS) and dynamic reaction cell (DRC-ICP-MS) were evaluated for sequential determination of As, Cd, Co, Cr, Cu, Mn, Pb, Se, Tl, V and Zn in blood. The method requires as little as 100 μL of blood. Prior to analysis, samples (100 μL) were diluted 1:50 in a solution containing 0.01% (v/v) Triton X-100 and 0.5% (v/v) nitric acid. The use of the DRC was only mandatory for Cr, Cu, V and Zn. For the other elements the equipment may be operated in a standard mode (q-ICP-MS). Ammonia was used as reaction gas. Selection of best flow rate of ammonium gas and optimization of the quadrupole dynamic band-pass tuning parameter (RPq) were carried out, using a ovine base blood for Cr and V and a synthetic matrix solution (SMS) for Zn and Cu diluted 1:50 and spiked to contain 1 μg L -1 of each element. Method detection limits (3 s) for 75 As, 114 Cd, 59 Co, 51 Cr, 63 Cu 55 Mn, 208 Pb, 82 Se, 205 Tl, 51 V, and 64 Zn were 14.0, 3.0, 11.0, 7.0, 280, 9.0, 3.0, 264, 0.7, 6.0 and 800 ng L -1 , respectively. Method validation was accomplished by the analysis of blood Reference Materials produced by the L'Institut National de Sante Publique du Quebec (Canada).

  20. Dynamically biased statistical model for the ortho/para conversion in the H2 + H3+ → H3+ + H2 reaction.

    Science.gov (United States)

    Gómez-Carrasco, Susana; González-Sánchez, Lola; Aguado, Alfredo; Sanz-Sanz, Cristina; Zanchet, Alexandre; Roncero, Octavio

    2012-09-07

    In this work we present a dynamically biased statistical model to describe the evolution of the title reaction from statistical to a more direct mechanism, using quasi-classical trajectories (QCT). The method is based on the one previously proposed by Park and Light [J. Chem. Phys. 126, 044305 (2007)]. A recent global potential energy surface is used here to calculate the capture probabilities, instead of the long-range ion-induced dipole interactions. The dynamical constraints are introduced by considering a scrambling matrix which depends on energy and determine the probability of the identity/hop/exchange mechanisms. These probabilities are calculated using QCT. It is found that the high zero-point energy of the fragments is transferred to the rest of the degrees of freedom, what shortens the lifetime of H(5)(+) complexes and, as a consequence, the exchange mechanism is produced with lower proportion. The zero-point energy (ZPE) is not properly described in quasi-classical trajectory calculations and an approximation is done in which the initial ZPE of the reactants is reduced in QCT calculations to obtain a new ZPE-biased scrambling matrix. This reduction of the ZPE is explained by the need of correcting the pure classical level number of the H(5)(+) complex, as done in classical simulations of unimolecular processes and to get equivalent quantum and classical rate constants using Rice-Ramsperger-Kassel-Marcus theory. This matrix allows to obtain a ratio of hop/exchange mechanisms, α(T), in rather good agreement with recent experimental results by Crabtree et al. [J. Chem. Phys. 134, 194311 (2011)] at room temperature. At lower temperatures, however, the present simulations predict too high ratios because the biased scrambling matrix is not statistical enough. This demonstrates the importance of applying quantum methods to simulate this reaction at the low temperatures of astrophysical interest.

  1. Dynamically biased statistical model for the ortho/para conversion in the H2+H3+ --> H3++ H2 reaction

    Science.gov (United States)

    Gómez-Carrasco, Susana; González-Sánchez, Lola; Aguado, Alfredo; Sanz-Sanz, Cristina; Zanchet, Alexandre; Roncero, Octavio

    2012-09-01

    In this work we present a dynamically biased statistical model to describe the evolution of the title reaction from statistical to a more direct mechanism, using quasi-classical trajectories (QCT). The method is based on the one previously proposed by Park and Light [J. Chem. Phys. 126, 044305 (2007), 10.1063/1.2430711]. A recent global potential energy surface is used here to calculate the capture probabilities, instead of the long-range ion-induced dipole interactions. The dynamical constraints are introduced by considering a scrambling matrix which depends on energy and determine the probability of the identity/hop/exchange mechanisms. These probabilities are calculated using QCT. It is found that the high zero-point energy of the fragments is transferred to the rest of the degrees of freedom, what shortens the lifetime of H_5^+ complexes and, as a consequence, the exchange mechanism is produced with lower proportion. The zero-point energy (ZPE) is not properly described in quasi-classical trajectory calculations and an approximation is done in which the initial ZPE of the reactants is reduced in QCT calculations to obtain a new ZPE-biased scrambling matrix. This reduction of the ZPE is explained by the need of correcting the pure classical level number of the H_5^+ complex, as done in classical simulations of unimolecular processes and to get equivalent quantum and classical rate constants using Rice-Ramsperger-Kassel-Marcus theory. This matrix allows to obtain a ratio of hop/exchange mechanisms, α(T), in rather good agreement with recent experimental results by Crabtree et al. [J. Chem. Phys. 134, 194311 (2011), 10.1063/1.3587246] at room temperature. At lower temperatures, however, the present simulations predict too high ratios because the biased scrambling matrix is not statistical enough. This demonstrates the importance of applying quantum methods to simulate this reaction at the low temperatures of astrophysical interest.

  2. Dynamics of Control and Resistance: Reactions to the Modern Policy of Assimilation of the Travellers in Norway

    Directory of Open Access Journals (Sweden)

    Rune Halvorsen

    2004-07-01

    Full Text Available For much of the 20th century, the Norwegian authorities pursued a strict assimilation policy towards Travellers (tatere/ romanifolket and their culture. As was the case in many other countries, Travellers were constructed as "the other" (Riggins 1997, MacLaughlin 1999. When compared to other Western European countries, it is, however, surprising that Norwegian Travellers were seen as such a serious problem and threat during the 20th century. The 1845 census counted 1145 Travellers out of a total population of 1.3 million in Norway (Sundt 1852, SSB 1968: Table 13. A private charity organisation acting on behalf of the state registered 5129 "itinerants" in their archives from 1900 to 1959 (Haave 2000. These were the figures that worried the elites. This paper examines the modern assimilation policy and Travellers' reactions to this policy. In particular the paper analyses the internal relation between the modern assimilation policy and the emergence of collective demands for recognition as an ethnic minority and moral redress among Travellers in the 1990s.

  3. Photoinitiated reactions in weakly bonded complexes

    International Nuclear Information System (INIS)

    Wittig, C.

    1993-01-01

    This paper discusses photoinitiated reactions in weakly bonded binary complexes in which the constituents are only mildly perturbed by the intermolecular bond. Such complexes, with their large zero point excursions, set the stage for events that occur following electronic excitation of one of the constituents. This can take several forms, but in all cases, entrance channel specificity is imposed by the character of the complex as well as the nature of the photoinitiation process. This has enabled us to examine aspects of bimolecular processes: steric effects, chemical branching ratios, and inelastic scattering. Furthermore, monitoring reactions directly in the time domain can reveal mechanisms that cannot be inferred from measurements of nascent product excitations. Consequently, we examined several systems that had been studied previously by our group with product state resolution. With CO 2 /HI, in which reaction occurs via a HOCO intermediate, the rates agree with RRKM predictions. With N 2 O/HI, the gas phase single collision reaction yielding OH + N 2 has been shown to proceed mainly via an HNNO intermediate that undergoes a 1,3-hydrogen shift to the OH + N 2 channel. With complexes, ab initio calculations and high resolution spectroscopic studies of analogous systems suggest that the hydrogen, while highly delocalized, prefers the oxygen to the nitrogen. We observe that OH is produced with a fast risetime (< 250 fs) which can be attributed to either direct oxygen-side attack or rapid HNNO decomposition and/or a termolecular contribution involving the nearby iodine

  4. Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

    International Nuclear Information System (INIS)

    Cao, Jun

    2015-01-01

    In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π * transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π * excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S 1 ( 1 ππ * ) and S 2 ( 1 n N π * ) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles

  5. Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Jun, E-mail: caojunbnu@mail.bnu.edu.cn [Guizhou Provincial Key Laboratory of Computational Nano-Material Sciences, Guizhou Normal College, Guiyang, Guizhou 550018, China and Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)

    2015-06-28

    In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

  6. Photoinduced reactions of both 2-formyl-2H-azirine and isoxazole: A theoretical study based on electronic structure calculations and nonadiabatic dynamics simulations

    Science.gov (United States)

    Cao, Jun

    2015-06-01

    In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π* transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π* excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S1(1ππ*) and S2(1nNπ*) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.

  7. Dynamical observation of lithium insertion/extraction reaction during charge-discharge processes in Li-ion batteries by in situ spatially resolved electron energy-loss spectroscopy.

    Science.gov (United States)

    Shimoyamada, Atsushi; Yamamoto, Kazuo; Yoshida, Ryuji; Kato, Takehisa; Iriyama, Yasutoshi; Hirayama, Tsukasa

    2015-12-01

    All-solid-state Li-ion batteries (LIBs) with solid electrolytes are expected to be the next generation devices to overcome serious issues facing conventional LIBs with liquid electrolytes. However, the large Li-ion transfer resistance at the electrode/solid-electrolyte interfaces causes low power density and prevents practical use. In-situ-formed negative electrodes prepared by decomposing the solid electrolyte Li(1+x+3z)Alx(Ti,Ge)(2-x)Si(3z)P(3-z)O12 (LASGTP) with an excess Li-ion insertion reaction are effective electrodes providing low Li-ion transfer resistance at the interfaces. Prior to our work, however, it had still been unclear how the negative electrodes were formed in the parent solid electrolytes. Here, we succeeded in dynamically visualizing the formation by in situ spatially resolved electron energy-loss spectroscopy in a transmission electron microscope mode (SR-TEM-EELS). The Li-ions were gradually inserted into the solid electrolyte region around 400 nm from the negative current-collector/solid-electrolyte interface in the charge process. Some of the ions were then extracted in the discharge process, and the rest were diffused such that the distribution was almost flat, resulting in the negative electrodes. The redox reaction of Ti(4+)/Ti(3+) in the solid electrolyte was also observed in situ during the Li insertion/extraction processes. The in situ SR-TEM-EELS revealed the mechanism of the electrochemical reaction in solid-state batteries. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Dynamic Time-Resolved Chirped-Pulse Rotational Spectroscopy of Vinyl Cyanide Photoproducts in a Room Temperature Flow Reactor

    Science.gov (United States)

    Zaleski, Daniel P.; Prozument, Kirill

    2017-06-01

    Chirped-pulsed (CP) Fourier transform rotational spectroscopy invented by Brooks Pate and coworkers a decade ago is an attractive tool for gas phase chemical dynamics and kinetics studies. A good reactor for such a purpose would have well-defined (and variable) temperature and pressure conditions to be amenable to accurate kinetic modeling. Furthermore, in low pressure samples with large enough number of molecular emitters, reaction dynamics can be observable directly, rather than mediated by supersonic expansion. In the present work, we are evaluating feasibility of in situ time-resolved CP spectroscopy in a room temperature flow tube reactor. Vinyl cyanide (CH_2CHCN), neat or mixed with inert gasses, flows through the reactor at pressures 1-50 μbar (0.76-38 mTorr) where it is photodissociated by a 193 nm laser. Millimeter-wave beam of the CP spectrometer co-propagates with the laser beam along the reactor tube and interacts with nascent photoproducts. Rotational transitions of HCN, HNC, and HCCCN are detected, with ≥10 μs time-steps for 500 ms following photolysis of CH_2CHCN. The post-photolysis evolution of the photoproducts' rotational line intensities is investigated for the effects of rotational and vibrational thermalization of energized photoproducts. Possible contributions from bimolecular and wall-mediated chemistry are evaluated as well.

  9. Computational fluid dynamics tracking of UF6 reaction products release into a gaseous diffusion plant cell housing

    International Nuclear Information System (INIS)

    Wendel, M.W.; Chen, N.C.J.; Kim, S.H.; Taleyarkhan, R.P.; Keith, K.D.; Schmidt, R.W.

    1996-01-01

    A three-dimensional (3-D) computational fluid dynamics (CFD) model has been developed using CFDS-FLOW3D Version 3.3 to model the transport of aerosol products formed during a release of uranium hexafluoride (UF 6 ) into a gaseous diffusion plant (GDP) process building. As part of a facility-wide safety evaluation, a one-dimensional (1-D) analysis of aerosol/vapor transport following such an hypothesized severe accident is being performed. The objective of this study is to supplement the 1-D analysis with more detailed 3-D results. Specifically, the goal is to quantify the distribution of aerosol passing out of the process building during the hypothetical accident. This work demonstrates a useful role for CFD in large 3-D problems, where some experimental data are available for calibrating key parameters and the desired results are global (total time-integrated aerosol flow rates across a few boundary surfaces) as opposed to local velocities, temperatures, or heat transfer coefficients

  10. Nuclear reaction studies

    International Nuclear Information System (INIS)

    Alexander, J.M.; Lacey, R.A.

    1994-01-01

    Research focused on the statistical and dynamical properties of ''hot'' nuclei formed in symmetric heavy-ion reactions. Theses included ''flow'' measurements and the mechanism for multifragment disassembly. Model calculations are being performed for the reactions C+C, Ne+Al, Ar+Sc, Kr+Nb, and Xe+La. It is planned to study 40 Ar reactions from 27 to 115 MeV/nucleon. 2 figs., 41 refs

  11. BGK-type models in strong reaction and kinetic chemical equilibrium regimes

    International Nuclear Information System (INIS)

    Monaco, R; Bianchi, M Pandolfi; Soares, A J

    2005-01-01

    A BGK-type procedure is applied to multi-component gases undergoing chemical reactions of bimolecular type. The relaxation process towards local Maxwellians, depending on mass and numerical densities of each species as well as common velocity and temperature, is investigated in two different cases with respect to chemical regimes. These cases are related to the strong reaction regime characterized by slow reactions, and to the kinetic chemical equilibrium regime where fast reactions take place. The consistency properties of both models are stated in detail. The trend to equilibrium is numerically tested and comparisons for the two regimes are performed within the hydrogen-air and carbon-oxygen reaction mechanism. In the spatial homogeneous case, it is also shown that the thermodynamical equilibrium of the models recovers satisfactorily the asymptotic equilibrium solutions to the reactive Euler equations

  12. Reaction dynamics of O({sup 1}D) + HCOOD/DCOOH investigated with time-resolved Fourier-transform infrared emission spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Shang-Chen; Putikam, Raghunath; Lin, M. C., E-mail: chemmcl@emory.edu, E-mail: tsuchis@sepia.plala.or.jp, E-mail: yplee@mail.nctu.edu.tw; Tsuchiya, Soji, E-mail: chemmcl@emory.edu, E-mail: tsuchis@sepia.plala.or.jp, E-mail: yplee@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Nghia, N. T. [School of Chemical Engineering - Hanoi University of Science and Technology, Hanoi (Viet Nam); Nguyen, Hue M. T. [Center for Computational Science and Faculty of Chemistry, Hanoi National University of Education, Hanoi (Viet Nam); Lee, Yuan-Pern, E-mail: chemmcl@emory.edu, E-mail: tsuchis@sepia.plala.or.jp, E-mail: yplee@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan (China)

    2014-10-21

    We investigated the reaction dynamics of O({sup 1}D) towards hydrogen atoms of two types in HCOOH. The reaction was initiated on irradiation of a flowing mixture of O{sub 3} and HCOOD or DCOOH at 248 nm. The relative vibration-rotational populations of OH and OD (1 ≦ v ≦ 4, J ≤ 15) states were determined from time-resolved IR emission recorded with a step-scan Fourier-transform spectrometer. In the reaction of O({sup 1}D) + HCOOD, the rotational distribution of product OH is nearly Boltzmann, whereas that of OD is bimodal. The product ratio [OH]/[OD] is 0.16 ± 0.05. In the reaction of O({sup 1}D) + DCOOH, the rotational distribution of product OH is bimodal, but the observed OD lines are too weak to provide reliable intensities. The three observed OH/OD channels agree with three major channels of production predicted with quantum-chemical calculations. In the case of O({sup 1}D) + HCOOD, two intermediates HOC(O)OD and HC(O)OOD are produced in the initial C−H and O−D insertion, respectively. The former undergoes further decomposition of the newly formed OH or the original OD, whereas the latter produces OD via direct decomposition. Decomposition of HOC(O)OD produced OH and OD with similar vibrational excitation, indicating efficient intramolecular vibrational relaxation, IVR. Decomposition of HC(O)OOD produced OD with greater rotational excitation. The predicted [OH]/[OD] ratio is 0.20 for O({sup 1}D) + HCOOD and 4.08 for O({sup 1}D) + DCOOH; the former agrees satisfactorily with experiments. We also observed the v{sub 3} emission from the product CO{sub 2}. This emission band is deconvoluted into two components corresponding to internal energies E = 317 and 96 kJ mol{sup −1} of CO{sub 2}, predicted to be produced via direct dehydration of HOC(O)OH and secondary decomposition of HC(O)O that was produced via decomposition of HC(O)OOH, respectively.

  13. Applications of a simple dynamical model to the reaction path Hamiltonian: tunneling corrections to rate constants, product state distributions, line widths of local mode overtones, and mode specificity in unimolecular decomposition

    International Nuclear Information System (INIS)

    Cerjan, C.J.; Shi, S.; Miller, W.H.

    1982-01-01

    A simple but often reasonably accurate dynamical model--a synthesis of the semiclassical perturbation (SCP) approximation of Miller and Smith and the infinite order sudden (IOS) approximation--has been shown previously to take an exceptionally simple form when applied to the reaction path Hamiltonian derived by Miller, Handy, and Adams. This paper shows how this combined SCP-IOS reaction path model can be used to provide a simple but comprehensive description of a variety of phenomena in the dynamics of polyatomic molecules

  14. Biochemical Stability and Molecular Dynamic Characterization of Aspergillus fumigatus Cystathionine γ-Lyase in Response to Various Reaction Effectors

    KAUST Repository

    El-Sayed, Ashraf S.A.; Abdel-Azeim, Safwat; Ibrahim, Hend M.; Yassin, Marwa A.; Abdel-Ghany, Salah E.; Esener, Sadik; Ali, Gul Shad

    2015-01-01

    Cystathionine γ-lyase (CGL) is a key enzyme in the methionine-cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8 U/mg. The melting temperature (Tm) of CGL in potassium phosphate buffer (pH 7.0-8.0) was 73.3 °C, with ∼3 °C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris-HCl, HEPES (pH 7.0) and CAPS (pH 9.0-10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under

  15. Biochemical Stability and Molecular Dynamic Characterization of Aspergillus fumigatus Cystathionine γ-Lyase in Response to Various Reaction Effectors

    KAUST Repository

    El-Sayed, Ashraf S.A.

    2015-08-11

    Cystathionine γ-lyase (CGL) is a key enzyme in the methionine-cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8 U/mg. The melting temperature (Tm) of CGL in potassium phosphate buffer (pH 7.0-8.0) was 73.3 °C, with ∼3 °C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris-HCl, HEPES (pH 7.0) and CAPS (pH 9.0-10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under

  16. Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: implications for replication and genome packaging.

    Science.gov (United States)

    Chaturvedi, Sonali; Rao, A L N

    2014-09-01

    In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein-protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

    International Nuclear Information System (INIS)

    Chaturvedi, Sonali; Rao, A.L.N.

    2014-01-01

    In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER

  18. Live cell imaging of interactions between replicase and capsid protein of Brome mosaic virus using Bimolecular Fluorescence Complementation: Implications for replication and genome packaging

    Energy Technology Data Exchange (ETDEWEB)

    Chaturvedi, Sonali; Rao, A.L.N., E-mail: arao@ucr.edu

    2014-09-15

    In Brome mosaic virus, it was hypothesized that a physical interaction between viral replicase and capsid protein (CP) is obligatory to confer genome packaging specificity. Here we tested this hypothesis by employing Bimolecular Fluorescent Complementation (BiFC) as a tool for evaluating protein–protein interactions in living cells. The efficacy of BiFC was validated by a known interaction between replicase protein 1a (p1a) and protein 2a (p2a) at the endoplasmic reticulum (ER) site of viral replication. Additionally, co-expression in planta of a bona fide pair of interacting protein partners of p1a and p2a had resulted in the assembly of a functional replicase. Subsequent BiFC assays in conjunction with mCherry labeled ER as a fluorescent cellular marker revealed that CP physically interacts with p2a, but not p1a, and this CP:p2a interaction occurs at the cytoplasmic phase of the ER. The significance of the CP:p2a interaction in BMV replication and genome packaging is discussed. - Highlights: • YFP fusion proteins of BMV p1a and p2a are biologically active. • Self-interaction was observed for p1a, p2a and CP. • CP interacts with p2a but not p1a. • Majority of reconstituted YFP resulting from bona fide fusion protein partners localized on ER.

  19. Entropy-based critical reaction time for mixing-controlled reactive transport

    DEFF Research Database (Denmark)

    Chiogna, Gabriele; Rolle, Massimo

    2017-01-01

    Entropy-based metrics, such as the dilution index, have been proposed to quantify dilution and reactive mixing in solute transport problems. In this work, we derive the transient advection dispersion equation for the entropy density of a reactive plume. We restrict our analysis to the case where...... the concentration distribution of the transported species is Gaussian and we observe that, even in case of an instantaneous complete bimolecular reaction, dilution caused by dispersive processes dominates the entropy balance at early times and results in the net increase of the entropy density of a reactive species...

  20. Simultaneous determination of Cr(iii) and Cr(vi) using reversed-phased ion-pairing liquid chromatography with dynamic reaction cell inductively coupled plasma mass spectrometry

    Science.gov (United States)

    Wolf, R.E.; Morrison, J.M.; Goldhaber, M.B.

    2007-01-01

    A method for the simultaneous determination of Cr(iii) and Cr(vi) species in waters, soil leachates and synthetic bio-fluids is described. The method uses reversed-phase ion-pairing liquid chromatography to separate the chromium species and a dynamic reaction cell (DRC??) equipped ICP-MS for detection of chromium. Separation of the chromium species is carried out in less than 2 min. Cr(iii) is complexed with ethylenediaminetetraacetic acid (EDTA) prior to separation by mixing samples with the mobile phase containing 2.0 mM tetrabutylammonium hydroxide (TBAOH), 0.5 mM EDTA (dipotassium salt), and 5% (vol/vol) methanol, adjusted to pH 7.6. The interfering 40Ar 12C+ background peak at mass 52 was reduced by over four orders of magnitude to less than 200 cps by using 0.65 mL min-1 ammonia as a reaction gas and an RPq setting on the DRC of 0.75. Method detection limits (MDLs) of 0.09 ??g L-1 for Cr(iii) and 0.06 ??g L-1 for Cr(vi) were obtained based on peak areas at mass 52 for 50 ??L injections of low level spikes. Reproducibility at 2 ??g L-1 was 3% RSD for 5 replicate injections. The tolerance of the method to various levels of common cations and anions found in natural waters and to matrix constituents found in soil leachates and simulated gastric and lung fluids was tested by performing spike recovery calculations for a variety of samples. ?? The Royal Society of Chemistry.

  1. Dynamics

    CERN Document Server

    Goodman, Lawrence E

    2001-01-01

    Beginning text presents complete theoretical treatment of mechanical model systems and deals with technological applications. Topics include introduction to calculus of vectors, particle motion, dynamics of particle systems and plane rigid bodies, technical applications in plane motions, theory of mechanical vibrations, and more. Exercises and answers appear in each chapter.

  2. Determination of (90)Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS).

    Science.gov (United States)

    Feuerstein, J; Boulyga, S F; Galler, P; Stingeder, G; Prohaska, T

    2008-11-01

    A rapid method is reported for the determination of (90)Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of (90)Zr, which is present in soils at concentrations higher by more than six orders of magnitude than (90)Sr. Zirconium was separated from strontium in two steps to reduce the interference by (90)Zr(+) ions by a factor of more than 10(7): (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from (88)Sr on mass 90 u was found to be about 3 x 10(-9). Detection limits of 4 fg g(-1) (0.02 Bq g(-1)) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 microg g(-1) Sr and 50 ng g(-1) Zr a detection limit of 0.2 pg g(-1) soil (1 Bq g(-1) soil) was determined. (90)Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66+/-0.27, 13.48+/-0.68 and 12.9+/-1.5 pg g(-1) corresponding to specific activities of 23.7+/-1.3, 68.6+/-3.5 and 65.6+/-7.8 Bq g(-1), respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level (90)Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g(-1).

  3. Determination of 90Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS)

    International Nuclear Information System (INIS)

    Feuerstein, J.; Boulyga, S.F.; Galler, P.; Stingeder, G.; Prohaska, T.

    2008-01-01

    A rapid method is reported for the determination of 90 Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of 90 Zr, which is present in soils at concentrations higher by more than six orders of magnitude than 90 Sr. Zirconium was separated from strontium in two steps to reduce the interference by 90 Zr + ions by a factor of more than 10 7 : (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from 88 Sr on mass 90 u was found to be about 3 x 10 -9 . Detection limits of 4 fg g -1 (0.02 Bq g -1 ) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 μg g -1 Sr and 50 ng g -1 Zr a detection limit of 0.2 pg g -1 soil (1 Bq g -1 soil) was determined. 90 Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66 ± 0.27, 13.48 ± 0.68 and 12.9 ± 1.5 pg g -1 corresponding to specific activities of 23.7 ± 1.3, 68.6 ± 3.5 and 65.6 ± 7.8 Bq g -1 , respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level 90 Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g -1

  4. Determination of {sup 90}Sr in soil samples using inductively coupled plasma mass spectrometry equipped with dynamic reaction cell (ICP-DRC-MS)

    Energy Technology Data Exchange (ETDEWEB)

    Feuerstein, J.; Boulyga, S.F.; Galler, P.; Stingeder, G. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria); Prohaska, T. [Department of Chemistry, Division of Analytical Chemistry-VIRIS Laboratory, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna (Austria)], E-mail: thomas.prohaska@boku.ac.at

    2008-11-15

    A rapid method is reported for the determination of {sup 90}Sr in contaminated soil samples in the vicinity of the Chernobyl Nuclear Power Plant by ICP-DRC-MS. Sample preparation and measurement procedures focus on overcoming the isobaric interference of {sup 90}Zr, which is present in soils at concentrations higher by more than six orders of magnitude than {sup 90}Sr. Zirconium was separated from strontium in two steps to reduce the interference by {sup 90}Zr{sup +} ions by a factor of more than 10{sup 7}: (i) by ion exchange using a Sr-specific resin and (ii) by reaction with oxygen as reaction gas in a dynamic reaction cell (DRC) of a quadrupole ICP-MS. The relative abundance sensitivity of the ICP-MS was studied systematically and the peak tailing originating from {sup 88}Sr on mass 90 u was found to be about 3 x 10{sup -9}. Detection limits of 4 fg g{sup -1} (0.02 Bq g{sup -1}) were achieved when measuring Sr solutions containing no Zr. In digested uncontaminated soil samples after matrix separation as well as in a solution of 5 {mu}g g{sup -1} Sr and 50 ng g{sup -1} Zr a detection limit of 0.2 pg g{sup -1} soil (1 Bq g{sup -1} soil) was determined. {sup 90}Sr concentrations in three soil samples collected in the vicinity of the Chernobyl Nuclear Power Plant were 4.66 {+-} 0.27, 13.48 {+-} 0.68 and 12.9 {+-} 1.5 pg g{sup -1} corresponding to specific activities of 23.7 {+-} 1.3, 68.6 {+-} 3.5 and 65.6 {+-} 7.8 Bq g{sup -1}, respectively. The ICP-DRC-MS results were compared to the activities measured earlier by radiometry. Although the ICP-DRC-MS is inferior to commonly used radiometric methods with respect to the achievable minimum detectable activity it represents a time- and cost-effective alternative technique for fast monitoring of high-level {sup 90}Sr contamination in environmental or nuclear industrial samples down to activities of about 1 Bq g{sup -1}.

  5. Nonadiabatic ab initio molecular dynamics of photoisomerization reaction between 1,3-cyclohexadiene and 1,3,5-cis-hexatriene

    International Nuclear Information System (INIS)

    Ohta, Ayumi; Kobayashi, Osamu; Danielache, Sebastian O.; Nanbu, Shinkoh

    2015-01-01

    Highlights: • The photoisomerization between cyclohexadiene and hexatriene was simulated. • Nonadiabatic ab initio MD simulations were employed to elucidate the mechanism. • Each excitations to S_1 and S_2 were simulated using full-dimensional model. • Specific molecular motions at CoIns and molecular vibrations on S_1 PES were found. • The one-sided product branching ratio was obtained at the photoexcitation to S_2. - Abstract: The photoisomerization process between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) has been studied by nonadiabatic ab initio molecular dynamics based on trajectory surface-hopping approach with a full-dimensional reaction model. The quantum chemical calculations were treated at MS-MR-CASPT2 level for 8 electrons in 8 orbitals with the cc-pVDZ basis set. The Zhu–Nakamura formula was employed to evaluate nonadiabatic transition probabilities. S_1 and S_2 states were included in the photoisomerization dynamics. Lifetimes and CHD:HT branching ratios were computationally estimated on the basis of statistical analysis of multiple executed trajectories. The analysis of trajectories suggested that the nonadiabatic transitions at the S_0/S_1 and S_1/S_2 conical intersections (CoIn) are correlated to the Kekulé-type vibration and the C3–C4–C5 bending motion, respectively. The one-sided branching ratio was obtained by excitations to the S_2 state; 70:30. The critical branching process was found to be dominated by the location of CoIn in potential energy hypersurface of the excited state.

  6. TRIMOLECULAR REACTIONS OF URANIUM HEXAFLUORIDE WITH WATER

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, M.; Becnel, J.; Garrison, S.

    2010-02-25

    The hydrolysis reaction of uranium hexafluoride (UF{sub 6}) is a key step in the synthesis of uranium dioxide (UO{sub 2}) powder for nuclear fuels. Mechanisms for the hydrolysis reactions are studied here with density functional theory and the Stuttgart small-core scalar relativistic pseudopotential and associated basis set for uranium. The reaction of a single UF{sub 6} molecule with a water molecule in the gas phase has been previously predicted to proceed over a relatively sizeable barrier of 78.2 kJ {center_dot} mol{sup -1}, indicating this reaction is only feasible at elevated temperatures. Given the observed formation of a second morphology for the UO{sub 2} product coupled with the observations of rapid, spontaneous hydrolysis at ambient conditions, an alternate reaction pathway must exist. In the present work, two trimolecular hydrolysis mechanisms are studied with density functional theory: (1) the reaction between two UF{sub 6} molecules and one water molecule, and (2) the reaction of two water molecules with a single UF{sub 6} molecule. The predicted reaction of two UF{sub 6} molecules with one water molecule displays an interesting 'fluorine-shuttle' mechanism, a significant energy barrier of 69.0 kJ {center_dot} mol{sup -1} to the formation of UF{sub 5}OH, and an enthalpy of reaction ({Delta}H{sub 298}) of +17.9 kJ {center_dot} mol{sup -1}. The reaction of a single UF{sub 6} molecule with two water molecules displays a 'proton-shuttle' mechanism, and is more favorable, having a slightly lower computed energy barrier of 58.9 kJ {center_dot} mol{sup -1} and an exothermic enthalpy of reaction ({Delta}H{sub 298}) of -13.9 kJ {center_dot} mol{sup -1}. The exothermic nature of the overall UF{sub 6} + 2 {center_dot} H{sub 2}O trimolecular reaction and the lowering of the barrier height with respect to the bimolecular reaction are encouraging; however, the sizable energy barrier indicates further study of the UF{sub 6} hydrolysis reaction

  7. Modified reaction mechanism of aerated n-dodecane liquid flowing over heated metal tubes

    Science.gov (United States)

    Reddy, K. T.; Cernansky, N. P.; Cohen, R. S.

    1988-01-01

    The degradation mechanism of the n-dodecane was studied using a modified jet fuel thermal oxidation tester containing a sample withdrawal system as a reaction vessel. The reaction products were identified using gas chromatography and mass spectorometry. The soluble products were found to consist mainly of C5-C10 n-alkanes and 1-alkenes, C7-C10 aldehydes, tetrahydrofuran derivatives, dodecanol and dodecanone isomers, dodecyl hydroperoxide (ROOH) decomposition products, and C24 alkane isomers. The data from the experiments agreed with those of Hazlett et al. (1977). It was found that alkyl peroxide radical reactions dominate in the autooxidation temperature regime (at T not above 300 C); the dominant path is for the alkyl peroxyl radical to react bimolecularly with fuel to yield primarily alkyl hydroperoxides. The alkyl peroxide radical also undergoes self-termination and unimolecular isomerization and decomposition reactions, to yield smaller amounts of C12 alcohol plus ketone products and tetrahydrofuran derivatives, respectively.

  8. Reaction dynamics of the four-centered elimination CH2OH + --> CHO + +H2: Measurement of kinetic energy release distribution and classical trajectory calculation

    Science.gov (United States)

    Lee, Tae Geol; Park, Seung C.; Kim, Myung Soo

    1996-03-01

    Mass-analyzed ion kinetic energy (MIKE) spectrum of CHO+ generated in the unimolecular dissociation of CH2OH+ was measured. Kinetic energy release distribution (KERD) was evaluated by analyzing the spectrum according to the algorithm developed previously. The average kinetic energy release evaluated from the distribution was extraordinarily large, 1.63 eV, corresponding to 75% of the reverse barrier of the reaction. A global analytical potential energy surface was constructed such that the experimental energetics was represented and that various features in the ab initio potential energy surface were closely reproduced. Classical trajectory calculation was carried out with the global analytical potential energy surface to investigate the causes for the extraordinarily large kinetic energy release. Based on the detailed dynamical calculations, it was found that the strained bending forces at the transition state and strengthening of the CO bond from double to triple bond character were mainly responsible for such a significant kinetic energy release. In addition, the dissociation products H2 and CHO+ ion were found to be rotationally excited in the trajectory calculations. This was attributed to the asymmetry of the transition state and the release of asymmetric bending forces. Also, the bending vibrational modes of CHO+ and the H2 stretching mode, which are coupled with the bending coordinates, were found to be moderately excited.

  9. Liquid chromatography-electrospray ionization tandem mass spectrometry and dynamic multiple reaction monitoring method for determining multiple pesticide residues in tomato.

    Science.gov (United States)

    Andrade, G C R M; Monteiro, S H; Francisco, J G; Figueiredo, L A; Botelho, R G; Tornisielo, V L

    2015-05-15

    A quick and sensitive liquid chromatography-electrospray ionization tandem mass spectrometry method, using dynamic multiple reaction monitoring and a 1.8-μm particle size analytical column, was developed to determine 57 pesticides in tomato in a 13-min run. QuEChERS (quick, easy, cheap, effective, rugged, and safe) method for samples preparations and validations was carried out in compliance with EU SANCO guidelines. The method was applied to 58 tomato samples. More than 84% of the compounds investigated showed limits of detection equal to or lower than 5 mg kg(-1). A mild (50%) matrix effect was observed for 72%, 25%, and 3% of the pesticides studied, respectively. Eighty-one percent of the pesticides showed recoveries ranging between 70% and 120%. Twelve pesticides were detected in 35 samples, all below the maximum residue levels permitted in the Brazilian legislation; 15 samples exceeded the maximum residue levels established by the EU legislation for methamidophos; and 10 exceeded limits for acephate and four for bromuconazole. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. A new potential energy surface of the OH2+ system and state-to-state quantum dynamics studies of the O+ + H2 reaction.

    Science.gov (United States)

    Li, Wentao; Yuan, Jiuchuang; Yuan, Meiling; Zhang, Yong; Yao, Minghai; Sun, Zhigang

    2018-01-03

    A new global potential energy surface (PES) of the O + + H 2 system was constructed with the permutation invariant polynomial neural network method, using about 63 000 ab initio points, which were calculated by employing the multi-reference configuration interaction method with aug-cc-pVTZ and aug-cc-pVQZ basis sets. For improving the accuracy of the PES, the basis set was extrapolated to the complete basis set limit by the two-point extrapolation method. The root mean square error of fitting was only 5.28 × 10 -3 eV. The spectroscopic constants of the diatomic molecules were calculated and compared with previous theoretical and experimental results, which suggests that the present results agree well with the experiment. On the newly constructed PES, reaction dynamics studies were performed using the time-dependent wave packet method. The calculated integral cross sections (ICSs) were compared with the available theoretical and experimental results, where a good agreement with the experimental data was seen. Significant forward and backward scatterings were observed in the whole collision energy region studied. At the same time, the differential cross sections biased the forward scattering, especially at higher collision energies.

  11. Dynamics of high energy reactions

    International Nuclear Information System (INIS)

    Field, R.D.

    1979-01-01

    During last several years, a new framework to describe strong interaction physics has emerged, i.e. quantum chromodynamics (QCD). It is the simplest field theory which incorporates color-dependent force among quarks. This force is generated by the exchange of colored vector gluons coupled to the quarks in gauge-invariant manner. The theory is closely related to the most successful quantum field theory, QED, and the only but very important difference is the gauge group involved. Although the theory is well defined, precisely what it predicts is not yet clearly known. However, at very high energy or momentum transfer Q, the effective coupling between quarks and gluons decreases toward zero with increasing Q 2 , and the calculation of a process involving high Q 2 is possible by the use of perturbation theory. In this paper, many applications of QCD to the processes involving high momentum transfer are examined. The effective coupling resulting from strong interaction between quarks and gluons, the scale violation in deep inelastic lepton scattering, large mass muon pair production, quark and gluon fragmentation functions, large transverse momentum meson and jet production in hadron-hadron collision, and the search for three-jet events are discussed. (Kako, I.)

  12. Chemical kinetics and reaction dynamics

    CERN Document Server

    Houston, Paul L

    2006-01-01

    This text teaches the principles underlying modern chemical kinetics in a clear, direct fashion, using several examples to enhance basic understanding. It features solutions to selected problems, with separate sections and appendices that cover more technical applications.Each chapter is self-contained and features an introduction that identifies its basic goals, their significance, and a general plan for their achievement. This text's important aims are to demonstrate that the basic kinetic principles are essential to the solution of modern chemical problems, and to show how the underlying qu

  13. Recent results on solvation dynamics of electron and spur reactions of solvated electron in polar solvents studied by femtosecond laser spectroscopy and picosecond pulse radiolysis

    International Nuclear Information System (INIS)

    Mostafavi, M.

    2006-01-01

    Here, we report several studies done recently at ELYSE laboratory on the solvation dynamics of electron and on the kinetics of solvated electron in the spur reactions, performed by femtosecond laser spectroscopy and picosecond pulse radiolysis, respectively. Solvated electrons have been produced in polyol (1,2-Etanediol, 1,2-Propanediol and 1,3-Propanediol) by two-photon ionization of the solvent with 263 nm femtosecond laser pulses at room temperature. The two-photon absorption coefficient of these solvents at 263 nm has been determined. The dynamics of electron solvation in polyols has been studied by pump-probe transient absorption spectroscopy. So, time resolved absorption spectra ranging from 430 to 720 nm have been measured (Figure 1). A blue shift of the spectra is observed for the first tens of picoseconds. Using Bayesian data analysis method, the observed solvation dynamics are reconstructed with different models: stepwise mechanisms, continuous relaxation models or combinations of stepwise and continuous relaxation. That analysis clearly indicates that it is not obvious to select a unique model to describe the solvation dynamics of electron in diols. We showed that several models are able to reproduce correctly the data: a two-step model, a heterogeneous or bi-exponential continuous relaxation model and even a hybrid model with a stepwise transition and homogeneous continuous relaxation. Nevertheless, the best fits are given by the continuous spectral relaxation models. The fact that the time-evolution of the absorption spectrum of the solvated electron in diols can be accurately described by the temperature dependent absorption spectrum of the ground state solvated electron suggests that the spectral blue shift is mostly caused by the continuous relaxation of the electron trapped in a large distribution of solvent cages. Similar trends on electron solvation dynamics are observed in the cases of 1,2-ethanediol, 1,3-propanediol and 1,2 propanediol

  14. Tetronic Star Block Copolymer Micelles: Photophysical Characterisation of Microenvironments and Applicability for Tuning Electron Transfer Reactions.

    Science.gov (United States)

    Samanta, Papu; Rane, Sonal; Bahadur, Pratap; Dutta Choudhury, Sharmistha; Pal, Haridas

    2018-05-10

    Detailed photophysical investigations have been carried out using a probe dye, Coumarin-153 (C153), to understand the microenvironments of micelles formed by the newly introduced Tetronic star block copolymers, T1304 and T1307, having the same polypropylene oxide (PPO) block size but different polyethylene oxide (PEO) block sizes. Ground state absorption, steady-state fluorescence and time-resolved fluorescence measurements have been used to estimate the micropolarity, microviscosity and solvation dynamics within the two micelles. To the best of our knowledge this is the first report on these important physicochemical parameters for this new class of the star block copolymer micelles. Our results indicate that T1307 micelle offers a relatively more polar and less viscous microenvironment in the corona region, compared to T1304. The effect of the two micellar systems has subsequently been investigated on the bimolecular photoinduced electron transfer (ET) reactions between coumarin dyes (electron acceptors) and aromatic amines (electron donors). On correlating the energetics and kinetics of the ET reactions, clear Marcus Inversion (MI) behavior is observed in both the micellar media. Interestingly, the ET rates for all the donor-acceptor pairs are much higher in T1307 than in T1304, and the onset of MI also appears at a relatively higher exergenocity (-Δ G 0 ) in the former micelle (~0.45 eV for T1307) than the latter (~0.37 eV for T1304). Effect of added NaCl salt studied selectively in T1307 micelle, shows that the ET rate decreases significantly along with a shift in the onset of MI toward lower exergenocity region, so that in the presence of 2 M NaCl the system becomes quite comparable to T1304. Based on the observed results, it is realized that the micropolarity and hence the dynamics of ET process can be tuned very effectively either by changing the constitution of the star block copolymer or by using a suitable additive as a modifier of the micellar

  15. Laser ablation-inductively coupled plasma-dynamic reaction cell-mass spectrometry for the multi-element analysis of polymers

    International Nuclear Information System (INIS)

    Resano, M.; Garcia-Ruiz, E.; Vanhaecke, F.

    2005-01-01

    In this work, the potential of laser ablation-inductively coupled plasma-mass spectrometry for the fast analysis of polymers has been explored. Different real-life samples (polyethylene shopping bags, an acrylonitrile butadiene styrene material and various plastic bricks) as well as several reference materials (VDA 001 to 004, Cd in polyethylene) have been selected for the study. Two polyethylene reference materials (ERM-EC 680 and 681), for which a reference or indicative value for the most relevant metals is available, have proved their suitability as standards for calibration. Special attention has been paid to the difficulties expected for the determination of Cr at the μg g -1 level in this kind of materials, due to the interference of ArC + ions on the most abundant isotopes of Cr. The use of ammonia as a reaction gas in a dynamic reaction cell is shown to alleviate this problem, resulting in a limit of detection of 0.15 μg g -1 for this element, while limiting only modestly the possibilities of the technique for simultaneous multi-element analysis. In this regard, As is the analyte most seriously affected by the use of ammonia, and its determination has to be carried out in vented mode, at the expense of measuring time. In all cases studied, accurate results could be obtained for elements ranging in content from the sub-μg g -1 level to tens of thousands of μg g -1 . However, the use of an element of known concentration as internal standard may be needed for materials with a matrix significantly different from that of the standard (polyethylene in this work). Precision ranged between 5% and 10% RSD for elements found at the 10 μg g -1 level or higher, while this value could deteriorate to 20% for analytes found at the sub-μg g -1 level. Overall, the technique evaluated presents many advantages for the fast and accurate multi-element analysis of these materials, avoiding laborious digestion procedures and minimizing the risk of analyte losses due to the

  16. Multi-element analysis of urine using dynamic reaction cell inductively coupled plasma mass spectrometry (ICP-DRC-MS — A practical application

    Directory of Open Access Journals (Sweden)

    Renata Brodzka

    2013-04-01

    Full Text Available Objectives: The method for the determination of As, Al, Cd, Ni, Pb (toxic elements and Cr, Co, Cu, Fe, Mn, Zn (essential elements in human urine by the use of Inductively Coupled Plasma Mass Spectrometry (quadrupole ICP-MS DRCe Elan, Perkin Elmer with the dynamic reaction cell (DRC was developed. Materials and Methods: The method has been applied for multi-element analysis of the urine of 16 non-exposed healthy volunteers and 27 workers employed in a copper smelter. The analysis was conducted after initial 10-fold dilution of the urine samples with 0,1% nitric acid. Rhodium was used as an internal standard. The method validation parameters such as detection limit, sensitivity, precision were described for all elements. Accuracy of the method was checked by the regular use of certified reference materials ClinCheck®-Control Urine (Recipe as well as by participation of the laboratory in the German External Quality Assessment Scheme (G-EQUAS. Results: The detection limits (DL 3s of the applied method were 0.025, 0.007, 0.002, 0.004, 0.004, 0.086, 0.037, 0.009, 0.016, 0.008, 0.064 (μg/l for Al, As, Cd, Cr, Co, Cu, Fe, Mn, Ni, Pb, Zn in urine, respectively. For each element linearity with correlation coefficient of at least 0.999 was determined. Spectral interferences from some of the ions were removed using DRC-e with addition of alternative gas: methane for cobalt, copper, cadmium, chromium, iron, manganese, nickel and rhodium, and oxygen for arsenic. Conclusions: The developed method allows to determine simultaneously eleven elements in the urine with low detection limits, high sensitivity and good accuracy. Moreover, the method is appropriate for the assessment of both environmental and occupational exposure.

  17. Mass yield distributions for the reactions Ca+Ca, Nb+Nb and Ca+Ca at E/A=800 MeV in the molecular-dynamical model

    International Nuclear Information System (INIS)

    Kiselev, S.M.

    1987-01-01

    Mass yield distributions obtained on the basis of the molecular-dynamical model are presented for the Ca+Ca, Nb+Nb reactions at E/A=400 MeV and Ca+Ca reaction at E/A=800 MeV. For the fragments with masses upto quarter of the mass of initial nucleus the model predicts a power law for mass spectra with almost the same value of the exponent. Such the behaviour is roughly a result of the superposition of the fireball breakup and the disintegration of spectator regions rather than the evidence of a liquid-gas-like phase transition in hot nuclear matter

  18. Dynamics of {sup 40,48}Ca+{sup 238}U→{sup 278,286}112{sup ⁎} reactions across the Coulomb barrier using dynamical cluster decay model

    Energy Technology Data Exchange (ETDEWEB)

    Sandhu, Kirandeep; Kaur, Gurvinder; Sharma, Manoj K., E-mail: msharma@thapar.edu

    2014-01-15

    The role of deformations and related orientations (optimum or compact) is investigated in reference to dynamics of {sup 40,48}Ca+{sup 238}U→{sup 278,286}112{sup ⁎} reactions using dynamical cluster decay model (DCM). The use of quadrupole and hexadecapole deformations in the decay of compound system suggest that the degree of compactness changes with addition of higher order deformations. The decay cross-sections are calculated in reference to the available data, including β{sub 2}-static deformations within ‘optimum’ orientation approach. The comparative analysis of spherical, β{sub 2}-static and dynamic alongwith β{sub 4}-static deformations is investigated at comparable center of mass energy of 230 MeV for both nuclei. To address the specific role of optimized orientations in the decay of {sup 278}112{sup ⁎} and {sup 286}112{sup ⁎} nuclei, the calculations are done using equatorial compact and polar elongated orientations. Using hot equatorial collisions, symmetric fission is observed as the dominant decay mode across the barrier, which otherwise becomes asymmetric for cold elongated approach. The calculated cross-sections match nicely with experimental data using hot configuration but the same are overestimated for the use of cold (polar) orientation approach at deep sub-barrier region. This overestimation in the deep sub-barrier region may be associated with the quasi-fission decay channel. The contribution of QF in both {sup 278}112{sup ⁎} and {sup 286}112{sup ⁎} nuclei are predicted through the overestimated cross-sections being more for neutron-deficient {sup 278}112{sup ⁎} nucleus, in agreement with experimental results. Larger barrier modification ΔV{sub B} is observed at sub-barrier energies for both isotopes of Z=112 nucleus. Also the contribution of ΔV{sub B} at lower incident energies is relatively higher for cold elongated polar configuration as compared to hot compact equatorial configuration, causing overestimation of cross

  19. Reactions of OH Radicals with Tris (1,10-Phenanthroline) Iron (II) Studied by Pulse Radiolysis

    DEFF Research Database (Denmark)

    Siekierska Floryan, E.; Pagsberg, Palle Bjørn

    1976-01-01

    The reaction of OH radicals with aqueous tris(1,10-phenanthroline)iron(II) leads to the formation of an adduct, which exhibits a broad absorption band at rmpH = 6, λmax = 460 nm, and epsilon (Porson)460 = 6700 (molar, decadic, 1 mol−1 cm−1). The rate of formation of the adduct is first order...... in complex concentration with a bimolecular rate constant Image independent of pH in the range pH 3–11. The adduct decays by mixed-order kinetics, but at 310 nm a second-order formation of a decay product can be directly observed. The reaction of OH radicals with aqueous 1,10-phenanthroline leads also...... to the formation of an adduct which absorbs in the whole visible region with a maximum at 425 nm and ε425 = 2612 (molar, decadic, 1 mol−1 cm−1) in neutral solution. The adduct exhibits a red shift in acidic and alkaline media. The formation is first order in 1,10-phenanthroline with a bimolecular rate constant...

  20. Detection of Heteromers Formed by Cannabinoid CB1, Dopamine D2, and Adenosine A2A G-Protein-Coupled Receptors by Combining Bimolecular Fluorescence Complementation and Bioluminescence Energy Transfer

    Science.gov (United States)

    Navarro, Gemma; Carriba, Paulina; Gandí, Jorge; Ciruela, Francisco; Casadó, Vicent; Cortés, Antoni; Mallol, Josefa; Canela, Enric I.; Lluis, Carmen; Franco, Rafael

    2008-01-01

    Functional interactions in signaling occur between dopamine D2 (D2R) and cannabinoid CB1 (CB1R) receptors, between CB1R and adenosine A2A (A2AR) receptors, and between D2R and A2AR. Furthermore, direct molecular interactions have been reported for the pairs CB1R-D2R, A2AR-D2R, and CB1R-A2AR. Here a combination of bimolecular fluorescence complementation and bioluminescence energy transfer techniques was used to identify the occurrence of D2R-CB1R-A2AR hetero-oligomers in living cells. PMID:18956124

  1. Detection of Heteromers Formed by Cannabinoid CB1, Dopamine D2, and Adenosine A2A G-Protein-Coupled Receptors by Combining Bimolecular Fluorescence Complementation and Bioluminescence Energy Transfer

    Directory of Open Access Journals (Sweden)

    Gemma Navarro

    2008-01-01

    Full Text Available Functional interactions in signaling occur between dopamine D2 (D2R and cannabinoid CB1 (CB1R receptors, between CB1R and adenosine A2A (A2AR receptors, and between D2R and A2AR. Furthermore, direct molecular interactions have been reported for the pairs CB1R-D2R, A2AR-D2R, and CB1R-A2AR. Here a combination of bimolecular fluorescence complementation and bioluminescence energy transfer techniques was used to identify the occurrence of D2R-CB1R-A2AR hetero-oligomers in living cells.

  2. Kinetics of subdiffusion-assisted reactions: non-Markovian stochastic Liouville equation approach

    International Nuclear Information System (INIS)

    Shushin, A I

    2005-01-01

    Anomalous specific features of the kinetics of subdiffusion-assisted bimolecular reactions (time-dependence, dependence on parameters of systems, etc) are analysed in detail with the use of the non-Markovian stochastic Liouville equation (SLE), which has been recently derived within the continuous-time random-walk (CTRW) approach. In the CTRW approach, subdiffusive motion of particles is modelled by jumps whose onset probability distribution function is of a long-tailed form. The non-Markovian SLE allows for rigorous describing of some peculiarities of these reactions; for example, very slow long-time behaviour of the kinetics, non-analytical dependence of the reaction rate on the reactivity of particles, strong manifestation of fluctuation kinetics showing itself in very slowly decreasing behaviour of the kinetics at very long times, etc

  3. Lipase-catalyzed asymmetric synthesis of naphtho[2,3-c]furan-1(3H)-one derivatives by a one-pot dynamic kinetic resolution/intramolecular Diels-Alder reaction: Total synthesis of (-)-himbacine.

    Science.gov (United States)

    Sugiyama, Koji; Kawanishi, Shinji; Oki, Yasuhiro; Kamiya, Marin; Hanada, Ryosuke; Egi, Masahiro; Akai, Shuji

    2018-04-01

    One-pot sequential reactions using the acyl moieties installed by enzymatic dynamic kinetic resolution of alcohols have been little investigated. In this work, the acryloyl moiety installed via the lipase/oxovanadium combo-catalyzed dynamic kinetic resolution of a racemic dienol [4-(cyclohex-1-en-1-yl)but-3-en-2-ol or 1-(cyclohex-1-en-1-yl)but-2-en-1-ol] with a (Z)-3-(phenylsulfonyl)acrylate underwent an intramolecular Diels-Alder reaction in a one-pot procedure to produce an optically active naphtho[2,3-c]furan-1(3H)-one derivative (98% ee). This method was successfully applied to the asymmetric total synthesis of (-)-himbacine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Nuclear reactions

    International Nuclear Information System (INIS)

    Lane, A.M.

    1980-01-01

    In reviewing work at Harwell over the past 25 years on nuclear reactions it is stated that a balance has to be struck in both experiment and theory between work on cross-sections of direct practical relevance to reactors and on those relevant to an overall understanding of reaction processes. The compound nucleus and direct process reactions are described. Having listed the contributions from AERE, Harwell to developments in nuclear reaction research in the period, work on the optical model, neutron capture theory, reactions at doorway states with fine structure, and sum-rules for spectroscopic factors are considered in more detail. (UK)

  5. Development of a method based on inductively coupled plasma-dynamic reaction cell-mass spectrometry for the simultaneous determination of phosphorus, calcium and strontium in bone and dental tissue

    International Nuclear Information System (INIS)

    De Muynck, David; Vanhaecke, Frank

    2009-01-01

    A method, based on the use of a quadrupole-based inductively coupled plasma-mass spectrometry instrument equipped with a quadrupole-based collision/reaction cell (dynamic reaction cell, DRC), was developed for the simultaneous determination of phosphorus, calcium and strontium in bone and dental (enamel and dentine) tissue. The use of NH 3 , introduced at a gas flow rate of 0.8 mL min -1 in the dynamic reaction cell, combined with a rejection parameter q (RPq) setting of 0.65, allows interference-free determination of calcium via its low-abundant isotopes 42 Ca, 43 Ca and 44 Ca, and of strontium via its isotopes 86 Sr and 88 Sr that are freed from overlap due to the occurrence of ArCa + and/or Ca 2 + ions. Also the determination of phosphorus ( 31 P, mono-isotopic) was shown to be achievable using the same dynamic reaction cell operating conditions. The bone certified reference materials NIST SRM 1400 Bone Ash and NIST SRM 1486 Bone Meal were used for validation of the measurement protocol that was shown capable of providing accurate and reproducible results. Detection limits of P, Ca and Sr in dental tissue digests were established as 3 μg L -1 for P, 2 μg L -1 for Ca and 0.2 μg L -1 for Sr. This method can be used to simultaneously (i) evaluate the impact of diagenesis on the elemental and isotopic composition of buried skeletal tissue via its Ca/P ratio and (ii) determine its Sr concentration. The measurement protocol was demonstrated as fit-for-purpose by the analysis of a set of teeth of archaeological interest for their Ca/P ratio and Sr concentration.

  6. Temperature-Dependent Rate Coefficients for the Reaction of CH2OO with Hydrogen Sulfide.

    Science.gov (United States)

    Smith, Mica C; Chao, Wen; Kumar, Manoj; Francisco, Joseph S; Takahashi, Kaito; Lin, Jim Jr-Min

    2017-02-09

    The reaction of the simplest Criegee intermediate CH 2 OO with hydrogen sulfide was measured with transient UV absorption spectroscopy in a temperature-controlled flow reactor, and bimolecular rate coefficients were obtained from 278 to 318 K and from 100 to 500 Torr. The average rate coefficient at 298 K and 100 Torr was (1.7 ± 0.2) × 10 -13 cm 3 s -1 . The reaction was found to be independent of pressure and exhibited a weak negative temperature dependence. Ab initio quantum chemistry calculations of the temperature-dependent reaction rate coefficient at the QCISD(T)/CBS level are in reasonable agreement with the experiment. The reaction of CH 2 OO with H 2 S is 2-3 orders of magnitude faster than the reaction with H 2 O monomer. Though rates of CH 2 OO scavenging by water vapor under atmospheric conditions are primarily controlled by the reaction with water dimer, the H 2 S loss pathway will be dominated by the reaction with monomer. The agreement between experiment and theory for the CH 2 OO + H 2 S reaction lends credence to theoretical descriptions of other Criegee intermediate reactions that cannot easily be probed experimentally.

  7. The Paterno-Buchi reaction

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Yding; Schalk, Oliver; Boguslavskiy, Andrey E.

    2012-01-01

    The Paternò-Büchi (PB) reaction between an excited carbonyl compound and an alkene has been widely studied, but so far little is known about the excited-state dynamics of the reaction. In this investigation, we used a compound in which a formyl and a vinyl group are attached to a [2.......2]paracyclophane in order to obtain a model system in pre-reactive conformation for the PB reaction. We studied the excited-state dynamics of the isolated molecule in a molecular beam using femtosecond time-resolved photoelectron spectroscopy and ab initio calculations. The results show that inter-system crossing...... within two picoseconds competes efficiently with the reaction in the singlet manifold. Thus, the PB reaction in this model system takes place in the triplet state on a time scale of nanoseconds. This result stresses the importance of triplet states in the excited-state pathway of the PB reaction...

  8. Studying Chemical Reactions, One Bond at a Time, with Single Molecule AFM Techniques

    Science.gov (United States)

    Fernandez, Julio M.

    2008-03-01

    The mechanisms by which mechanical forces regulate the kinetics of a chemical reaction are unknown. In my lecture I will demonstrate how we use single molecule force-clamp spectroscopy and protein engineering to study the effect of force on the kinetics of thiol/disulfide exchange. Reduction of disulfide bond via the thiol/disulfide exchange chemical reaction is crucial in regulating protein function and is of common occurrence in mechanically stressed proteins. While reduction is thought to proceed through a substitution nucleophilic bimolecular (SN2) reaction, the role of a mechanical force in modulating this chemical reaction is unknown. We apply a constant stretching force to single engineered disulfide bonds and measure their rate of reduction by dithiothreitol (DTT). We find that while the reduction rate is linearly dependent on the concentration of DTT, it is exponentially dependent on the applied force, increasing 10-fold over a 300 pN range. This result predicts that the disulfide bond lengthens by 0.34 å at the transition state of the thiol/disulfide exchange reaction. In addition to DTT, we also study the reduction of the engineered disulfide bond by the E. coli enzyme thioredoxin (Trx). Thioredoxins are enzymes that catalyze disulfide bond reduction in all organisms. As before, we apply a mechanical force in the range of 25-450 pN to the engineered disulfide bond substrate and monitor the reduction of these bonds by individual enzymes. In sharp contrast with the data obtained with DTT, we now observe two alternative forms of the catalytic reaction, the first requiring a reorientation of the substrate disulfide bond, causing a shortening of the substrate polypeptide by 0.76±0.07 å, and the second elongating the substrate disulfide bond by 0.21±0.01 å. These results support the view that the Trx active site regulates the geometry of the participating sulfur atoms, with sub-ångström precision, in order to achieve efficient catalysis. Single molecule

  9. Toward the first study of chemical reaction dynamics of Mu with vibrational-state-selected reactants in the gas phase: The Mu+H2*(v=1) reaction by stimulated Raman pumping

    International Nuclear Information System (INIS)

    Bakule, Pavel; Sukhorukov, Oleksandr; Matsuda, Yasuyuki; Pratt, Francis; Gumplinger, Peter; Momose, Takamasa; Torikai, Eiko; Fleming, Donald

    2009-01-01

    Stimulated Raman pumping (SRP) is used to produce H 2 in its first vibrational state, in order to measure, for the first time, the Mu+H 2 *(v=1)→MuH+H reaction rate at room temperature, as a prototypical example of new directions in gas-phase muonium chemistry, utilizing the pulsed muon beam and a new dedicated laser system at the RIKEN/RAL Laboratory. Reported here is a preliminary result but the final results are expected to provide definitive new tests of reaction rate theory on the highly accurate H 3 potential energy surface. The major difficulty in this experiment, compared to the standard SRP process, is to ensure a homogeneous excitation over a volume of several cm 3 and of sufficient intensity to ensure a measurable Mu relaxation rate. The techniques used to accomplish this are described. The experiment utilizes the 2nd harmonic output of a Nd:YAG laser (532 nm) with pulse energies up to 500 mJ at a repetition rate of 25 Hz. Different optical setups have been constructed and tested in order to optimize the number of laser-pumped H 2 molecules and their overlap with the stopping profile of the muon beam in the reaction cell (total volume ∼100x40x4mm 3 ). The first result of this experiment gives a measured relaxation rate due to laser excitation of λ*=0.085±0.051μs -1 , consistent with theory but limited by both low statistics and particularly a high background relaxation rate.

  10. Reaction between aminoalkyl radicals and akyl halides: Dehalogenation by electron transfer?

    Science.gov (United States)

    Lalevée, J.; Fouassier, J. P.; Blanchard, N.; Ingold, K. U.

    2011-07-01

    Aminoalkyl radicals, such as Et2NCrad HCH3, have low oxidation potentials and are therefore powerful reducing agents. We have found that Et2NCrad HCH3 reacts with CCl4 and CBr4 in di-tert-butyl peroxide with bimolecular rate constants (measured by LFP) close, or equal, to the diffusion-controlled limit. For the less reactive halide, CH2Br2, the reaction rate is increased substantially by the addition of acetonitrile as a co-solvent. It is tentatively concluded that these reactions occur by electron-transfer from the aminoalkyl to the organohalide with formation of the iminium ion, Et2N+dbnd CHCH3 (NMR detection), halide ion and a halomethyl radical, e.g., rad CCl3 and rad CHCl2 (ESR, spin-trapping detection).

  11. Nickel group cluster anion reactions with carbon monoxide: Rate coefficients and chemisorption efficiency

    Science.gov (United States)

    Hintz, Paul A.; Ervin, Kent M.

    1994-04-01

    Reactions of Ni-n(n=3-10), Pd-n(n=3-8), and Pt-n(n=3-7) with CO are studied in a flow tube reactor. Bimolecular rate coefficients are measured for the association reaction of CO adsorbing on the cluster surface. The rate coefficients range from about 10% of the collision rate for the trimer anions to near the collision rate for clusters larger than four atoms. The maximum number of CO molecules that bind to each cluster is determined. Whereas the saturation limits for nickel are typical for an 18 electron transition metal, the limits for platinum are lower, reflecting the electron deficient structures observed in condensed phase chemistry. The CO saturated palladium clusters represent the first examples of saturated binary palladium carbonyl compounds. Comparisons are made to similar studies on metal cation and neutral clusters and also to surface scattering studies of nickel group metals.

  12. Cooperative protein structural dynamics of homodimeric hemoglobin linked to water cluster at subunit interface revealed by time-resolved X-ray solution scattering

    Directory of Open Access Journals (Sweden)

    Jong Goo Kim

    2016-03-01

    Full Text Available Homodimeric hemoglobin (HbI consisting of two subunits is a good model system for investigating the allosteric structural transition as it exhibits cooperativity in ligand binding. In this work, as an effort to extend our previous study on wild-type and F97Y mutant HbI, we investigate structural dynamics of a mutant HbI in solution to examine the role of well-organized interfacial water cluster, which has been known to mediate intersubunit communication in HbI. In the T72V mutant of HbI, the interfacial water cluster in the T state is perturbed due to the lack of Thr72, resulting in two less interfacial water molecules than in wild-type HbI. By performing picosecond time-resolved X-ray solution scattering experiment and kinetic analysis on the T72V mutant, we identify three structurally distinct intermediates (I1, I2, and I3 and show that the kinetics of the T72V mutant are well described by the same kinetic model used for wild-type and F97Y HbI, which involves biphasic kinetics, geminate recombination, and bimolecular CO recombination. The optimized kinetic model shows that the R-T transition and bimolecular CO recombination are faster in the T72V mutant than in the wild type. From structural analysis using species-associated difference scattering curves for the intermediates, we find that the T-like deoxy I3 intermediate in solution has a different structure from deoxy HbI in crystal. In addition, we extract detailed structural parameters of the intermediates such as E-F distance, intersubunit rotation angle, and heme-heme distance. By comparing the structures of protein intermediates in wild-type HbI and the T72V mutant, we reveal how the perturbation in the interfacial water cluster affects the kinetics and structures of reaction intermediates of HbI.

  13. Dynamics of the π-p→π0π0n reaction for pπ-<750 MeV/c

    International Nuclear Information System (INIS)

    Craig, K.; Comfort, J.R.; Ramirez, A.F.; Allgower, C.E.; Spinka, H.; Bekrenev, V.; Koulbardis, A.; Kozlenko, N.; Kruglov, S.; Lopatin, I.; Berger, E.; Clajus, M.; McDonald, S.; Nefkens, B.M.K.; Phaisangittisakul, N.; Prakhov, S.; Price, J.W.; Pulver, M.; Tippens, W.B.; Briscoe, W.J.

    2003-01-01

    Data are presented for the reaction π - p→π 0 π 0 n in the range from threshold to p π - =750 MeV/c. The systematics of the data and multipole analyses are examined for sensitivity to a f 0 (600) (''σ'') meson. A one-pion-exchange mechanism is found to be very weak, or absent. The reaction appears to become dominated by sequential π 0 decays through the Δ(1232) resonance as the beam momentum increases, along with substantial interference effects from several competing mechanisms

  14. Mean field interaction in biochemical reaction networks

    KAUST Repository

    Tembine, Hamidou; Tempone, Raul; Vilanova, Pedro

    2011-01-01

    In this paper we establish a relationship between chemical dynamics and mean field game dynamics. We show that chemical reaction networks can be studied using noisy mean field limits. We provide deterministic, noisy and switching mean field limits

  15. A new global analytical potential energy surface of NaH2+ system and dynamical calculation for H(2S) + NaH+(X2Σ+) → Na+(1S) + H2(X1Σg+) reaction

    Science.gov (United States)

    Yuan, Meiling; Li, Wentao; Yuan, Jiuchuang

    2018-05-01

    A new global potential energy surface (PES) of the NaH2+ system is constructed by fitting 27,621 ab initio energy points with the neural network method. The root mean square error of the new PES is only 4.1609 × 10-4 eV. Based on the new PES, dynamical calculations have been performed using the time-dependent quantum wave packet method. These results are then compared with the H(2S) + LiH+(X2Σ+) → Li+(1S) + H2(X1Σg+) reaction. The direct abstract mechanism is found to play an important role in the reaction because only forward scattering signals on the differential cross section results for all calculated collision energies.

  16. Quasielastic reactions

    International Nuclear Information System (INIS)

    Henning, W.

    1979-01-01

    Quasielastic reaction studies, because of their capability to microscopically probe nuclear structure, are still of considerable interest in heavy-ion reactions. The recent progress in understanding various aspects of the reaction mechanism make this aim appear closer. The relation between microscopic and macroscopic behavior, as suggested, for example, by the single proton transfer data to individual final states or averaged excitation energy intervals, needs to be explored. It seems particularly useful to extend measurements to higher incident energies, to explore and understand nuclear structure aspects up to the limit of the energy range where they are important

  17. Study of photo-activated electron transfer reactions in the first excited singlet state by picosecond and nanosecond laser spectroscopy

    International Nuclear Information System (INIS)

    Doizi, Denis

    1983-01-01

    Picosecond laser spectroscopy has been used to study two photo-activated electron transfer reactions: - a bimolecular electron transfer reaction between a sensitizer, DODCI, and an electron acceptor, methylviologen. The two radical ions created with an electron transfer efficiency γ ≅ 0.07 have been identified in picosecond and nanosecond laser absorption spectroscopy by adding selective solutes such as para-benzoquinone (an electron acceptor) or L(+) ascorbic acid (an electron donor). - an intramolecular electron transfer reaction in a triad molecule consisting of a tetra-aryl-porphyrin covalently linked to both a carotenoid and a quinone. The photoinduced charge separation occurs within 30 ps and leads, with a yield of 25 pc, to the formation of a zwitterion whose half-life is 2.5 μs. The experimental results obtained in these two studies show an effective decrease in the recombination rate of the two radical ions created in the encounter pair. (author) [fr

  18. Observed side feeding in incomplete fusion dynamics in 16O + 160Gd reaction at energy ∼5.6 MeV/A: Spin distribution measurements

    Science.gov (United States)

    Ali, Rahbar; Afzal Ansari, M.; Singh, D.; Kumar, Rakesh; Singh, D. P.; Sharma, M. K.; Gupta, Unnati; Singh, B. P.; Shidling, P. D.; Negi, Dinesh; Muralithar, S.; Singh, R. P.; Bhowmik, R. K.

    2017-12-01

    Spin distributions of various residues populated via complete fusion (CF) and incomplete fusion (ICF) reactions in the interaction of 16O with 160Gd at the projectile energy Eproj ∼ 5.6 MeV/A have been studied. The experimentally measured spin distributions of the residues associated with the ICF reactions are found to be distinctly different from those populated via the CF reactions. An attempt has been made to extract the side-feeding pattern from the spin distributions of CF and ICF reaction products. It has been observed that the CF products are strongly fed over a broad spin range. But, no side-feeding takes place in the low observed spins as low partial waves are strongly hindered in the fast α-emission channels (associated with ICF) in the forward direction. It has also been observed that the mean input angular momentum for direct α-emitting (ICF) channels is relatively higher than evaporation α-emitting (CF) channels, and it increases with direct α-multiplicity in forward direction.

  19. Relationships between Static and Dynamic Balance and Anticipation Time, Reaction Time in School Children at the Age of 10-12 Years

    Science.gov (United States)

    Bozkurt, Sinan; Erkut, Oya; Akkoç, Orkun

    2017-01-01

    The aim of this study is to investigate the relationship between anticipation time, reaction time and balance characteristics in school children at the age of 10-12 years. 11 males and 12 females, 23 students in total, studying at Istanbul Sancaktepe Ibn-i Sina Elementary School, whose average age was 11.06 years, average height was 142.78 cm and…

  20. Dynamical fission life-times deduced from gamma-ray emission observed in the fusion-fission reaction : Ne-20 on Bi-209.

    NARCIS (Netherlands)

    vanderPloeg, H; Bacelar, JCS; Buda, A; Dioszegi, [No Value; vantHof, G; vanderWoude, A

    1996-01-01

    The gamma-ray emission spectra between 4 and 20 MeV have been measured for the fusion-fission reactions Ne-20 on Bi-209 --> Np-229* at beam energies 150, 186 and 220 MeV. In addition for the latter experiment the angular dependence of the gamma-ray emission with respect to the spin axis has been