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Sample records for bimolecular reaction dynamics

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

    OpenAIRE

    Allen, Joshua W.; Green, William H; Suleimanov, Yu. V.

    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 ...

  2. 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.

  3. Recent Advances in Quantum Dynamics of Bimolecular Reactions.

    Science.gov (United States)

    Zhang, Dong H; Guo, Hua

    2016-05-27

    In this review, we survey the latest advances in theoretical understanding of bimolecular reaction dynamics in the past decade. The remarkable recent progress in this field has been driven by more accurate and efficient ab initio electronic structure theory, effective potential-energy surface fitting techniques, and novel quantum scattering algorithms. Quantum mechanical characterization of bimolecular reactions continues to uncover interesting dynamical phenomena in atom-diatom reactions and beyond, reaching an unprecedented level of sophistication. In tandem with experimental explorations, these theoretical developments have greatly advanced our understanding of key issues in reaction dynamics, such as microscopic reaction mechanisms, mode specificity, product energy disposal, influence of reactive resonances, and nonadiabatic effects. PMID:26980305

  4. 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.

  5. 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

  6. 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}}, NCO{sup {minus}} and NCS{sup {minus}}. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH{sub 3}0H,F + C{sub 2}H{sub 5}OH,F + OH and F + H{sub 2}. A time dependent framework for the simulation and interpretation of the bound {yields} free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH {yields} O({sup 3}P, {sup 1}D) + HF and F + H{sub 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{sub 2} system, comparisons with three-dimensional quantum calculations are made.

  7. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    International Nuclear Information System (INIS)

    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 + 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

  8. Generation of radicals by bimolecular reactions

    Energy Technology Data Exchange (ETDEWEB)

    Denisov, Evgenii T; Denisova, Taisa G [Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)

    2002-05-31

    The published data on bimolecular processes of radical generation in chain degradation, polymerisation, oxidation and halogenation reactions of organic compounds are systematised and analysed within the framework of the parabolic model of homolytic bimolecular reactions. The specific features of these highly endothermic reactions are discussed with a special emphasis on their striking similarity to radical abstraction processes with identical reaction centres in the transition state. The feasibility of theoretical evaluation of the activation energies and the rate constants of bimolecular reactions in radical generation is demonstrated. The bibliography includes 86 references.

  9. An exact solution to Brownian dynamics of a reversible bimolecular reaction in one dimension

    OpenAIRE

    Smith, Stephen; Grima, Ramon

    2016-01-01

    Brownian dynamics is a popular fine-grained method for simulating systems of interacting particles, such as chemical reactions. Though the method is simple to simulate, it is generally assumed that the dynamics is impossible to solve exactly and analytically, aside from some trivial systems. We here give the first exact analytical solution to a non-trivial Brownian dynamics system: the reaction $A+B\\xrightleftharpoons[]{}C$ in equilibrium in one-dimensional periodic space. The solution is a f...

  10. Molecular beam studies of unimolecular and bimolecular chemical reaction dynamics using VUV synchrotron radiation as a product probe

    Energy Technology Data Exchange (ETDEWEB)

    Blank, D.A.

    1997-08-01

    This dissertation describes the use of a new molecular beam apparatus designed to use tunable VUV synchrotron radiation for photoionization of the products from scattering experiments. The apparatus was built at the recently constructed Advanced Light Source at Lawrence Berkeley National Laboratory, a third generation 1-2 GeV synchrotron radiation source. The new apparatus is applied to investigations of the dynamics of unimolecular reactions, photodissociation experiments, and bimolecular reactions, crossed molecular beam experiments. The first chapter describes the new apparatus and the VUV radiation used for photoionization. This is followed by a number of examples of the many advantages provided by using VUV photoionization in comparison with the traditional technique of electron bombardment ionization. At the end of the chapter there is a discussion of the data analysis employed in these scattering experiments. The remaining four chapters are complete investigations of the dynamics of four chemical systems using the new apparatus and provide numerous additional examples of the advantages provided by VUV photoionizaiton of the products. Chapters 2-4 are photofragment translational spectroscopy studies of the photodissociation dynamics of dimethyl sulfoxide, acrylonitrile, and vinyl chloride following absorption at 193 mn. All of these systems have multiple dissociation channels and provide good examples of the ability of the new apparatus to unravel the complex UV photodissociation dynamics that can arise in small polyatomic molecules.

  11. Resonance Reaction in Diffusion-Influenced Bimolecular Reactions

    CERN Document Server

    Kolb, Jakob J; Dzubiella, Joachim

    2016-01-01

    We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance the standard reciprocal additivity law for diffusion and surface reaction rates is violated due to the dynamical coupling of multiple kinetic processes. Together, these findings may have important repercussions on the correct interpretation of various kinetic reaction problems in complex systems, as, e.g., in biomolecular association or catalysis.

  12. Communication: Resonance reaction in diffusion-influenced bimolecular reactions

    Science.gov (United States)

    Kolb, Jakob J.; Angioletti-Uberti, Stefano; Dzubiella, Joachim

    2016-02-01

    We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new "resonant reaction" behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance, the standard reciprocal additivity law for diffusion and surface reaction rates is violated due to the dynamical coupling of multiple kinetic processes. Together, these findings may have important repercussions on the correct interpretation of various kinetic reaction problems in complex systems, as, e.g., in biomolecular association or catalysis.

  13. Resonance Reaction in Diffusion-Influenced Bimolecular Reactions

    OpenAIRE

    Kolb, Jakob J.; Angioletti-Uberti, Stefano; Dzubiella, Joachim

    2016-01-01

    We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance the standard reciprocal additivity law for diffusion and surface reaction rates is viola...

  14. Theory of Crowding Effects on Bimolecular Reaction Rates.

    Science.gov (United States)

    Berezhkovskii, Alexander M; Szabo, Attila

    2016-07-01

    An analytical expression for the rate constant of a diffusion-influenced bimolecular reaction in a crowded environment is derived in the framework of a microscopic model that accounts for: (1) the slowdown of diffusion due to crowding and the dependence of the diffusivity on the distance between the reactants, (2) a crowding-induced attractive short-range potential of mean force, and (3) nonspecific reversible binding to the crowders. This expression spans the range from reaction to diffusion control. Crowding can increase the reaction-controlled rate by inducing an effective attraction between reactants but decrease the diffusion-controlled rate by reducing their relative diffusivity. PMID:27096470

  15. Morse bifurcations of transition states in bimolecular reactions

    Science.gov (United States)

    MacKay, R. S.; Strub, D. C.

    2015-12-01

    The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo Morse bifurcations, in which they change diffeomorphism class, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces.

  16. Morse bifurcations of transition states in bimolecular reactions

    CERN Document Server

    MacKay, Robert S

    2015-01-01

    The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces. The reduction of the $n$-body systems representing the reactions is discussed and reviewed with comments on the difficulties associated with choosing appropriate charts and the global geometry of the reduced spaces.

  17. The power-law reaction rate coefficient for an elementary bimolecular reaction

    OpenAIRE

    Yin, Cangtao; Du, Jiulin

    2013-01-01

    The power-law TST reaction rate coefficient for an elementary bimolecular reaction is studied when the reaction takes place in a nonequilibrium system with power-law distributions. We derive a generalized TST rate coefficient, which not only depends on a power-law parameter but also on the reaction coordinate frequency of transition state. The numerical analyses show a very strong dependence of TST rate coefficient on the power-law parameter, and clearly indicate that a tiny deviation from un...

  18. Bimolecular recombination reactions: K-adiabatic and K-active forms of the bimolecular master equations and analytic solutions

    Science.gov (United States)

    Ghaderi, Nima

    2016-03-01

    Expressions for a K-adiabatic master equation for a bimolecular recombination rate constant krec are derived for a bimolecular reaction forming a complex with a single well or complexes with multiple well, where K is the component of the total angular momentum along the axis of least moment of inertia of the recombination product. The K-active master equation is also considered. The exact analytic solutions, i.e., the K-adiabatic and K-active steady-state population distribution function of reactive complexes, g(EJK) and g(EJ), respectively, are derived for the K-adiabatic and K-active master equation cases using properties of inhomogeneous integral equations (Fredholm type). The solutions accommodate arbitrary intermolecular energy transfer models, e.g., the single exponential, double exponential, Gaussian, step-ladder, and near-singularity models. At the high pressure limit, the krec for both the K-adiabatic and K-active master equations reduce, respectively, to the K-adiabatic and K-active bimolecular Rice-Ramsperger-Kassel-Marcus theory (high pressure limit expressions). Ozone and its formation from O + O2 are known to exhibit an adiabatic K. The ratio of the K-adiabatic to the K-active recombination rate constants for ozone formation at the high pressure limit is calculated to be ˜0.9 at 300 K. Results on the temperature and pressure dependence of the recombination rate constants and populations of O3 will be presented elsewhere.

  19. Kinetics and mechanism of bimolecular electron transfer reaction in quinone-amine systems in micellar solution

    International Nuclear Information System (INIS)

    Photoinduced electron transfer (ET) reactions between anthraquinone derivatives and aromatic amines have been investigated in sodium dodecyl sulphate (SDS) micellar solutions. Significant static quenching of the quinone fluorescence due to high amine concentration in the micellar phase has been observed in steady-state measurements. The bimolecular rate constants for the dynamic quenching in the present systems kqTR, as estimated from the time-resolved measurements, have been correlated with the free energy changes ΔG0 for the ET reactions. Interestingly it is seen that the kqTR vs ΔG0 plot displays an inversion behavior with maximum kqTR at around 0.7 eV, a trend similar to that predicted in Marcus ET theory. Like the present results, Marcus inversion in the kqTR values was also observed earlier in coumarin-amine systems in SDS and TX-100 micellar solutions, with maximum kqTR at around the same exergonicity. These results thus suggest that Marcus inversion in bimolecular ET reaction is a general phenomenon in micellar media. Present observations have been rationalized on the basis of the two-dimensional ET (2DET) theory, which seems to be more suitable for micellar ET reactions than the conventional ET theory. For the quinone-amine systems, it is interestingly seen that kqTR vs ΔG0 plot is somewhat wider in comparison to that of the coumarin-amine systems, even though the maxima in the kqTR vs ΔG0 plots appear at almost similar exergonicity for both the acceptor-donor systems. These observations have been rationalized on the basis of the differences in the reaction windows along the solvation axis, as envisaged within the framework of the 2DET theory, and arise due to the differences in the locations of the quinones and coumarin dyes in the micellar phase

  20. A transition in the spatially integrated reaction rate of bimolecular reaction-diffusion systems

    Science.gov (United States)

    Arshadi, Masoud; Rajaram, Harihar

    2015-09-01

    Numerical simulations of diffusion with bimolecular reaction demonstrate a transition in the spatially integrated reaction rate—increasing with time initially, and transitioning to a decrease with time. In previous work, this reaction-diffusion problem has been analyzed as a Stefan problem involving a distinct moving boundary (reaction front), leading to predictions that front motion scales as √t, and correspondingly the spatially integrated reaction rate decreases as the square root of time 1/√t. We present a general nondimensionalization of the problem and a perturbation analysis to show that there is an early time regime where the spatially integrated reaction rate scales as √t rather than 1/√t. The duration of this early time regime (where the spatially integrated reaction rate is kinetically rather than diffusion controlled) is shown to depend on the kinetic rate parameters, diffusion coefficients, and initial concentrations of the two species. Numerical simulation results confirm the theoretical estimates of the transition time. We present illustrative calculations in the context of in situ chemical oxidation for remediation of fractured rock systems where contaminants are largely dissolved in the rock matrix. We consider different contaminants of concern (COCs), including TCE, PCE, MTBE, and RDX. While the early time regime is very short lived for TCE, it can persist over months to years for MTBE and RDX, due to slow oxidation kinetics.

  1. Differences in the Abilities to Mechanically Eliminate Activation Energies for Unimolecular and Bimolecular Reactions

    Science.gov (United States)

    Kochhar, Gurpaul S.; Mosey, Nicholas J.

    2016-03-01

    Mechanochemistry, i.e. the application of forces, F, at the molecular level, has attracted significant interest as a means of controlling chemical reactions. The present study uses quantum chemical calculations to explore the abilities to mechanically eliminate activation energies, ΔE‡, for unimolecular and bimolecular reactions. The results demonstrate that ΔE‡ can be eliminated for unimolecular reactions by applying sufficiently large F along directions that move the reactant and/or transition state (TS) structures parallel to the zero-F reaction coordinate, S0. In contrast, eliminating ΔE‡ for bimolecular reactions requires the reactant to undergo a force-induced shift parallel to S0 irrespective of changes in the TS. Meeting this requirement depends upon the coupling between F and S0 in the reactant. The insights regarding the differences in eliminating ΔE‡ for unimolecular and bimolecular reactions, and the requirements for eliminating ΔE‡, may be useful in practical efforts to control reactions mechanochemically.

  2. Detonation wave solutions and linear stability in a four component gas with bimolecular chemical reaction

    OpenAIRE

    Carvalho, Filipe; De Silva, A.W.; Soares, A. J.

    2015-01-01

    We consider a four component gas undergoing a bimolecular chemical reaction of type A1 + A2 = A3 + A4, described by the Boltzmann equation (BE) for chemically reactive mixtures. We adopt hard-spheres elastic cross sections and modified line-of-centers reactive cross sections depending on both the activation energy and geometry of the reactive collisions. Then we consider the hydrodynamic limit specified by the reactive Euler equations, in an earlier stage of the chemical reaction, when the ga...

  3. 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.

  4. Irreversible bimolecular reactions with inertia: from the trapping to the target setting at finite densities.

    Science.gov (United States)

    Piazza, Francesco; Foffi, Giuseppe; De Michele, Cristiano

    2013-06-19

    We investigate numerically pseudo-first-order irreversible bimolecular reactions of the type A + B → B between hard spheres undergoing event-driven Brownian dynamics. We study the encounter rate and the survival probability of A particles as functions of the packing fraction ϕ in the trapping (a single particle diffusing among static non-overlapping traps) and target (many traps diffusing in the presence of a single static target particle) settings, as well as in the case of diffusing traps and particles (full mobility). We show that, since inertial effects are accounted for in our simulation protocol, the standard Smoluchowski theory of coagulation of non-interacting colloids is recovered only at times greater than a characteristic time Δt, marking the transition from the under-damped to the over-damped regime. We show that the survival probability S(t) decays exponentially during this first stage, with a rate 1/τ0 is proportional to φ. Furthermore, we work out a simple analytical expression that is able to capture to an excellent extent the numerical results for t < Δt at low and intermediate densities. Moreover, we demonstrate that the time constant of the asymptotic exponential decay of S(t) for diffusing traps and particles is k(S)(-1), where kS = 4π(DA + DB)Rρ is the Smoluchowski rate. Detailed analyses of the effective decay exponent β = d [log(-logS(t))]/d (logt) and of the steady-state encounter rate reveal that the full mobility and trapping problem are characterized by very similar kinetics, rather different from the target problem. Our results do not allow one to ascertain whether the prediction S(t) is proportional to exp(-at(3/2)) (a = const.) as t → ∞ for the trapping problem in 3D is indeed recovered. In fact, at high density, S(t) is dominated by short encounter times, which makes it exceedingly hard to record the events corresponding to the exploration of large, trap-free regions. As a consequence, at high densities the steady

  5. On the Temperature Dependence of the Rate Constant of the Bimolecular Reaction of two Hydrated Electrons

    Directory of Open Access Journals (Sweden)

    S.L. Butarbutar

    2013-08-01

    Full Text Available It has been a longstanding issue in the radiation chemistry of water that, even though H2 is a molecular product, its “escape” yield g(H2 increases with increasing temperature. A main source of H2 is the bimolecular reaction of two hydrated electrons (eaq. The temperature dependence of the rate constant of this reaction (k1, measured under alkaline conditions, reveals that the rate constant drops abruptly above ~150°C. Recently, it has been suggested that this temperature dependence should be regarded as being independent of pH and used in high-temperature modeling of near-neutral water radiolysis. However, when this drop in the eaq self-reaction rate constant is included in low (isolated spurs and high (cylindrical tracks linear energy transfer (LET modeling calculations, g(H2 shows a marked downward discontinuity at ~150°C which is not observed experimentally. The consequences of the presence of this discontinuity in g(H2 for both low and high LET radiation are briefly discussed in this communication. It is concluded that the applicability of the sudden drop in k1 observed at ~150°C in alkaline water to near-neutral water is questionable and that further measurements of the rate constant in pure water are highly desirable.

  6. Modeling Bimolecular Reactions and Transport in Porous Media Via Particle Tracking

    Energy Technology Data Exchange (ETDEWEB)

    Dong Ding; David Benson; Amir Paster; Diogo Bolster

    2012-01-01

    We use a particle-tracking method to simulate several one-dimensional bimolecular reactive transport experiments. In this numerical method, the reactants are represented by particles: advection and dispersion dominate the flow, and molecular diffusion dictates, in large part, the reactions. The particle/particle reactions are determined by a combination of two probabilities dictated by the physics of transport and energetics of reaction. The first is that reactant particles occupy the same volume over a short time interval. The second is the conditional probability that two collocated particles favorably transform into a reaction. The first probability is a direct physical representation of the degree of mixing in an advancing displacement front, and as such lacks empirical parameters except for the user-defined number of particles. This number can be determined analytically from concentration autocovariance, if this type of data is available. The simulations compare favorably to two physical experiments. In one, the concentration of product, 1,2-naphthoquinoe-4-aminobenzene (NQAB) from reaction between 1,2-naphthoquinone-4-sulfonic acid (NQS) and aniline (AN), was measured at the outflow of a column filled with glass beads at different times. In the other, the concentration distribution of reactants (CuSO_4 and EDTA^{4-}) and products (CuEDTA^{4-}) were quantified by snapshots of transmitted light through a column packed with cryloite sand. The thermodynamic rate coefficient in the latter experiment was 10^7 times greater than the former experiment, making it essentially instantaneous. When compared to the solution of the advection-dispersion-reaction equation (ADRE) with the well-mixed reaction coefficient, the experiments and the particle-tracking simulations showed on the order of 20% to 40% less overall product, which is attributed to poor mixing. The poor mixing also leads to higher product concentrations on the edges of the mixing zones, which the particle

  7. 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)

    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 3000C. The high-energy unimolecular elimination of H2O from ethanol in the presence of 2-propanol and HBr can be selectively induced with a pulsed CO2 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 H2O 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

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

    International Nuclear Information System (INIS)

    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

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

    International Nuclear Information System (INIS)

    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>∼1.2-1.3 eV) much higher than that observed in SDS and TX-100 micelles (-ΔG0>∼0.7 eV), 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

  10. 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. PMID:27586911

  11. Luminescence Spectroscopy and Bimolecular Quenching

    Science.gov (United States)

    Demas, J. N.

    1975-01-01

    Describes an undergraduate physical chemistry experiment in which a low cost spectrofluorimeter is used to carry out elementary emission measurements on a transition metal complex. The students measure uncorrected emission and excitation spectra, and determine the rate constant for an exceedingly fast bimolecular reaction, the deactivation of an…

  12. Kinetics of the unimolecular reaction of CH2OO and the bimolecular reactions with the water monomer, acetaldehyde and acetone under atmospheric conditions.

    Science.gov (United States)

    Berndt, Torsten; Kaethner, Ralf; Voigtländer, Jens; Stratmann, Frank; Pfeifle, Mark; Reichle, Patrick; Sipilä, Mikko; Kulmala, Markku; Olzmann, Matthias

    2015-08-14

    Stabilized Criegee Intermediates (sCIs) have been identified as oxidants of atmospheric trace gases such as SO2, NO2, carboxylic acids or carbonyls. The atmospheric sCI concentrations, and accordingly their importance for trace gas oxidation, are controlled by the rate of the most important loss processes, very likely the unimolecular reactions and the reaction with water vapour (monomer and dimer) ubiquitously present at high concentrations in the troposphere. In this study, the rate coefficients of the unimolecular reaction of the simplest sCI, formaldehyde oxide, CH2OO, and its bimolecular reaction with the water monomer have been experimentally determined at T = (297 ± 1) K and at atmospheric pressure by using a free-jet flow system. CH2OO was produced by the reaction of ozone with C2H4, and CH2OO concentrations were probed indirectly by detecting H2SO4 after titration with SO2. Time-resolved experiments yield a rate coefficient of the unimolecular reaction of k(uni) = (0.19 ± 0.07) s(-1), a value that is supported by quantum-chemical and statistical rate theory calculations as well as by additional measurements performed under CH2OO steady-state conditions. A rate coefficient of k(CH2OO+H2O) = (3.2 ± 1.2) × 10(-16) cm(3) molecule(-1) s(-1) has been determined for sufficiently low H2O concentrations (<10(15) molecule cm(-3)) that allow separation from the CH2OO reaction with the water dimer. In order to evaluate the accuracy of the experimental approach, the rate coefficients of the reactions with acetaldehyde and acetone were reinvestigated. The obtained rate coefficients k(CH2OO+acetald) = (1.7 ± 0.5) × 10(-12) and k(CH2OO+acetone) = (3.4 ± 0.9) × 10(-13) cm(3) molecule(-1) s(-1) are in good agreement with literature data. PMID:26159709

  13. Roaming dynamics in radical addition-elimination reactions

    Science.gov (United States)

    Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Suits, Arthur G.; Mebel, Alexander M.

    2014-06-01

    Radical addition-elimination reactions are a major pathway for transformation of unsaturated hydrocarbons. In the gas phase, these reactions involve formation of a transient strongly bound intermediate. However, the detailed mechanism and dynamics for these reactions remain unclear. Here we show, for reaction of chlorine atoms with butenes, that the Cl addition-HCl elimination pathway occurs from an abstraction-like Cl-H-C geometry rather than a conventional three-centre or four-centre transition state. Furthermore, access to this geometry is attained by roaming excursions of the Cl atom from the initially formed adduct. In effect, the alkene π cloud serves to capture the Cl atom and hold it, allowing many subsequent opportunities for the energized intermediate to find a suitable approach to the abstraction geometry. These bimolecular roaming reactions are closely related to the roaming radical dynamics recently discovered to play an important role in unimolecular reactions.

  14. Non-innocent electrolyte effects on bimolecular pseudo-self-exchange reactions of ruthenium ammine complexes: Evidence for electron-transfer catalysis in H-bonded ternary assemblies

    International Nuclear Information System (INIS)

    The kinetics of bimolecular pseudo-self-exchange reactions such as that between pentaammine(pyridine)ruthenium(II) and pentaammine(3-fluoropyridine)ruthenium(III) shown below,(NH3)5RuII(py)2++(NH3)5RuIII(3-Fpy)3+-bar kex(NH3)5RuIII(py)3++(NH3)5RuII(3-Fpy)2+reveal a novel form of non-covalently mediated electron transfer over distance when salts of non-innocent electrolytes such as the conjugated dicarboxylic acid anions trans,trans-muconate2- or terephthalate2- are added to the solution. The kinetic accelerations are distinct from those seen with simple electrolytes such as KCl or CaCl2, and are thus outside the realm of classical electrolyte effects described by the Debye-Huckel theory of ion atmospheres. Kinetic simulations are presented, and the rate acceleration is interpreted in the context of possible superexchange-type interactions taking place in hydrogen-bonded ternary (or higher) association complexes which create new kinetic pathways for electron transfer over distance in aqueous solution

  15. New methods for quantum mechanical reaction dynamics

    International Nuclear Information System (INIS)

    Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L2) representation of the outgoing wave scattering Green's function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green's function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC- can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC- geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H3O- system, providing information about the potential energy surface for the OH + H2 reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the Boltzmannized flux operator

  16. 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.

  17. Reaction dynamics and photochemistry of divalent systems

    Energy Technology Data Exchange (ETDEWEB)

    Davis, H.F.

    1992-05-01

    Results are presented of molecular beam studies of bimolecular and unimolecular reactions of Ba. Chapter 1 discusses the reaction Ba + NO{sub 2}. Formation of the dominant BaO({sup 1}{Sigma}) + NO products resulted primarily from decay of long-lived Ba{sup +}NO{sub 2}{sup {minus}} collision complexes. Secondary mechanisms led to formation of forward scattered, internally excited BaO, and BaNO + O. D{sub o}(Ba-NO) = 65{plus_minus}20 kcal/mol. Reactions of ground state and electronically excited Ba with water and alcohols are examined in Chapter 2. Reaction of Ba({sup 1}S) + H{sup 2}O led to BaO + H{sub 2}, whereas excited state Ba({sup 1}D) + H{sub 2}O reacted to form BaOH + H. Collisions between Ba and CH{sub 3}OH led to BaOCH{sub 3} + H. Radical channels involve H-atom migration and are promoted by excitation of the incident Ba atom. In Chapter 3, reactions of Ba({sup 1}S) with ClO{sub 2}2 and O{sub 3} are discussed. Again, direct and complex mechanisms were observed. Formation of BaCl + O{sub 2} from decomposition of Ba{sup +}ClO{sub 2}{sup {minus}} accounted for 10% of total reaction crass section. Although Ba + O{sub 3} {yields} BaO + 0{sub 2} occurs primarily by direct reaction mechanisms, the secondary channel Ba + 0{sub 3} {yields} BaO{sub 2} + 0 involved decay of long lived Ba{sup +}O{sub 3}{sup {minus}} intermediates. D{sub o}(Ba{minus}O{sub 2}) = 120 {plus_minus}20 kcal/mol. Photodissociation dynamics of NO{sub 3} is explored in chapter 4. Visible excitation leads to formation of NO + 0{sub 2} and NO{sub 2} + O. Wavelength dependence of branching ratios is investigated. D{sub o}(O-NO{sub 2}) = 48.55 kcal/mole ;and calculate {Delta}H{sub f}(NO{sub 3}) = 17.75 kcal/mole (298K). Chapter 5 discusses the photodissociation of OClO in a molecular beam. Although ClO({sup 2}II) + O({sup 3}P) is dominant, Cl({sup 2}P) + O{sub 2} also forms, with a max yield of 3.9{plus_minus}0.8% near 404nm.

  18. Dynamics of anion-molecule reactions at low energy

    International Nuclear Information System (INIS)

    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 (SN2) 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 SN2 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 SN2-, 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 SN2 mechanism involving CH3-rotation. (orig.)

  19. 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.)

  20. Semiclassical methods in chemical reaction dynamics

    International Nuclear Information System (INIS)

    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

  1. Semiclassical methods in chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  2. Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions

    Science.gov (United States)

    Schultz, Emeric

    2008-01-01

    A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…

  3. Some Concepts in Reaction Dynamics

    Science.gov (United States)

    Polannyi, John C.

    1972-01-01

    In 1929 London 1 published a very approximate solution of the Schroedinger equation for a system of chemical interest: H3. To the extent that chemistry can be regarded as existing separately from physics, this was a landmark in the history of chemistry, comparable in importance to the landmark in the history of physics marked by the appearance of the Heitler-London equation for H2. The expression for H3, was, of necessity, even less accurate than that for H2, but chemists, like the habitual poor, were accustomed to this sort of misfortune. Together with the physicists they enjoyed the sensation of living in a renaissance. The physicists still could not calculate a great deal that was of interest to them, and the chemists could calculate less, but both could now dream. It would be too easy to say that their dreams were dreams of unlimited computer time. Their dreams were a lot more productive than that. Two years after London published his equation, H. Eyring and M. Polanyi obtained the first numerical energy surface for H3. They infused the London equation with a measure of empiricism to produce an energy surface which, whether or not it was correct in its details, provided a basis for further speculations of an important sort. The existence of a tangible energy surface in 1931 stimulated speculation along two different lines. The following year Pelzer and Wigner used this London-Eyring-Polanyi (LEP) energy surface for a thermodynamic treatment of the reaction rate in H + H2. This important development reached its full flowering a few years later. In these remarks I shall be concerned with another line of development. A second more-or-less distinct category of speculation that began with (and, indeed, in) the 1931 paper has to do with the dynamics of individual reactive encounters under the influence of specified interaction potentials.

  4. Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?

    International Nuclear Information System (INIS)

    We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H2, D + MuH, and F + H2, and the prototypical polyatomic reaction H + CH4. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method

  5. The reaction dynamics of alkali dimer molecules and electronically excited alkali atoms with simple molecules

    Energy Technology Data Exchange (ETDEWEB)

    Hou, H [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1995-12-01

    This dissertation presents the results from the crossed molecular beam studies on the dynamics of bimolecular collisions in the gas phase. The primary subjects include the interactions of alkali dimer molecules with simple molecules, and the inelastic scattering of electronically excited alkali atoms with O2. The reaction of the sodium dimers with oxygen molecules is described in Chapter 2. Two reaction pathways were observed for this four-center molecule-molecule reaction, i.e. the formations of NaO2 + Na and NaO + NaO. NaO2 products exhibit a very anisotropic angular distribution, indicating a direct spectator stripping mechanism for this reaction channel. The NaO formation follows the bond breaking of O2, which is likely a result of a charge transfer from Na2 to the excited state orbital of O2-. The scattering of sodium dimers from ammonium and methanol produced novel molecules, NaNH3 and Na(CH3OH), respectively. These experimental observations, as well as the discussions on the reaction dynamics and the chemical bonding within these molecules, will be presented in Chapter 3. The lower limits for the bond dissociation energies of these molecules are also obtained. Finally, Chapter 4 describes the energy transfer between oxygen molecules and electronically excited sodium atoms.

  6. Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damk\\"ohler numbers

    CERN Document Server

    Bandopadhyay, Aditya; Méheust, Yves; Dentz, Marco

    2016-01-01

    Mixing fronts, where fluids of different chemical compositions mix with each other, are typically subjected to velocity gradients, ranging from the pore scale to the catchment scale due to permeability variations and flow line geometries. A common trait of these processes is that the mixing interface is strained by shear. Depending on the P\\'eclet number $Pe$, which represents the ratio of the characteristic diffusion time to the characteristic advection time, and the Damk\\"ohler number $Da$, which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. This impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either very low or very high $Da$. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damk\\"ohler numbers, for a bimolecular reaction and an initial interface with separated reactants....

  7. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    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

  8. Markovian Dynamics on Complex Reaction Networks

    CERN Document Server

    Goutsias, John

    2012-01-01

    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 underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the 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...

  9. Chemical Reaction Dynamics in Nanoscle Environments

    Energy Technology Data Exchange (ETDEWEB)

    Evelyn M. Goldfield

    2006-09-26

    The major focus of the research in this program is the study of the behavior of molecular systems confined in nanoscale environments. The goal is to develop a theoretical framework for predicting how chemical reactions occur in nanoscale environments. To achieve this goal we have employed ab initio quantum chemistry, classical dynamics and quantum dynamics methods. Much of the research has focused on the behavior of molecules confined within single-walled carbon nanotubes (SWCNTs). We have also studied interactions of small molecules with the exterior surface of SWCNTs. Nonequilibrium molecular dynamics of interfaces of sliding surface interfaces have also been performed.

  10. 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.

  11. Markovian dynamics on complex reaction networks

    Science.gov (United States)

    Goutsias, J.; Jenkinson, G.

    2013-08-01

    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.

  12. 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.

  13. Molecular dynamics of bimolecular reactions : the equilibrium constant of dimerisation of carbon dioxide : rebinding molecular dynamics of nitric oxide to the V68F myoglobin mutant

    OpenAIRE

    Tsintsarska, Stefka

    2007-01-01

    1.1 Carbon dioxide 1.1.1 Significance Theoretical and experimental investigations of weakly bound molecular complexes are of fundamental importance for understanding of molecular interactions responsible for properties of condensed phases. The carbon dioxide clusters provide a simple model for such studies. Carbon dioxide has been a subject of many papers in recent years. Some deal with its role in the biosphere, mainly the greenhouse effect. The greenhouse effect is the ris...

  14. A dynamical model of surrogate reactions

    CERN Document Server

    Aritomo, Y; Nishio, K

    2010-01-01

    A new dynamical model is developed to describe the whole process of surrogate reactions; transfer of several nucleons at an initial stage, thermal equilibration of residues leading to washing out of shell effects and decay of populated compound nuclei are treated in a unified framework. Multi-dimensional Langevin equations are employed to describe time-evolution of collective coordinates with a time-dependent potential energy surface corresponding to different stages of surrogate reactions. The new model is capable of calculating spin distributions of the compound nuclei, one of the most important quantity in the surrogate technique. Furthermore, various observables of surrogate reactions can be calculated, e.g., energy and angular distribution of ejectile, and mass distributions of fission fragments. These features are important to assess validity of the proposed model itself, to understand mechanisms of the surrogate reactions and to determine unknown parameters of the model. It is found that spin distribut...

  15. Quantum effects in unimolecular reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Gezelter, J.D.

    1995-12-01

    This work is primarily concerned with the development of models for the quantum dynamics of unimolecular isomerization and photodissociation reactions. We apply the rigorous quantum methodology of a Discrete Variable Representation (DVR) with Absorbing Boundary Conditions (ABC) to these models in an attempt to explain some very surprising results from a series of experiments on vibrationally excited ketene. Within the framework of these models, we are able to identify the experimental signatures of tunneling and dynamical resonances in the energy dependence of the rate of ketene isomerization. Additionally, we investigate the step-like features in the energy dependence of the rate of dissociation of triplet ketene to form {sup 3}B{sub 1} CH{sub 2} + {sup 1}{sigma}{sup +} CO that have been observed experimentally. These calculations provide a link between ab initio calculations of the potential energy surfaces and the experimentally observed dynamics on these surfaces. Additionally, we develop an approximate model for the partitioning of energy in the products of photodissociation reactions of large molecules with appreciable barriers to recombination. In simple bond cleavage reactions like CH{sub 3}COCl {yields} CH{sub 3}CO + Cl, the model does considerably better than other impulsive and statistical models in predicting the energy distribution in the products. We also investigate ways of correcting classical mechanics to include the important quantum mechanical aspects of zero-point energy. The method we investigate is found to introduce a number of undesirable dynamical artifacts including a reduction in the above-threshold rates for simple reactions, and a strong mixing of the chaotic and regular energy domains for some model problems. We conclude by discussing some of the directions for future research in the field of theoretical chemical dynamics.

  16. 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.

  17. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T.

    1987-03-01

    Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.

  18. Neural Networks in Chemical Reaction Dynamics

    CERN Document Server

    Raff, Lionel; Hagan, Martin

    2011-01-01

    This monograph presents recent advances in neural network (NN) approaches and applications to chemical reaction dynamics. Topics covered include: (i) the development of ab initio potential-energy surfaces (PES) for complex multichannel systems using modified novelty sampling and feedforward NNs; (ii) methods for sampling the configuration space of critical importance, such as trajectory and novelty sampling methods and gradient fitting methods; (iii) parametrization of interatomic potential functions using a genetic algorithm accelerated with a NN; (iv) parametrization of analytic interatomic

  19. 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.

  20. Catalytic reaction dynamics in inhomogeneous networks.

    Science.gov (United States)

    Watanabe, Akitomo; Yakubo, Kousuke

    2014-05-01

    Biochemical reactions in a cell can be modeled by a catalytic reaction network (CRN). It has been reported that catalytic chain reactions occur intermittently in the CRN with a homogeneous random-graph topology and its avalanche-size distribution obeys a power law with the exponent 4/3 [A. Awazu and K. Kaneko, Phys. Rev. E 80, 010902(R) (2009)]. This fact indicates that the catalytic reaction dynamics in homogeneous CRNs exhibits self-organized criticality (SOC). Structures of actual CRNs are, however, known to be highly inhomogeneous. We study the influence of various types of inhomogeneities found in real-world metabolic networks on the universality class of SOC. Our numerical results clarify that SOC keeps its universality class even for networks possessing structural inhomogeneities such as the scale-free property, community structures, and degree correlations. In contrast, if the CRN has inhomogeneous catalytic functionality, the universality class of SOC depends on how widely distributed the number of reaction paths catalyzed by a single chemical species is. PMID:25353843

  1. Iodine-benzene complex as a candidate for a real-time control of a bimolecular reaction. Spectroscopic studies of the properties of the 1:1 complex isolated in solid krypton.

    Science.gov (United States)

    Kiviniemi, Tiina; Hulkko, Eero; Kiljunen, Toni; Pettersson, Mika

    2009-06-01

    The properties of the 1:1 iodine-benzene complex isolated in a solid Kr matrix at low temperatures have been studied using UV-vis absorption, FTIR, resonance Raman, and femtosecond coherent anti-Stokes Raman spectroscopy (fs-CARS). The use of all these techniques on similar samples provides a wide view on the spectroscopic properties of the complex and allows comparison and combination of the results from different methods. The results for the complex cover its structure, the changes in the iodine molecule's vibrational frequencies and electronic absorption spectrum upon complexation, and the dynamics of the complexed I(2) molecule on both ground and excited electronic states. In addition, polarization beats between uncomplexed benzene and iodine molecules are detected in the fs-CARS spectra, showing an amplification of an electronically nonresonant CARS signal by the resonant iodine signal. The possibility of controlling the charge-transfer reaction of the I(2)-Bz complex using the excitation of a well-defined ground-state vibrational wavepacket, according to the Tannor-Rice-Kosloff scheme, is discussed on the basis of the experimental findings. PMID:19425545

  2. 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

  3. 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.

  4. Mode specificity in unimolecular reaction dynamics

    International Nuclear Information System (INIS)

    Theoretical studies on mode specificity in unimolecular reaction dynamics are presented, based on essentially exact quantum mechanical methods, a semi-classical multichannel branching model, and classical trajectory methods. The principal aim is to discover the relevant factors governing whether a unimolecular system exhibits mode specificity in its individual state rate constants, i.e., whether quasi-degenerate metastable states decay with significantly different rates. Model studies of two nonlinearly coupled oscillators (one of which can dissociate) demonstrate the effects of various features of potential energy surfaces on the character of the rates (e.g., degeneracy of modes, reaction path curvature, frequency modulation, etc.). These results and those obtained for the Henon-Heiles potential energy surface indicate and apparent absence of correlation between the quasi-periodic/ergodic motion of classical mechanics and the mode specific/statistical behavior of the unimolecular rate constants

  5. Predictions of dynamic changes in reaction rates as a consequence of incomplete mixing using pore scale reactive transport modeling on images of porous media.

    Science.gov (United States)

    Alhashmi, Z; Blunt, M J; Bijeljic, B

    2015-08-01

    We present a pore scale model capable of simulating fluid/fluid reactive transport on images of porous media from first principles. We use a streamline-based particle tracking method for simulating flow and transport, while for reaction to occur, both reactants must be within a diffusive distance of each other during a time-step. We assign a probability of reaction (Pr), as a function of the reaction rate constant (kr) and the diffusion length. Firstly, we validate our model for reaction against analytical solutions for the bimolecular reaction (A+B→C) in a free fluid. Then, we simulate transport and reaction in a beadpack to validate the model through predicting the fluid/fluid reaction experimental results provided by Gramling et al. (2002). Our model accurately predicts the experimental data, as it takes into account the degree of incomplete mixing present at the sub-pore (image voxel) level, in contrast to advection-dispersion-reaction equation (ADRE) model that over-predicts pore scale mixing. Finally, we show how our model can predict dynamic changes in the reaction rate accurately accounting for the local geometry, topology and flow field at the pore scale. We demonstrate the substantial difference between the predicted early-time reaction rate in comparison to the ADRE model. PMID:26142546

  6. 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 ve

  7. The molecular dynamics of atmospheric reaction

    Science.gov (United States)

    Polanyi, J. C.

    1971-01-01

    Detailed information about the chemistry of the upper atmosphere took the form of quantitative data concerning the rate of reaction into specified states of product vibration, rotation and translation for exothermic reaction, as well as concerning the rate of reaction from specified states of reagent vibration, rotation and translation for endothermic reaction. The techniques used were variants on the infrared chemiluminescence method. Emphasis was placed on reactions that formed, and that removed, vibrationally-excited hydroxyl radicals. Fundamental studies were also performed on exothermic reactions involving hydrogen halides.

  8. Mode-coupling theory for reaction dynamics in liquids

    OpenAIRE

    Shental, Nurit; Rabani, Eran

    2003-01-01

    A theory for chemical reaction dynamics in condensed phase systems based on the generalized Langevin formalism of Grote and Hynes is presented. A microscopic approach to calculate the dynamic friction is developed within the framework of a combination of kinetic and mode-coupling theories. The approach provides a powerful analytic tool to study chemical reactions in realistic condensed phase environments. The accuracy of the approach is tested for a model isomerization reaction in a Lennard-J...

  9. 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}.

  10. 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.

  11. Electromagnetic reactions and few-nucleon dynamics

    International Nuclear Information System (INIS)

    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 medium mass nuclei in coupled-cluster theory, highlighted by the recent application to the 16O photo-nuclear cross section. (author)

  12. 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.

  13. Dynamics of fission and heavy ion reactions

    International Nuclear Information System (INIS)

    Recent advances in a unified macroscopic-microscopic description of large-amplitude collective nuclear motion such as occurs in fission and heavy ion reactions are discussed. With the goal of finding observable quantities that depend upon the magnitude and mechanism of nuclear dissipation, one-body dissipation and two-body viscosity within the framework of a generalized Fokker-Planck equation for the time dependence of the distribution function in phase space of collective coordinates and momenta are considered. Proceeding in two separate directions, the generalized Hamilton equations of motion for the first moments of the distribution function with a new shape parametrization and other technical innovations are first solved. This yields the mean translational fission-fragment kinetic energy and mass of a third fragment that sometimes forms between the two end fragments, as well as the energy required for fusion in symmetric heavy-ion reactions and the mass transfer and capture cross section in asymmetric heavy-ion reactions. In a second direction, we specialize to an inverted-oscillator fission barrier and use Kramers' stationary solution to calculate the mean time from the saddle point to scission for a heavy-ion-induced fission reaction for which experimental information is becoming available. 25 references

  14. Testing string dynamics in lepton nucleus reactions

    International Nuclear Information System (INIS)

    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

  15. The hunt for the dynamical resonances in chemical reaction dynamics: a perspective on historical advances

    OpenAIRE

    Yu Angyang; Zhonghua Yang

    2015-01-01

    The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly obser...

  16. 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...

  17. 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.

  18. Skeletal Isomerization and Inter-molecular Hydrogen Transfer Reactions in Catalytic Cracking

    Institute of Scientific and Technical Information of China (English)

    Gao Yongcan; Zhang Jiushun; Xie Chaogang; Long Jun

    2002-01-01

    Bimolecular hydrogen transfer and skeletal isomerization are the important secondary reac tions among catalytic cracking reactions, which affect product yield distribution and product quality.Catalyst properties and operating parameters have great impact on bimolecular hydrogen transfer and skeletal isomerization reactions. Bimolecular hydrogen transfer activity and skeletal isomerization activity of USY-containing catalysts are higher than that of ZSM-5-containing catalyst. Coke deposition on the active sites of catalyst may suppress bimolecular hydrogen transfer activity and skeletal isomerization activity of catalyst in different degrees. Short reaction time causes a decrease of hydrogen trans fer reaction, but an increase of skeletal isomerization reaction compared to cracking reaction in catalytic cracking process.

  19. 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.

  20. Crossed molecular beam studies of unimolecular reaction dynamics

    International Nuclear Information System (INIS)

    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 CF3I 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

  1. Roaming dynamics in the MgH + H→Mg + H 2 reaction: Quantum dynamics calculations

    Science.gov (United States)

    Takayanagi, Toshiyuki; Tanaka, Tomokazu

    2011-03-01

    Reaction mechanisms of the MgH + H→Mg + H 2 reaction have been investigated using quantum reactive scattering methods on a global ab initio potential energy surface. There exist two microscopic mechanisms in the dynamics of this reaction. One is a direct hydrogen abstraction reaction and the other proceeds via initial formation of a HMgH complex in the deep potential well. The result of the present quantum dynamics calculations suggests that the HMgH complex formed in the reaction mainly decays into the Mg + H 2 channel via a 'roaming mechanism' without going through the saddle point region.

  2. Many-body quantum reaction dynamics near the fusion barrier

    International Nuclear Information System (INIS)

    The understanding of quantum effects in determining nuclear reaction outcomes is evolving as improved experimental techniques reveal new facets of interaction dynamics. Whilst the phenomenon of coupling-enhanced quantum tunnelling is understood to arise due to quantum superposition, the observed inhibition of fusion at energies well below the barrier is not yet quantitatively understood. Collisions involving weakly-bound nuclei, which have low energy thresholds against breakup, present further challenges. Recent coincidence measurements for reactions of weakly bound stable nuclei have not only provided a complete picture of the physical mechanisms triggering breakup, but have also shown how information on reaction dynamics occurring on time-scales of ∼ zepto-seconds can be obtained experimentally. These new experimental findings demand major developments in quantum models of near-barrier nuclear reactions. (authors)

  3. Many-body Quantum Reaction Dynamics near the Fusion Barrier

    Directory of Open Access Journals (Sweden)

    Dasgupta M.

    2014-03-01

    Full Text Available The understanding of quantum effects in determining nuclear reaction outcomes is evolving as improved experimental techniques reveal new facets of interaction dynamics. Whilst the phenomenon of coupling-enhanced quantum tunnelling is understood to arise due to quantum superposition, the observed inhibition of fusion at energies well below the barrier is not yet quantitatively understood. Collisions involving weakly-bound nuclei, which have low energy thresholds against breakup, present further challenges. Recent coincidence measurements for reactions of weakly bound stable nuclei have not only provided a complete picture of the physical mechanisms triggering breakup, but have also shown how information on reaction dynamics occurring on time-scales of ~zepto-seconds can be obtained experimentally. These new experimental findings demand major developments in quantum models of near-barrier nuclear reactions.

  4. Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.

    Science.gov (United States)

    Preston, Thomas J; Hornung, Balázs; Pandit, Shubhrangshu; Harvey, Jeremy N; Orr-Ewing, Andrew J

    2016-07-14

    Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics. PMID:26812395

  5. Dynamical dipole mode in heavy-ion fusion reactions

    International Nuclear Information System (INIS)

    The dynamical dipole mode, excited in charge asymmetric heavy-ion collisions, was investigated in the mass region of the 192Pb compound nucleus, formed by using the 40,48Ca + 152,144Sm reactions at ∼11 MeV/nucleon. Preliminary results of this measurement, concerning both fusion-evaporation and fission events are presented. As a fast cooling mechanism on the fusion path, the dynamical dipole mode could be useful for the synthesis of super heavy elements through 'hot' fusion reactions.

  6. Simulation of chemical reaction dynamics on an NMR quantum computer

    CERN Document Server

    Lu, Dawei; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-01-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

  7. 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.

  8. Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation

    OpenAIRE

    Mauguière, F. A. L.; Collins, P.; Ezra, G. S.; Farantos, S. C.; Wiggins, S

    2014-01-01

    A model Hamiltonian for the reaction CH$_4^+ \\rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom ...

  9. The hunt for the dynamical resonances in chemical reaction dynamics: a perspective on historical advances

    Directory of Open Access Journals (Sweden)

    Yu Angyang

    2015-06-01

    Full Text Available The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly observed by the researchers of the Chinese Academy of Sciences in 2006. Besides, the partial wave resonances in the chemical reactions have been observed for the first time in 2010.

  10. Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

    Science.gov (United States)

    Menon, Madhu

    1998-01-01

    In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.

  11. Finite temperature amplitudes and reaction rates in Thermofield dynamics

    CERN Document Server

    Rakhimov, A M

    2001-01-01

    We propose a method for calculating the reaction rates and transition amplitudes of generic process taking place in a many body system in equilibrium. The relationship of the scattering and decay amplitudes as calculated in Thermo Field Dynamics the conventional techniques is established. It is shown that in many cases the calculations are relatively easy in TFD.

  12. Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics.

    Science.gov (United States)

    Marchand, Adrien; Ferreira, Rubén; Tateishi-Karimata, Hisae; Miyoshi, Daisuke; Sugimoto, Naoki; Gabelica, Valérie

    2013-10-17

    Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely sensitive to the sequence and to the chemical environment, for example, solvation. Dehydrating conditions are known to stabilize G-quadruplex structures, but information on how solvation influences the individual rates of folding and unfolding of G-quadruplexes remains scarce. Here, we used electrospray mass spectrometry for the first time to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands, in the presence of common organic cosolvents (methanol, ethanol, isopropanol, and acetonitrile). Based on the ammonium ion distribution, the total dimer signal was decomposed into contributions from the parallel and antiparallel structures to obtain individual reaction rates, and the antiparallel G-quadruplex structure was found to form faster than the parallel one. A dimeric reaction intermediate, in rapid equilibrium with the single strands, was also identified. Organic cosolvents increase the stability of the final structures mainly by increasing the folding rates. Our quantitative analysis of reaction rate dependence on cosolvent percentage shows that organic cosolvent molecules can be captured or released upon G-quadruplex formation, highlighting that they are not inert with DNA. In contrast to the folding rates, the G-quadruplex unfolding rates are almost insensitive to solvation effects, but are instead governed by the sequence and by the final structure: parallel dimers dissociate slower than antiparallel dimers only when thymine bases are present at the 5'-end. These results contribute unraveling the folding pathways of telomeric G-quadruplexes. The solvent effects revealed here enlighten that G-quadruplex structure in dehydrated, and molecularly crowded environments are modulated by the nature of cosolvent (e.g., methanol favors antiparallel structures) due to direct interactions, and by the time scale of the reaction, with >200-fold acceleration of

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

    International Nuclear Information System (INIS)

    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

  14. Quantum Dynamics of Radical-Ion-Pair Reactions

    CERN Document Server

    Kominis, I K

    2010-01-01

    Radical-ion-pair reactions were recently shown to represent a rich biophysical laboratory for the application of quantum measurement theory methods and concepts, casting doubt on the validity of the theoretical treatment of these reactions and the results thereof that has been at the core of spin chemistry for several decades now. The ensued scientific debate, although exciting, is plagued with several misconceptions. We will here provide a comprehensive treatment of the quantum dynamics of radical-ion-pair reactions, generalizing our recent work and elaborating on the analogy with the double-slit experiment having partial "which-path" information. This analogy directly leads to the general treatment of radical-ion pair reactions covering the whole range between the two extremes, that of perfect singlet-triplet coherence and that of complete incoherence.

  15. Entrance channel effects in fusion reactions near the barrier: Reaction dynamics or nuclear structure?

    International Nuclear Information System (INIS)

    The origin of previously reported entrance channel effects by symmetric and asymmetric fusion reactions leading to rare earth nuclei near the Coulomb barrier is critically reviewed. Possible influences of reaction dynamics or structure effects due to the proximity of superdeformation are discussed using new charged-particle spectra and angular distributions associated with specific axn exit channels. For axn channels, nonstatistical effects in the fusion of the asymmetric entrance channel are responsible for the large difference in the spin distributions in the evaporation residues formed by symmetric and asymmetric entrance channels. Whereas GDR spectra show significant entrance channel effects, the authors find no influence on the subbarrier α spectra from possible elongated shapes associated with early reaction dynamics. New data and analyses of γ-ray multiplicity distributions from the xn exit channels show that previously reported entrance channel effects are due to mapping from l to residue spin and then to γ-ray multiplicity

  16. Roaming dynamics in ion-molecule reactions: phase space reaction pathways and geometrical interpretation

    CERN Document Server

    Mauguière, F A L; Ezra, G S; Farantos, S C; Wiggins, S

    2014-01-01

    A model Hamiltonian for the reaction CH$_4^+ \\rightarrow$ CH$_3^+$ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and product...

  17. Understanding bimolecular machines: Theoretical and experimental approaches

    Science.gov (United States)

    Goler, Adam Scott

    This dissertation concerns the study of two classes of molecular machines from a physical perspective: enzymes and membrane proteins. Though the functions of these classes of proteins are different, they each represent important test-beds from which new understanding can be developed by the application of different techniques. HIV1 Reverse Transcriptase is an enzyme that performs multiple functions, including reverse transcription of RNA into an RNA/DNA duplex, RNA degradation by the RNaseH domain, and synthesis of dsDNA. These functions allow for the incorporation of the retroviral genes into the host genome. Its catalytic cycle requires repeated large-scale conformational changes fundamental to its mechanism. Motivated by experimental work, these motions were studied theoretically by the application of normal mode analysis. It was observed that the lowest order modes correlate with largest amplitude (low-frequency) motion, which are most likely to be catalytically relevant. Comparisons between normal modes obtained via an elastic network model to those calculated from the essential dynamics of a series of all-atom molecular dynamics simulations show the self-consistency between these calculations. That similar conformational motions are seen between independent theoretical methods reinforces the importance of large-scale subdomain motion for the biochemical action of DNA polymerases in general. Moreover, it was observed that the major subunits of HIV1 Reverse Transcriptase interact quasi-harmonically. The 5HT3A Serotonin receptor and P2X1 receptor, by contrast, are trans-membrane proteins that function as ligand gated ion channels. Such proteins feature a central pore, which allows for the transit of ions necessary for cellular function across a membrane. The pore is opened by the ligation of binding sites on the extracellular portion of different protein subunits. In an attempt to resolve the individual subunits of these membrane proteins beyond the diffraction

  18. Structure, dynamics, and surface reactions of bioactive glasses

    Science.gov (United States)

    Zeitler, Todd R.

    Three bioactive glasses (45S5, 55S4.3, and 60S3.8) have been investigated using atomic-scale molecular dynamics simulations in attempt to explain differences in observed macroscopic bioactivity. Bulk and surface structures and bulk dynamics have been characterized. Ion exchange and hydrolysis reactions, the first two stages in Hench's model describing the reactions of bioactive glass surfaces in vivo, have been investigated in detail. The 45S5 composition shows a much greater network fragmentation: it is suggested that this fragmentation can play a role in at least the first two stages of Hench's model for HCA formation on the surfaces of bioactive glasses. In terms of dynamic behavior, long-range diffusion was only observed for sodium. Calcium showed only jumps between adjacent sites, while phosphorus showed only local vibrations. Surface simulations show the distinct accumulation of sodium at the immediate surface for each composition. Surface channels are also shown to exist and are most evident for 45S5 glass. Results for a single ion exchange showed that the ion-exchange reaction is preferred (more exothermic) for Na+ ions near Si, rather than P. A range of reaction energies were found, due to a range of local environments, as expected for a glass surface. The average reaction energies are not significantly different among the three glass compositions. The results for bond hydrolysis on as-created surfaces show no significant differences among the three compositions for simulations involving Si-O-Si or Si-O-P. All average values are greater than zero, indicating endothermic reactions that are not favorable by themselves. However, it is shown that the hydrolysis reactions became more favorable (in fact, exothermic for 45S5 and 55S4.3) when simulated on surfaces that had already been ion-exchanged. This is significant because it gives evidence supporting Hench's proposed reaction sequence. Perhaps even more significantly, the reaction energies for hydrolysis

  19. Crossed molecular beam studies of atmospheric chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jingsong

    1993-04-01

    The dynamics of several elementary chemical reactions that are important in atmospheric chemistry are investigated. The reactive scattering of ground state chlorine or bromine atoms with ozone molecules and ground state chlorine atoms with nitrogen dioxide molecules is studied using a crossed molecular beams apparatus with a rotatable mass spectrometer detector. The Cl + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at four collision energies ranging from 6 kcal/mole to 32 kcal/mole. The derived product center-of-mass angular and translational energy distributions show that the reaction has a direct reaction mechanism and that there is a strong repulsion on the exit channel. The ClO product is sideways and forward scattered with respect to the Cl atom, and the translational energy release is large. The Cl atom is most likely to attack the terminal oxygen atom of the ozone molecule. The Br + O{sub 3} {yields} ClO + O{sub 2} reaction has been studied at five collision energies ranging from 5 kcal/mole to 26 kcal/mole. The derived product center-of-mass angular and translational energy distributions are quite similar to those in the Cl + O{sub 3} reaction. The Br + O{sub 3} reaction has a direct reaction mechanism similar to that of the Cl + O{sub 3} reaction. The electronic structure of the ozone molecule seems to play the central role in determining the reaction mechanism in atomic radical reactions with the ozone molecule. The Cl + NO{sub 2} {yields} ClO + NO reaction has been studied at three collision energies ranging from 10.6 kcal/mole to 22.4 kcal/mole. The center-of-mass angular distribution has some forward-backward symmetry, and the product translational energy release is quite large. The reaction proceeds through a short-lived complex whose lifetime is less than one rotational period. The experimental results seem to show that the Cl atom mainly attacks the oxygen atom instead of the nitrogen atom of the NO{sub 2} molecule.

  20. 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.

  1. Untangling knots via reaction-diffusion dynamics of vortex strings

    CERN Document Server

    Maucher, Fabian

    2016-01-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  2. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    Science.gov (United States)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541

  3. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    Science.gov (United States)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  4. Simulation of chemical reaction dynamics on an NMR quantum computer

    OpenAIRE

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-01-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical ...

  5. Fluid dynamic modeling of nano-thermite reactions

    Energy Technology Data Exchange (ETDEWEB)

    Martirosyan, Karen S., E-mail: karen.martirosyan@utb.edu [Department of Physics and Astronomy, University of Texas, Brownsville, 80 Fort Brown, Brownsville, Texas 78520 (United States); Zyskin, Maxim [Rutgers University, 110 Frelinghusen Road, Piscataway, New Jersey 08854-8019 (United States); Jenkins, Charles M.; Horie, Yasuyuki [Air Force Research Laboratory, Munitions Directorate, 2306 Perimeter Road, Eglin AFB, Florida 32542 (United States)

    2014-03-14

    This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of “slower” reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.

  6. Fluid dynamic modeling of nano-thermite reactions

    Science.gov (United States)

    Martirosyan, Karen S.; Zyskin, Maxim; Jenkins, Charles M.; Yuki Horie, Yasuyuki

    2014-03-01

    This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of "slower" reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.

  7. Fluid dynamic modeling of nano-thermite reactions

    International Nuclear Information System (INIS)

    This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of “slower” reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor

  8. Reaction dynamics studies for the system 7Be+58Ni

    Science.gov (United States)

    Torresi, D.; Mazzocco, M.; Acosta, L.; Boiano, A.; Boiano, C.; Diaz-Torres, A.; Fierro, N.; Glodariu, T.; Grilj, L.; Guglielmetti, A.; Keeley, N.; La Commara, M.; Martel, I.; Mazzocchi, C.; Molini, P.; Pakou, A.; Parascandolo, C.; Parkar, V. V.; Patronis, N.; Pierroutsakou, D.; Romoli, M.; Rusek, K.; Sanchez-Benitez, A. M.; Sandoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Stiliaris, E.; Strano, E.; Stroe, L.; Zerva, K.

    2015-04-01

    The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].

  9. [2+2] Photocycloaddition reaction dynamics of triplet pyrimidines.

    Science.gov (United States)

    Yang, Chunfan; Yu, Youqing; Liu, Kunhui; Song, Di; Wu, Lidan; Su, Hongmei

    2011-06-01

    Taking the 266 nm excited pyrimidine (uracil or thymine) with cyclopentene as model reaction systems, we have examined the photoproduct formation dynamics from the [2 + 2] photocycloaddition reactions of triplet pyrimidines in solution and provided mechanistic insights into this important DNA photodamage reaction. By combining two compliment methods of nanosecond time-resolved transient IR and UV-vis laser flash-photolysis spectroscopy, the photoproduct formation dynamics as well as the triplet quenching kinetics are measured. Characteristic IR absorption bands due to photoproduct formation have been observed and product quantum yields are determined to be ∼0.91% for uracil and ∼0.41% for thymine. Compared to the measured large quenching rate constants of triplet uracil (1.5 × 10(9) M(-1)s(-1)) or thymine (0.6 × 10(9) M(-1)s(-1)) by cyclopentene, the inefficiency in formation of photoproducts indicates competitive physical quenching processes may exist on the route leading to photoproducts, resulting in very small product yields eventually. Such an energy wasting process is found to be resulted from T(1)/S(0) surface crossings by the hybrid density functional calculations, which compliments the experiments and reveals the reaction mechanism. PMID:21557584

  10. Switching dynamics in reaction networks induced by molecular discreteness

    International Nuclear Information System (INIS)

    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

  11. Data preprocessing for parameter estimation. An application to a reactive bimolecular transport model

    CERN Document Server

    Cuch, Daniel A; Hasi, Claudio D El

    2015-01-01

    In this work we are concerned with the inverse problem of the estimation of modeling parameters for a reactive bimolecular transport based on experimental data that is non-uniformly distributed along the interval where the process takes place. We proposed a methodology that can help to determine the intervals where most of the data should be taken in order to obtain a good estimation of the parameters. For the purpose of reducing the cost of laboratory experiments, we propose to simulate data where is needed and it is not available, a PreProcesing Data Fitting (PPDF).We applied this strategy on the estimation of parameters for an advection-diffusion-reaction problem in a porous media. Each step is explained in detail and simulation results are shown and compared with previous ones.

  12. Quantum mechanics of chemical reactions: Recent developments in reactive scattering and in reaction path Hamiltonians

    International Nuclear Information System (INIS)

    Two recent developments in the theory of chemical reaction dynamics are reviewed. First, it has recently been discovered that the S- matrix version of the Kohn variational principle is free of the ''Kohn anomalies'' that have plagued other versions and prevented its general use. This has considerably simplified quantum mechanical reactive scattering calculations, which provide the rigorous characterizations of bimolecular reactions. Second, a new kind of reaction path Hamiltonian has been developed, one based on the ''least motion'' path that interpolates linearly between the reactant and product geometry of the molecule (rather than the previously used minimum energy, or ''intrinsic'' reaction path). The form of Hamiltonian which results is much simpler than the original reaction path Hamiltonian, but more important is the fact that it provides a more physically correct description of hydrogen atom transfer reactions. 44 refs., 4 figs

  13. Use of bimolecular fluorescence complementation in yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Skarp, Kari-Pekka; Zhao, Xueqiang; Weber, Marion; Jantti, Jussi

    2008-01-01

    Visualization of protein-protein interactions in vivo offers a powerful tool to resolve spatial and temporal aspects of cellular functions. Bimolecular fluorescence complementation (BiFC) makes use of nonfluorescent fragments of green fluorescent protein or its variants that are added as "tags" to target proteins under study. Only upon target protein interaction is a fluorescent protein complex assembled and the site of interaction can be monitored by microscopy. In this chapter, we describe the method and tools for use of BiFC in the yeast Saccharomyces cerevisiae. PMID:19066026

  14. Roaming dynamics in ion-molecule reactions: Phase space reaction pathways and geometrical interpretation

    Science.gov (United States)

    Mauguière, Frédéric A. L.; Collins, Peter; Ezra, Gregory S.; Farantos, Stavros C.; Wiggins, Stephen

    2014-04-01

    A model Hamiltonian for the reaction CH_4^+ rArr CH_3^+ + H, parametrized to exhibit either early or late inner transition states, is employed to investigate the dynamical characteristics of the roaming mechanism. Tight/loose transition states and conventional/roaming reaction pathways are identified in terms of time-invariant objects in phase space. These are dividing surfaces associated with normally hyperbolic invariant manifolds (NHIMs). For systems with two degrees of freedom NHIMS are unstable periodic orbits which, in conjunction with their stable and unstable manifolds, unambiguously define the (locally) non-recrossing dividing surfaces assumed in statistical theories of reaction rates. By constructing periodic orbit continuation/bifurcation diagrams for two values of the potential function parameter corresponding to late and early transition states, respectively, and using the total energy as another parameter, we dynamically assign different regions of phase space to reactants and products as well as to conventional and roaming reaction pathways. The classical dynamics of the system are investigated by uniformly sampling trajectory initial conditions on the dividing surfaces. Trajectories are classified into four different categories: direct reactive and non-reactive trajectories, which lead to the formation of molecular and radical products respectively, and roaming reactive and non-reactive orbiting trajectories, which represent alternative pathways to form molecular and radical products. By analysing gap time distributions at several energies, we demonstrate that the phase space structure of the roaming region, which is strongly influenced by nonlinear resonances between the two degrees of freedom, results in nonexponential (nonstatistical) decay.

  15. Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics

    Directory of Open Access Journals (Sweden)

    Georgiev Nikola

    2006-01-01

    Full Text Available The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK—and STAT5a —protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation inherent to the model of ERK and STAT cross talk.

  16. Recycling probability and dynamical properties of germinal center reactions

    CERN Document Server

    Meyer-Hermann, M; Or-Guil, M; Meyer-Hermann, Michael; Deutsch, Andreas; Or-Guil, Michal

    2001-01-01

    We introduce a new model for the dynamics of centroblasts and centrocytes in a germinal center. The model reduces the germinal center reaction to the elements considered as essential and embeds proliferation of centroblasts, point mutations of the corresponding antibody types represented in a shape space, differentiation to centrocytes, selection with respect to initial antigens, differentiation of positively selected centrocytes to plasma or memory cells and recycling of centrocytes to centroblasts. We use exclusively parameters with a direct biological interpretation such that, once determined by experimental data, the model gains predictive power. Based on the experiment of Han et al.(1995) we predict that a high rate of recycling of centrocytes to centroblasts is necessary for the germinal center reaction to work reliably. Furthermore, we find a delayed start of the production of plasma and memory cells with respect to the start of point mutations, which turns to be necessary for the optimization process ...

  17. 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.

  18. 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

  19. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    Truhlar, Donald G.

    1993-04-01

    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

  20. Dynamics of GeV light-ion-induced reactions

    International Nuclear Information System (INIS)

    Recent results from studies of the 1.8 - 4.8 GeV 3He + natAg, 197Au 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.)

  1. Dynamics of GeV light-ion-induced reactions

    Energy Technology Data Exchange (ETDEWEB)

    Kwiatkowski, K.; Bracken, D.S.; Foxford, E.R.; Ginger, D.S.; Hsi, W.C.; Morley, K.B.; Viola, V.E.; Wang, G. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Korteling, R.G. [Simon Fraser Univ., Burnaby, BC (Canada). Dept. of Chemistry; Legrain, R. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. d`Astrophysique, de la Physique des Particules, de la Physique Nucleaire et de l`Instrumentation Associee] [and others

    1996-09-01

    Recent results from studies of the 1.8 - 4.8 GeV {sup 3}He + {sup nat}Ag, {sup 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.). 19 refs.

  2. Dynamics of helix-coil transition and isotope exchange reaction

    International Nuclear Information System (INIS)

    A dynamical theory is presented for the helix-coil transition and the isotope exchange reaction in a short polypeptide chain. In this theory it is assumed that there is always one and only one helical sequence. The boundaries of the helix are assumed to move randomly along the chain. If we assume slow movement of the boundaries, our model theory explains the experimental results, i.e., the very low rate of the isotope exchange in the central portion of the chain and the site dependence of the rate. (author)

  3. Adsorption Isotherms and Surface Reaction Kinetics

    Science.gov (United States)

    Lobo, L. S.; Bernardo, C. A.

    1974-01-01

    Explains an error that occurs in calculating the conditions for a maximum value of a rate expression for a bimolecular reaction. The rate expression is derived using the Langmuir adsorption isotherm to relate gas pressures and corresponding surface coverages. (GS)

  4. Reaction mechanisms in medium energy collisions: influence of dynamical fluctuations

    International Nuclear Information System (INIS)

    Dynamical fluctuations in heavy ion collisions at beam energies 20 - 200 MeV are discussed. The main topics are: fragment formation from dynamical instabilities; neck fragmentation and variances; dynamics of fluctuations. A detailed study between the fragment formation time and the freeze-out time has been performed. Different theoretical models are proposed. For more peripheral collisions a novel reaction mechanism is revealed, due to the onset of new neck instabilities coupled to an increasing amount of dynamical fluctuations. Expected consequences are: possibility of intermediate mass fragment emission from the neck region and larger variances in projectile-like and target-like observables. A great variety of sources for dynamically emitted particles are predicted. Isospin effects and possibilities of producing of highly exotic nuclear systems from neck ruptures are also expected. A fully consistent treatment of fluctuation dynamics is presented, including short range (Langevin type) and long range (mean field) correlations. A stochastic transport model is constructed with the presence of the random force related to consistent density fluctuations. The Boltzmann-Nordheim-Vlasov equation for a mean phase space trajectory is modified by a correlation term with the structure of a diffusion in momentum space. Effects for collective motions and for regions of mean field instabilities are discussed. Relevant contributions from fluctuations are predicted for the production of high energy photons with a coherent mechanism. In particular a soft component in the Bremsstrahlung gamma spectrum is strongly enhanced, with important consequences on the properties of hot giant resonances that can be extracted from experiments. 5 refs

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

    International Nuclear Information System (INIS)

    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

  6. 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.

  7. Reaction dynamics and photochemistry of divalent systems. [Reaction of Ba with NO sub 2 , H sub 2 O, methanol, ClO sub 2 , O sub 3; photodissociation of NO sub 3 radical and OClO

    Energy Technology Data Exchange (ETDEWEB)

    Davis, H.F.

    1992-05-01

    Results are presented of molecular beam studies of bimolecular and unimolecular reactions of Ba. Chapter 1 discusses the reaction Ba + NO{sub 2}. Formation of the dominant BaO({sup 1}{Sigma}) + NO products resulted primarily from decay of long-lived Ba{sup +}NO{sub 2}{sup {minus}} collision complexes. Secondary mechanisms led to formation of forward scattered, internally excited BaO, and BaNO + O. D{sub o}(Ba-NO) = 65{plus minus}20 kcal/mol. Reactions of ground state and electronically excited Ba with water and alcohols are examined in Chapter 2. Reaction of Ba({sup 1}S) + H{sup 2}O led to BaO + H{sub 2}, whereas excited state Ba({sup 1}D) + H{sub 2}O reacted to form BaOH + H. Collisions between Ba and CH{sub 3}OH led to BaOCH{sub 3} + H. Radical channels involve H-atom migration and are promoted by excitation of the incident Ba atom. In Chapter 3, reactions of Ba({sup 1}S) with ClO{sub 2}2 and O{sub 3} are discussed. Again, direct and complex mechanisms were observed. Formation of BaCl + O{sub 2} from decomposition of Ba{sup +}ClO{sub 2}{sup {minus}} accounted for 10% of total reaction crass section. Although Ba + O{sub 3} {yields} BaO + 0{sub 2} occurs primarily by direct reaction mechanisms, the secondary channel Ba + 0{sub 3} {yields} BaO{sub 2} + 0 involved decay of long lived Ba{sup +}O{sub 3}{sup {minus}} intermediates. D{sub o}(Ba{minus}O{sub 2}) = 120 {plus minus}20 kcal/mol. Photodissociation dynamics of NO{sub 3} is explored in chapter 4. Visible excitation leads to formation of NO + 0{sub 2} and NO{sub 2} + O. Wavelength dependence of branching ratios is investigated. D{sub o}(O-NO{sub 2}) = 48.55 kcal/mole ;and calculate {Delta}H{sub f}(NO{sub 3}) = 17.75 kcal/mole (298K). Chapter 5 discusses the photodissociation of OClO in a molecular beam. Although ClO({sup 2}II) + O({sup 3}P) is dominant, Cl({sup 2}P) + O{sub 2} also forms, with a max yield of 3.9{plus minus}0.8% near 404nm.

  8. Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

    OpenAIRE

    Gamallo Belmonte, Pablo; González Pérez, Miguel; Huarte Larrañaga, Fermín

    2013-01-01

    The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction N...

  9. 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.

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

    International Nuclear Information System (INIS)

    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

  11. Dynamical Monte Carlo methods for plasma-surface reactions

    Science.gov (United States)

    Guerra, Vasco; Marinov, Daniil

    2016-08-01

    Different dynamical Monte Carlo algorithms to investigate molecule formation on surfaces are developed, evaluated and compared with the deterministic approach based on reaction-rate equations. These include a null event algorithm, the n-fold way/BKL algorithm and an ‘hybrid’ variant of the latter. NO2 formation by NO oxidation on Pyrex and O recombination on silica with the formation of O2 are taken as case studies. The influence of the grid size on the CPU calculation time and the accuracy of the results is analysed. The role of Langmuir–Hinsehlwood recombination involving two physisorbed atoms and the effect of back diffusion and its inclusion in a deterministic formulation are investigated and discussed. It is shown that dynamical Monte Carlo schemes are flexible, simple to implement, describe easily elementary processes that are not straightforward to include in deterministic simulations, can run very efficiently if appropriately chosen and give highly reliable results. Moreover, the present approach provides a relatively simple procedure to describe fully coupled surface and gas phase chemistries.

  12. Femtosecond stimulated Raman spectroscopy of ultrafast biophysical reaction dynamics

    Science.gov (United States)

    McCamant, David William

    2004-12-01

    I have developed the technique of femtosecond stimulated Raman spectroscopy (FSRS), which enables the rapid acquisition of vibrational spectra with optical excitation to S2 (1Bu +) the molecule relaxes to S1 in 160 fs where it undergoes rapid two-step IVR with 200- and 450-fs time constants. In later work, the FSRS spectrum of S2 beta-carotene was observed, which consists of three intense and broad bands at ˜1100, 1300 and 1650 cm-1 that exhibit kinetics matching the decay of the S2 near-infrared absorption. These data show that there is no additional intermediate 1B u- electronic state involved in the relaxation pathway of beta-carotene. FSRS was also used to study the photoisomerization dynamics in bacteriorhodopsin (bR). Spectra obtained during bR's excited state lifetime exhibit dispersive lineshapes at the ground-state frequencies that decay in 250 fs and are attributed to a nonlinear emission process. This relaxation is significantly faster than the decay of the stimulated emission (˜500 fs), indicating that the excited population moves away from the ground-state geometry in 250 fs. Spectral changes between 1.5 to 100 ps reveal that a significant fraction of the isomerization occurs on the ground state photoproduct surface. The many benefits FSRS will make it a valuable tool for vibrational spectroscopy of reaction dynamics in ultrafast photochemical and photophysical processes.

  13. The power-law reaction rate coefficient for barrierless reactions

    OpenAIRE

    Yin, Cangtao; Du, Jiulin

    2014-01-01

    The power-law reaction rate coefficient for the barrierless reactions is studied if the reactions take place in systems with power-law distributions, and a generalized rate formula for the barrierless reactions in Gorin model is derived. We show that due to barrierless, different from those for bimolecular and unimolcular reactions, the power-law rate coefficient for the barrierless reactions does not have the factor of power-law distribution function and thus it is not very strongly dependen...

  14. 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

  15. Bimolecular recombination and complete photocurrent decay in metallophthalocyanine thin films

    Science.gov (United States)

    Noah, Ramsey S.

    Metallophthalocyanines (MPc) are a class of planar small molecule semiconductors that are of great interest due to their applications in organic solar cells. However, a thorough understanding of many of their charge transport properties, especially those related to trap states, is lacking. In previous works the increase of grain size in MPc thin films with higher substrate temperature during the thermal evaporation process was quantified. Here, we investigate the charge transport properties of phthalocyanine with varying grain sizes in five ways: 1) intensity-varied photocurrent measurements are used to study the order of recombination in zinc phthalocyanine (ZnPc) thin films; 2) the conduction dependence on oxygen doping in copper phthalocyanine (CuPc) and ZnPc is investigated through oxygen deprivation in a closed-cycle refrigerator; 3) the complete photocurrent decay in CuPc and ZnPc is explored; 4) the bandgap of CuPc and ZnPc is derived from wide temperature range (˜ 80K - 351K) resistance measurements; 5) thermally stimulated currents (TSC) in CuPc and ZnPc are induced using a modified Reber methodology. An explanation for oxygen doping in these type of thin films is presented and in addition to bimolecular recombination a second model is also applied to measurements of intensity-varied photocurrent. Our data suggest several interesting aspects of the charge transport properties in these organic semiconductors. Recombination may not be dominated by monomolecular processes but instead bimolecular. More amorphous (low deposition temperature) samples show a greater change in conductivity due to oxygen doping. The photocurrent of more crystalline samples decays more rapidly compared to amorphous samples, suggesting that deeper trap states are present in lower deposition temperature samples. The bandgap derived from temperature-varied resistance measurements is systematically low due to slow detrapping. Unlike TSC measurements in micrometer-thick organic films

  16. Study of the reaction dynamics of dissipative heavy ion reactions by a kinematical coincidence apparature and γ circular polarimeters

    International Nuclear Information System (INIS)

    The reaction dynamics of dissipative heavy ion reactions is studied by measurement of the circular polarization of the γ radiation which is emitted by the highly excited reaction products. The object of these measurements were the systems 86Kr+139La and 86Kr+166Er at incident energies of 705 MeG and 860 MeV. The experiments were performed at the heavy ion accelerator UNILAC of the GSI. From the measured γ circular polarizations the spin polarizations of the reaction fragments in direction of the scattering norm were obtained. (orig./HSI)

  17. Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS.

    Science.gov (United States)

    Zhang, Fan; Chen, Nanhao; Wu, Ruibo

    2016-05-23

    The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery. PMID:27082764

  18. Isospin dynamics on neck fragmentation in isotopic nuclear reactions

    CERN Document Server

    Feng, Zhao-Qing

    2016-01-01

    The neck dynamics in Fermi-energy heavy-ion collisions, to probe the nuclear symmetry energy in the domain of sub-saturation densities, is investigated within an isospin dependent transport model. The single and double ratios of neutron/proton from free nucleons and light clusters (complex particles) in the isotopic reactions are analyzed systematically. Isospin effects of particles produced from the neck fragmentations are explored, which are constrained within the midrapidities ($|y/y_{proj}|<$0.3) and azimuthal angles (70$^{o}\\sim$110$^{o}$, 250$^{o}\\sim$290$^{o}$) in semiperipheral nuclear collisions. It is found that the ratios of the energetic isospin particles strongly depend on the stiffness of nuclear symmetry energy and the effects increase with softening the symmetry energy, which would be a nice probe for extracting the symmetry energy below the normal density in experimentally. A flat structure appears at the tail spectra from the double ratio distributions. The neutron to proton ratio of ligh...

  19. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Energy Technology Data Exchange (ETDEWEB)

    Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)

    2015-02-14

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  20. Can post-error dynamics explain sequential reaction time patterns?

    Directory of Open Access Journals (Sweden)

    StephanieGoldfarb

    2012-07-01

    Full Text Available We investigate human error dynamics in sequential two-alternative choice tasks. When subjects repeatedly discriminate between two stimuli, their error rates and mean reaction times (RTs systematically depend on prior sequences of stimuli. We analyze these sequential effects on RTs, separating error and correct responses, and identify a sequential RT tradeoff: a sequence of stimuli which yields a relatively fast RT on error trials will produce a relatively slow RT on correct trials and vice versa. We reanalyze previous data and acquire and analyze new data in a choice task with stimulus sequences generated by a first-order Markov process having unequal probabilities of repetitions and alternations. We then show that relationships among these stimulus sequences and the corresponding RTs for correct trials, error trials, and averaged over all trials are significantly influenced by the probability of alternations; these relationships have not been captured by previous models. Finally, we show that simple, sequential updates to the initial condition and thresholds of a pure drift diffusion model can account for the trends in RT for correct and error trials. Our results suggest that error-based parameter adjustments are critical to modeling sequential effects.

  1. Molecular Dynamics Simulations of Chemical Reactions for Use in Education

    Science.gov (United States)

    Qian Xie; Tinker, Robert

    2006-01-01

    One of the simulation engines of an open-source program called the Molecular Workbench, which can simulate thermodynamics of chemical reactions, is described. This type of real-time, interactive simulation and visualization of chemical reactions at the atomic scale could help students understand the connections between chemical reaction equations…

  2. Quantum-classical transition for an analog of double-slit experiment in complex collisions: Dynamical decoherence in quantum many-body systems

    OpenAIRE

    Benet, L.; Chadderton, L. T.; Kun, S. Yu.; Qi, Wang

    2006-01-01

    We study coherent superpositions of clockwise and anti-clockwise rotating intermediate complexes with overlapping resonances formed in bimolecular chemical reactions. Disintegration of such complexes represents an analog of famous double-slit experiment. The time for disappearance of the interference fringes is estimated from heuristic arguments related to fingerprints of chaotic dynamics of a classical counterpart of the coherently rotating complex. Validity of this estimate is confirmed num...

  3. Visualization of protein interactions in living Drosophila embryos by the bimolecular fluorescence complementation assay

    Directory of Open Access Journals (Sweden)

    Merabet Samir

    2011-01-01

    Full Text Available Abstract Background Protein interactions control the regulatory networks underlying developmental processes. The understanding of developmental complexity will, therefore, require the characterization of protein interactions within their proper environment. The bimolecular fluorescence complementation (BiFC technology offers this possibility as it enables the direct visualization of protein interactions in living cells. However, its potential has rarely been applied in embryos of animal model organisms and was only performed under transient protein expression levels. Results Using a Hox protein partnership as a test case, we investigated the suitability of BiFC for the study of protein interactions in the living Drosophila embryo. Importantly, all BiFC parameters were established with constructs that were stably expressed under the control of endogenous promoters. Under these physiological conditions, we showed that BiFC is specific and sensitive enough to analyse dynamic protein interactions. We next used BiFC in a candidate interaction screen, which led to the identification of several Hox protein partners. Conclusion Our results establish the general suitability of BiFC for revealing and studying protein interactions in their physiological context during the rapid course of Drosophila embryonic development.

  4. Dynamical resonance in F+H2 chemical reaction and rotational excitation effect

    Institute of Scientific and Technical Information of China (English)

    YANG XueMing; XIE DaiQian; ZHANG DongHui

    2007-01-01

    Reaction resonance is a frontier topic in chemical dynamics research, and it is also essential to the understanding of mechanisms of elementary chemical reactions. This short article describes an important development in the frontier of research. Experimental evidence of reaction resonance has been detected in a full quantum state resolved reactive scattering study of the F+H2 reaction. Highly accurate full quantum scattering theoretical modeling shows that the reaction resonance is caused by two Feshbach resonance states. Further studies show that quantum interference is present between the two resonance states for the forward scattering product. This study is a significant step forward in our understanding of chemical reaction resonance in the benchmark F+H2 system. Further experimental studies on the effect of H2 rotational excitation on dynamical resonance have been carried out. Dynamical resonance in the F+H2 (j = 1) reaction has also been observed.

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

    International Nuclear Information System (INIS)

    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

  6. Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

    International Nuclear Information System (INIS)

    A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies

  7. Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach

    Energy Technology Data Exchange (ETDEWEB)

    Adomaitis, Raymond A., E-mail: adomaiti@umd.edu [Department of Chemical and Biomolecular Engineering, Institute for Systems Research, University of Maryland, College Park, Maryland 20742 (United States)

    2016-01-15

    A set of numerical tools for the analysis and dynamic dimension reduction of chemical vapor and atomic layer deposition (ALD) surface reaction models is developed in this work. The approach is based on a two-step process where in the first, the chemical species surface balance dynamic equations are factored to effectively decouple the (nonlinear) reaction rates, a process that eliminates redundant dynamic modes and that identifies conserved quantities. If successful, the second phase is implemented to factor out redundant dynamic modes when species relatively minor in concentration are omitted; if unsuccessful, the technique points to potential model structural problems. An alumina ALD process is used for an example consisting of 19 reactions and 23 surface and gas-phase species. Using the approach developed, the model is reduced by nineteen modes to a four-dimensional dynamic system without any knowledge of the reaction rate values. Results are interpreted in the context of potential model validation studies.

  8. Direct Dynamics Study on CH2O + CH·3 → CHO + CH4 Reaction

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    It is still a formidable challenge to study CH2O + CH·3 → CHO + CH4 reaction in the gas phase by traditional dynamics, because of the large number of freedom degrees for the system.In this paper, direct dynamics, in which trajectories were run directly on the DFT potential energy surface, have been applied to the reaction, which gave a direct look in the reaction processes.Two sets of trajectories at different initial orientations of reactants and temperature have been simulated. And the detailed reaction mechanisms have been described.

  9. An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction

    Science.gov (United States)

    Yu, Hua-Gen

    2011-08-01

    We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.

  10. Fission as a probe to understand heavy ion reaction mechanism and dynamics

    International Nuclear Information System (INIS)

    The study of nucleus-nucleus collisions provides a way to learn about the nuclear equilibration process in several collective degrees of freedom of much physical significance and their characteristics relaxation times. The reactions resulting from nucleus-nucleus collisions at intermediate energies can be broadly classified in four types: elastic (and quasi elastic) reaction, dinucleus reactions involving deep inelastic collisions, non-compound nucleus fusion reactions like fast-fission, quasi-fission and pre-equilibrium fission and true compound nucleus reactions. Experimentally, it is not always possible to identify uniquely the reaction products as belonging to the pre or post compound nucleus phase. This often leads to apparent anomaly in the interpretation of some of the experimental results in heavy ion reaction studies. Measurements of various observables in fission-like reactions provides information about the reaction mechanism and dynamics. Fission fragment angular distributions, which depend on the spin distributions and the shape parameters of the fissioning nucleus, give information about the fusion dynamics. Pre and post scission neutron multiplicities in fusion-fission reactions are used to determine pre-scission life times. Fragment-fragment angular correlation acts as a probe for linear momentum transfer characterising the reaction mechanism. The experimental results on the different aspects of the heavy ion fission studies and the information obtained on the dynamical features of the heavy ion collisions are summarised. (author). 36 refs., 12 figs

  11. Mass Action Dynamics of Coupled Reactions using Fluctuation Theory

    OpenAIRE

    Cannon, William R.; Baker, Scott E.

    2015-01-01

    Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary state...

  12. Uncertainty for calculating transport on Titan: a probabilistic description of bimolecular diffusion parameters

    CERN Document Server

    Plessis, Sylvain; Mandt, Kathy; Greathouse, Thomas; Luspay-Kuti, Adrienn

    2015-01-01

    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 u...

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

    International Nuclear Information System (INIS)

    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. 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: 1.972, year: 2014

  15. HYTAR : a Hybrid Telescope Array for Reaction dynamics

    International Nuclear Information System (INIS)

    HYTAR is an array of Hybrid detector telescopes developed at IUAC for the study of reaction mechanisms around coulomb barrier. The hybrid detector module is a combination of gas (ΔE) and silicon detector (stopping). They have been developed for heavy ion detection and particle identification in nuclear physics experiments in GPSC/NAND facility at IUAC. Currently the array has 13 such telescopes. The detector telescopes have been earlier used for studying the angular distribution of fission fragments. The detector system can also be used to identify projectile like fragments and thus can be used for studying quasi-elastic scattering, transfer and breakup reactions

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

    International Nuclear Information System (INIS)

    Isotopically resolved yields of particles and complex fragments from 12C and 18O induced reactions on 53Ni, 54Ni, Ag, and 197Au 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.)

  17. Theoretical studies of the dynamics of chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, A.F. [Argonne National Laboratory, IL (United States)

    1993-12-01

    Recent research effort has focussed on several reactions pertinent to combustion. The formation of the formyl radical from atomic hydrogen and carbon monoxide, recombination of alkyl radicals and halo-alkyl radicals with halogen atoms, and the thermal dissociation of hydrogen cyanide and acetylene have been studied by modeling. In addition, the inelastic collisions of NCO with helium have been investigated.

  18. Static and dynamic fusion barriers in heavy-ion reactions

    International Nuclear Information System (INIS)

    We have calculated the potential energy of two interacting nuclei within the liquid-drop model including the nuclear proximity energy. We use a two-parameter family of shapes which simply describes the path leading from two separated nuclei to the spherical compound nucleus. Double-humped fusion barriers appear when Z1Z2> or approx.1800+-100. The inner barrier is the highest for Z1Z2> or approx.2300+-100. The existence and the shape of the external minimum may be at origin of the development of fusion-fission or fast-fission phenomena. Our phenomenological dynamic model depends only on one parameter: the radial friction coefficient, fixed once and for all. The empirical barrier heights are very well reproduced. For very heavy systems (Z1Z2> or approx.2100+-100, alternatively (Z2/A)sub(eff)> or approx.38 or xsub(eff)> or approx.0.8), a dynamic fusion barrier appears, significantly higher than the static one and in close agreement with the experimental data. This dynamic barrier is mostly governed by the entrance channel, no evidence for dynamic deformations being found. The slope of the fusion cross sections is better reproduced if the angular momentum dissipation rule varies from the sticking limit for medium systems to the sliding limit for very heavy systems. The possibility of forming superheavy elements is strongly hindered by this double-humped dynamic barrier. (orig.)

  19. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Nichole Cates; Gysel, Roman; Sweetnam, Sean; McGehee, Michael D. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Cho, Eunkyung [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA (United States); Junk, Matthias J.N.; Chmelka, Bradley F. [Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA (United States); Risko, Chad; Kim, Dongwook; Bredas, Jean-Luc [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); Miller, Chad E. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States); Richter, Lee J.; Kline, R. Joseph [National Institute of Standards and Technology, Gaithersburg, MD (United States); Heeney, Martin; McCulloch, Iain [Department of Chemistry, Imperial College London (United Kingdom); Amassian, Aram [King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal (Saudi Arabia); Acevedo-Feliz, Daniel; Knox, Christopher [King Abdullah University of Science and Technology (KAUST), Visualization Core Laboratory, Thuwal (Saudi Arabia); Hansen, Michael Ryan; Dudenko, Dmytro [Max Planck Institute for Polymer Research, Mainz (Germany); Toney, Michael F. [Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States)

    2012-11-27

    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 copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. 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.

  2. Reaction dynamics for fusion of weakly-bound nuclei

    OpenAIRE

    Hagino, K.; Vitturi, A.

    2004-01-01

    We discuss several open problems of fusion reactions induced by weakly bound nuclei. For this purpose, we solve a one dimensional three-body Hamiltonian with the coupled-channels formalism. We show that the continuum-continuum couplings substantially reduce the total fusion probability at energies above the barrier compared with the no-breakup case, although the fusion probability remains enhanced at subbarrier energies. We then discuss a role of transfer process in fusion of weakly bound nuc...

  3. Space station structural dynamics/reaction control system interaction study

    Science.gov (United States)

    Pinnamaneni, M.; Murray, J.

    1987-01-01

    The performance of the Reaction Control System is impacted by the extreme flexibility of the space station structure. The method used to analyze the periodic thrust profile of a simple form of phase plane logic is presented. The results illustrate the effect on flexible body response of the type of phase plane logic utilized and the choice of control parameters: cycle period and attitude deadband.

  4. On the Compensation of Dynamic Reaction Forces in Stationary Machinery

    OpenAIRE

    Radermacher, Tobias; Lübbert, Jan; Weber, Jürgen

    2016-01-01

    This paper studies a method for active electrohydraulic force compensation in industrial scale high power applications. A valve controlled cylinder moves a mass using the force of inertia to compensate for the reaction forces of an industrial process. Two strategies for force compensation are developed and investigated in a 160 ton clamping unit of an injection moulding machine to significantly reduce the excitation. Results of the different strategies are shown and evaluated. Advantages and ...

  5. Ultrafast reaction dynamics and vibrational spectroscopy at surfaces

    OpenAIRE

    Hess, Christian

    2001-01-01

    A mechanistic understanding of the surface femtochemistry leading to the formation of hydrogen and the desorption and oxidation of CO from a Ru(001) single crystal surface is obtained by application of a variety of experimental methods. Among these are measurements of the translational energy distributions, two-pulse-correlations, isotope effects, and vibrational spectra of the reaction products after excitation with near-infrared (800 nm) femtosecond laser pulses. It is demonstrated t...

  6. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    Science.gov (United States)

    Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E

    2016-05-10

    Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks. PMID:26990904

  7. Low-energy heavy-ion reactions: a link between nuclear structure and reaction dynamics

    CERN Document Server

    Corradi, L; Beghini, S; Lin, C J; Montagnoli, G; Pollarolo, G; Scarlassara, F; Segato, G F; Stefanini, A M; Zheng, L F

    1999-01-01

    High precision data recently obtained in the study of multinucleon transfer and sub-barrier fusion reactions at LNL are presented. The studies of transfer channels in the systems sup 4 sup 0 sup , sup 4 sup 8 Ca+ sup 1 sup 2 sup 4 Sn and sup 6 sup 4 Ni+ sup 2 sup 3 sup 8 U revealed important effects not identified in the past, and demonstrated the possibility of a quantitative understanding of the role played by the various degrees of freedom in the reaction mechanism. Evidence of their influence on the fusion enhancements seem to show-up in the systems sup 4 sup 0 Ca+ sup 1 sup 2 sup 4 sup , sup 1 sup 1 sup 6 Sn and sup 4 sup 0 Ca+ sup 9 sup 0 sup , sup 9 sup 6 Zr, but, in general, the data still escape a consistent treatment.

  8. 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.

  9. Structural parameter identifiability analysis for dynamic reaction networks

    DEFF Research Database (Denmark)

    Davidescu, Florin Paul; Jørgensen, Sten Bay

    2008-01-01

    A fundamental problem in model identification is to investigate whether unknown parameters in a given model structure potentially can be uniquely recovered from experimental data. This issue of global or structural identifiability is essential during nonlinear first principles model development...... 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...

  10. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

    Bratu, P.; Brenig, W.; Gross, A.; Hartmann, M.; Höfer, U.; Kratzer, Peter; Russ, R.

    1996-01-01

    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...... 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...... five-dimensional model is presented taking lattice distortion, corrugation, and molecular vibrations into account within the framework of coupled-channel calculations. While the temperature dependence of the sticking is dominated by lattice distortion, the main effect of corrugation is a reduction of...

  11. 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...

  12. Electron-Wavepacket Reaction Dynamics in Proton Transfer of Formamide

    Science.gov (United States)

    Nagashima, Kengo; Takatsuka, Kazuo

    2009-10-01

    We apply the semiclassical Ehrenfest theory, which provides electron wavepacket dynamics coupled to nuclear motion, to a study of water-assisted proton relay in formamide compared with a forced proton transfer in gas phase, both of which are associated with the tautomerization. We start with the enol (imidic acid) form HO-CH═NH and track its proton transfer process to the keto (amide) form O═CH-NH2. Identifying the fact that this is indeed a "proton transfer process" rather than hydrogen-atom migration in terms of radical character on the proton, we show a collective quantum flux of electrons, which flows backward against the proton motion. This backward flux compensates the electrons tightly covering the proton, as represented in the Mulliken charge. The enol form formamide is one of the simplest species in the group O═CR1-NHR2, which is a unit of polypeptide. In the gas phase, the nitrogen atom may have a pyramidal structure as in the ammonium molecule; therefore, the C-N bond may allow low barrier rotation along it. This rotation is strongly prohibited by the formation of the double bond C═N induced by the proton transfer. Not only the dynamical process of proton transfer itself but also the electronic structures left behind are greatly affected by the presence of water molecule(s) and polar solvents. In discussing the relative stability of the formamide after the proton transfer, the following resonance structures are frequently mentioned, O--CH═N+H2 ↔ O═CH-NH2. Here we address the dynamical manifestation of the resonance structures in terms of our dynamical electron theory.

  13. Reduction of dynamical biochemical reactions networks in computational biology

    OpenAIRE

    Radulescu, O.; Gorban, A.N.; Zinovyev, A.; Noel, V.

    2012-01-01

    Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to...

  14. Optimal Sampling of a Reaction Coordinate in Molecular Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2005-01-01

    Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.

  15. Dynamics of fluctuations in a reactive system of low spatial dimension

    Science.gov (United States)

    Prakash, S.; Nicolis, G.

    1996-01-01

    We study, using master equation techniques, the time evolution of the average concentration and fluctuations in the two-species n-molecule reaction A+( n-1) X⇌ nX in one dimension described by a Glauber-type dynamical lattice model for the specific cases n=2 (bimolecular) and n=3 (trimolecular). The evolution is found to be quite different from that described by the Mean-Field equations even for the bimolecular case, where the steady state is meanfield. For the trimolecular process, the values of fluctuation correlations in the nonequilibrium steady state are well predicted by the fixed points of the dynamical equations obtained from the master equation. In addition, three-point fluctuation correlations are found to play an important role in both processes and are accounted for by an extended Bethe-type ansatz. The bimolecular system shows no memory effects of initial conditions, while the trimolecular system is characterized by memory effects in terms of the average concentration, fluctuations as well as the entropy. The spatial decay of fluctuation correlations is found to be short range at the steady state for the trimolecular system.

  16. 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.

  17. The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak

    Directory of Open Access Journals (Sweden)

    Jing Li

    2014-01-01

    Full Text Available The stability and bifurcations of multiple limit cycles for the physical model of thermonuclear reaction in Tokamak are investigated in this paper. The one-dimensional Ginzburg-Landau type perturbed diffusion equations for the density of the plasma and the radial electric field near the plasma edge in Tokamak are established. First, the equations are transformed to the average equations with the method of multiple scales and the average equations turn to be a Z2-symmetric perturbed polynomial Hamiltonian system of degree 5. Then, with the bifurcations theory and method of detection function, the qualitative behavior of the unperturbed system and the number of the limit cycles of the perturbed system for certain groups of parameter are analyzed. At last, the stability of the limit cycles is studied and the physical meaning of Tokamak equations under these parameter groups is given.

  18. The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak

    Science.gov (United States)

    Li, Jing; Quan, Tingting; Zhang, Wei; Deng, Wei

    2014-01-01

    The stability and bifurcations of multiple limit cycles for the physical model of thermonuclear reaction in Tokamak are investigated in this paper. The one-dimensional Ginzburg-Landau type perturbed diffusion equations for the density of the plasma and the radial electric field near the plasma edge in Tokamak are established. First, the equations are transformed to the average equations with the method of multiple scales and the average equations turn to be a Z2-symmetric perturbed polynomial Hamiltonian system of degree 5. Then, with the bifurcations theory and method of detection function, the qualitative behavior of the unperturbed system and the number of the limit cycles of the perturbed system for certain groups of parameter are analyzed. At last, the stability of the limit cycles is studied and the physical meaning of Tokamak equations under these parameter groups is given. PMID:24892099

  19. Three-dimensional wave packet dynamics of H2 + D2 reaction

    International Nuclear Information System (INIS)

    Research highlights: → Three-dimensional wave packet dynamics of H2(v1 = high) + D2(v2 = low) reaction. → Competitive processes were studied on the BMKP and ASP potential energy surfaces. → Orientation of the cold diatom did not greatly affect the reaction processes. → Orientation of the hot diatom had a significant effect on the reaction processes. → Reaction probabilities for H2 + D2 reaction were compared with H2 + H2 reaction. - Abstract: Initial state selected time-dependent wave packet calculations were carried out for the H2(v1 = high) + D2(v2 = low) reaction within a three degrees of freedom model. The probabilities for different competitive processes were studied on two realistic global potential energy surfaces (PESs) - BMKP and ASP. The orientation of the cold diatom did not greatly affect the reaction processes, while the orientation of the hot diatom had a significant effect. The BMKP surface generally gave lower energy thresholds than the ASP surface, except for the collision induced dissociation (CID) within the TII geometry where the hot diatom comes in head-on perpendicular to the cold diatom. Isotopic substitution effects were studied on the recent BMKP PES. The H2 + D2 reaction was more effective for CID and showed more structured probability curves for single exchange reaction (SE) and three-body complex formation (3BC) than the H2 + H2 reaction.

  20. A general expression for bimolecular association rates with orientational constraints

    CERN Document Server

    Schlosshauer, M; Schlosshauer, Maximilian; Baker, David

    2002-01-01

    We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact and properly aligned to within specified angular tolerances. This extends and generalizes previous approaches that considered only axially symmetric patches; the earlier solutions are shown to be limiting cases of our general expression. Previous numerical results on the rate of protein-protein association with high steric specificity are in very good agreement with the value computed from our analytic expression. Using the new expression, we investigate the influence of orientational constraints on the rate constant. We find that for angular constraints of ~5-15 degrees, a typical range for example in the case of protein-protein interactions, the reaction rate is about 2 to 3 orders of magnitude higher than expected from a simple geometric model.

  1. Crossed molecular beam studies of unimolecular reaction dynamics. [Angular and velocity distributions

    Energy Technology Data Exchange (ETDEWEB)

    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/sub 3/I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol/sup -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.

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

    Science.gov (United States)

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

    2008-06-01

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

  3. Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics

    Institute of Scientific and Technical Information of China (English)

    徐峥; 安田启司; 刘晓峻

    2015-01-01

    In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves.

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

    International Nuclear Information System (INIS)

    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 S1 → S0 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)

  5. 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.

  6. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    Science.gov (United States)

    Benjamin, Ilan; Pohorille, Andrew

    1993-01-01

    The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

  7. Averaging methods for stochastic dynamics of complex reaction networks: description of multi-scale couplings

    CERN Document Server

    Plyasunov, S

    2005-01-01

    This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and elimination of degrees of freedom via the renormalization of transition rates of slow reactions. The method suggested in this work is more general than other approaches presented previously: it is not limited to a particular type of stochastic processes and can be applied to different types of processes describing fast dynamics, and also provides crossover to the case when separation of time scales is not well pronounced. We derive a family of exact fluctuation-dissipation relations which establish the connection between effective rates and the statistics of the reaction events in fast reaction channels. An illustration of the technique is provided. Examples show that renormalized transition rates exhibit in general non-exponential relaxation behavior with a broad range of pos...

  8. 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.

  9. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    Science.gov (United States)

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. PMID:26747638

  10. Structural dynamics effects on the ultrafast chemical bond cleavage of a photodissociation reaction

    OpenAIRE

    Corrales, Maria E.; Loriot, Vincent; Balerdi, Garikoitz; González-Vázquez, Jesús; de Nalda, Rebeca; Bañares, Luis; Zewail, Ahmed H.

    2014-01-01

    The correlation between chemical structure and dynamics has been explored in a series of molecules with increasing structural complexity in order to investigate its influence on bond cleavage reaction times in a photodissociation event. Femtosecond time-resolved velocity map imaging spectroscopy reveals specificity of the ultrafast carbon–iodine (C–I) bond breakage for a series of linear (unbranched) and branched alkyl iodides, due to the interplay between the pure reaction coordinate and the...

  11. Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region

    Energy Technology Data Exchange (ETDEWEB)

    T.-S. H. Lee; A. Matsuyama; T. Sato

    2006-11-15

    A dynamical coupled-channel model is presented for investigating the nucleon resonances (N*) in the meson production reactions induced by pions and photons. Our objective is to extract the N* parameters and to investigate the meson production reaction mechanisms for mapping out the quark-gluon substructure of N* from the data. The model is based on an energy-independent Hamiltonian which is derived from a set of Lagrangians by using a unitary transformation method.

  12. Study of reaction dynamics in 16O+115In system using recoil range distribution

    International Nuclear Information System (INIS)

    The study of reaction dynamics of heavy ion (HI) induced reactions has been a topic of interest at incident energies from Coulomb barrier to 7 MeV/ nucleon. The Incomplete Fusion (ICF) reactions had been observed for the first time by H.C. Britt and A.R. Quinton at 10.5 MeV/nucleon energy. But recent studies show that the ICF competes with Complete Fusion (CF) even at energies just above the Coulomb barrier. It has been observed that ICF reaction dynamics depends on various entrance channel effects such as projectile energy, mass asymmetry of interacting ions and input angular momentum. To study the comparison between CF and ICF, Forward Recoil Range Distribution (FRRD) is used as a probe. Moreover, CF and ICF products can be disentangled on the basis of recoil velocity of reaction products, depending upon the degree of linear momentum transfer. Hence, the present work is carried out to study the interplay between CF and ICF reaction dynamics, using recoil range distribution in 16O+115In system at about 102 MeV energy

  13. End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide.

    Science.gov (United States)

    Cheng, Ryan R; Makarov, Dmitrii E

    2010-03-11

    The dynamics of surface-attached polymers play a key role in the operation of a number of biological sensors, yet its current understanding is rather limited. Here we use computer simulations to study the dynamics of a reaction between the free end of a polymer chain and a surface, to which its other end has been attached. We consider two limiting cases, the diffusion-controlled limit, where the reaction is accomplished whenever the free chain end diffuses to within a specified distance from the surface, and the reaction-controlled limit, where slow, intrinsic reaction kinetics rather than diffusion of the chain is rate limiting. In the diffusion-controlled limit, we find that the overall rate scales as N(-b), where N is the number of monomers in the chain and b approximately = 2.2 for excluded volume chains. This value of the scaling exponent b is close to that derived from a simple approximate theory treating the dynamics of the chain end relative to the surface as one-dimensional diffusion in an effective potential. In the reaction-controlled limit, the value of the scaling exponent b is close to 1. We compare our findings with those for the related (and better studied) problem of end-to-end reactions within an unconstrained polymer chain and discuss their implications for electrochemical DNA sensors. PMID:20151703

  14. Dislocation-dislocation and dislocation-twin reactions in nanocrystalline Al by molecular-dynamics simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Yamakov, V.; Wolf, D.; Phillpot, S. R.; Gleiter, H.; Materials Science Division; Forschungszentrum Karlsruhe

    2003-08-15

    We use massively parallel molecular dynamics simulations of polycrystal plasticity to elucidate the intricate dislocation dynamics that evolves during the process of deformation of columnar nanocrystalline Al microstructures of grain size between 30 and 100 nm. We analyze in detail the mechanisms of dislocation-dislocation and dislocation-twin boundary reactions that take place under sufficiently high stress. These reactions are shown to lead to the formation of complex twin networks, i.e. structures of coherent twin boundaries connected by stair-rod dislocations. Consistent with recent experimental observations, these twin networks may cause dislocation pile-ups and thus give rise to strain hardening.

  15. Modification of an amplification reaction in recursively dynamic compartments driven by stirring.

    Science.gov (United States)

    Ichii, Tetsuo; Tanahashi, Genya; Suzuki, Hiroaki; Yomo, Tetsuya

    2013-12-17

    In living systems, biochemical reactions are confined to cellular or subcellular compartments, such as the plasma membrane and the organelles within a cell. These biological compartments are usually subjected to recursive changes, such as combinations of growth, fusion, and division, to constitute repeating cell cycles. In such recursively dynamic compartments, the encapsulated biochemical reaction may exhibit dynamics that differ from those of the static compartment (i.e., test tubes) used in conventional biochemistry experiments. To test this hypothesis in a simplified model, we mechanically stirred femtoliter-sized water-in-oil emulsion droplets so that individual droplets were subjected to repeated coalescence and breakage. We show that recursive dynamics appeared in the emulsion, which were measured by the exponential propagation of a water-soluble dye. The rate of the propagation, μ, was controlled by modulating the pulse-width of stirring in an electromagnetic stirrer. Within this system, we studied the dynamics of an RNA-amplification reaction in recursively increasing reaction compartments at various values of μ. We showed that there was an optimal value of μ that maximized RNA amplification. This effect was explained by the balance between the opposing effects of supply of substrate and the dilution of amplified RNA both resulting from coalescence. Moreover, when we mixed two RNA species with different kinetic properties, we found a preferential amplification for one of the species only in the recursively dynamic emulsion. This effect was partly explained by a separation effect which preferentially amplifies the number of compartments for the molecular specie that can better follow the breakage dynamics of the compartments. The present work demonstrated how the recursive dynamics of compartments modifies the internal biochemical reaction. PMID:24219119

  16. Molecular dynamic simulation of thermite reaction of Al nanosphere/Fe2O3 nanotube

    Science.gov (United States)

    Zhu, Zhi-Yang; Ma, Bo; Tang, Cui-Ming; Cheng, Xin-Lu

    2016-01-01

    The letter presents thermite reactions of Al/Fe2O3 nanothermites simulated by using molecular dynamic method in combination with ReaxFF. The variations in chemical bonds are measured to elaborate reaction process and characterize ignition performance. It is found that the longer interval is, the higher ignition temperature and the longer ignition delay system has. Additionally, the heating rate has much effect on ignition temperature. Under the temperature of 1450 K, oxygen is directly released from hematite nanotube, thermite reaction is deemed as a multiphase process. And, release energy of System2 is about 3.96 kJ/g. However, much energy rises from alloy reaction. Thermite reactions do not follow the theoretical equation, but are a complicated process.

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

    International Nuclear Information System (INIS)

    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.)

  18. The ultrafast reaction dynamics of hydrogen and interfacial structure of water on the Ru(001)-surface

    OpenAIRE

    Denzler, Daniel N.

    2003-01-01

    The goal of this work is to acquire detailed insight into the fundamental interaction mechanisms in surface chemistry and physics. Therefore the dynamic and static-structural properties of two prototypical adsorbate systems have been investigated: The ultrafast reaction dynamics of hydrogen on the Ru(001)-surface, and the interfacial structure of water on Ru(001). The investigation of the recombinative hydrogen formation according to Had+Had -> H2,gas was performed by irradiation...

  19. Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects

    OpenAIRE

    Ramsey, S. A.; Hu, B. L.

    1997-01-01

    We present a detailed and systematic analysis of the nonperturbative, nonequilibrium dynamics of a quantum field in the reheating phase of inflatonary cosmology, including full back reactions of the quantum field on the curved spacetime, as well as the fluctuations on the mean field. We use the O(N) field theory with unbroken symmetry in a spatially flat FRW universe to study the dynamics of the inflaton in the post-inflaton, preheating stage. Oscillations of the inflaton's zero mode induce p...

  20. Bimolecular fluorescence complementation analysis of eukaryotic fusion products

    OpenAIRE

    Lin, Ho-Pi; Vincenz, Claudius; Eliceiri, Kevin W.; Kerppola, Tom K.; Ogle, Brenda M.

    2010-01-01

    Background information. Cell fusion is known to underlie key developmental processes in humans and is postulated to contribute to tissue maintenance and even carcinogenesis. The mechanistic details of cell fusion, especially between different cell types, have been difficult to characterize because of the dynamic nature of the process and inadequate means to track fusion products over time. Here we introduce an inducible system for detecting and tracking live cell fusion products in vitro and ...

  1. Measurement of the rate of bimolecular electron spin relaxation between pairs of reactive radicals using time-resolved electron spin-echo spectroscopy

    International Nuclear Information System (INIS)

    The time-resolved electron spin echo (ESE) method has been employed to measure the bimolecular contribution to electron spin relaxation in the acetate radical xCH2CO-2, formed by pulse radiolysis. Time-resolved ESE signals from solutions containing up to 4 x 10-4 M initial radical concentrations were analyzed using Bloch equations modified to include the effects of strong Heisenberg exchange, chemical reaction, and CIDEP. It is found that the electron exchange rate is approx.3 times faster than the chemical reaction rate, contrary to a simple model involving only statistical factors which predicts equal rates for the two processes. It is also found that the CIDEP enhancement factor is independent of initial radical concentration over the ten fold range of concentrations studied

  2. 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.

  3. Mechanisms of oxygen reduction reactions for carbon alloy catalysts via first principles molecular dynamics

    International Nuclear Information System (INIS)

    Carbon alloy catalysts (CACs) are one of promising candidates for platinum-substitute cathode catalysts for polymer electrolyte fuel cells. We have investigated possible mechanisms of oxygen reduction reactions (ORRs) for CACs via first-principles-based molecular dynamics simulations. In this contribution, we review possible ORRs at likely catalytic sites of CACs suggested from our simulations. (author)

  4. 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 c...

  5. 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: 1.972, year: 2014

  6. Dynamics of the Spiral Tip in a Closed Belousov-Zhabotinsky Reaction

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hui-Jie; WANG Peng-Ye; ZHAO Ying-Ying

    2005-01-01

    @@ Dynamics of spiral tip rotating in a closed system of the light sensitive Belousov-Zhabotinsky reaction is studied under a homogeneous and steady illumination. The time dependence of the kinematical parameters of meandering spiral is presented and the experimental evidence is obtained for self-synchronization of the spiral tip in a closed B-Z system without external feedback.

  7. Fusion and quasi-fission dynamics in nearly-symmetric reactions

    Science.gov (United States)

    Wang, Ning; Zhao, Kai; Li, ZhuXia

    2015-11-01

    Some nearly-symmetric fusion reactions are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. By introducing two-body inelastic scattering in the Fermi constraint procedure, the stability of an individual nucleus and the description of fusion cross sections at energies near the Coulomb barrier can be further improved. Simultaneously, the quasifission process in 154Sm+160Gd is also investigated with the microscopic dynamics model for the first time. We find that at energies above the Bass barrier, the fusion probability is smaller than 10-5 for this reaction, and the nuclear contact time is generally smaller than 1500 fm/ c. From the central collisions of Sm+Gd, the neutron-rich fragments such as 164,165Gd, 192W can be produced in the ImQMD simulations, which implies that the quasi-fission reaction could be an alternative way to synthesize new neutron-rich heavy nuclei.

  8. Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field

    Institute of Scientific and Technical Information of China (English)

    DU Jiulin; SHEN Hong

    2005-01-01

    The coupling of the sun's gravitational field with processes of diffusion and convection exerts a significant influence on the dynamical behavior of the core 3He nuclear reaction-diffusion system. Stability analyses of the system are made in this paper by using the theory of nonequilibrium dynamics. It is showed that, in the nuclear reaction regions extending from the center to about 0.38 times of the radius of the sun, the gravitational field enables the core 3He nuclear reaction-diffusion system to become unstable and, after the instability, new states to appear in the system have characteristic of time oscillation. This may change the production rates of both 7Be and 8B neutrinos.

  9. Fusion and quasi-fission dynamics in nearly-symmetric reactions

    CERN Document Server

    Wang, Ning; Li, Zhuxia

    2015-01-01

    Some nearly-symmetric fusion reactions are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. By introducing two-body inelastic scattering in the Fermi constraint procedure, the stability of an individual nucleus and the description of fusion cross sections at energies near the Coulomb barrier can be further improved. Simultaneously, the quasi-fission process in $^{154}$Sm+$^{160}$Gd is also investigated with the microscopic dynamics model for the first time. We find that at energies above the Bass barrier, the fusion probability is smaller than $10^{-5}$ for this reaction, and the nuclear contact-time is generally smaller than $1500$ fm/c. From the central collisions of Sm+Gd, the neutron-rich fragments such as $^{164,165}$Gd, $^{192}$W can be produced in the ImQMD simulations, which implies that the quasi-fission reaction could be an alternative way to synthesize new neutron-rich heavy nuclei.

  10. Dynamical Dipole mode in heavy-ion fusion reactions by using stable and radioactive beams

    International Nuclear Information System (INIS)

    The existence of the dynamical dipole mode in the 192Pb composite system was investigated through the study of its prompt decay employing the 40Ca + 152Sm and 48Ca + 144Sm reactions at E(lab)=11 and 10.1 MeV/u, respectively. The γ-rays and light charged particles were detected in coincidence with evaporation residues and fission fragments. First results of this experiment show that the dynamical dipole mode survives in collisions involving heavier mass reaction partners than those studied previously. As a fast cooling mechanism on the fusion path, the prompt dipole radiation could be of interest for the synthesis of super-heavy elements through 'hot' fusion reactions. Furthermore, by using radioactive beams and the prompt radiation as a probe we could get information on the symmetry energy at sub-saturation densities. (authors)

  11. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    Science.gov (United States)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  12. Quantum-classical transition for an analog of the double-slit experiment in complex collisions: Dynamical decoherence in quantum many-body systems

    International Nuclear Information System (INIS)

    We study coherent superpositions of clockwise and anticlockwise rotating intermediate complexes with overlapping resonances formed in bimolecular chemical reactions. Disintegration of such complexes represents an analog of a famous double-slit experiment. The time for disappearance of the interference fringes is estimated from heuristic arguments related to fingerprints of chaotic dynamics of a classical counterpart of the coherently rotating complex. Validity of this estimate is confirmed numerically for the H+D2 chemical reaction. Thus we demonstrate the quantum-classical transition in temporal behavior of highly excited quantum many-body systems in the absence of external noise and coupling to an environment

  13. Chiral Dynamics and Dubna-Mainz-Taipei Dynamical Model for Pion-Photoproduction Reaction

    CERN Document Server

    Yang, Shin Nan

    2010-01-01

    We demonstrate that the Dubna-Mainz-Taipei (DMT) meson-exchange dynamical model, which starts from an effective chiral Lagrangian, for pion photoproduction provides an excellent and economic framework to describe both the pi^0 threshold production and the Delta deformation, two features dictated by chiral dynamics.

  14. A Convergent Reaction-Diffusion Master Equation

    CERN Document Server

    Isaacson, Samuel A

    2012-01-01

    The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME has been shown to have the drawback of losing bimolecular reactions in the continuum limit that the lattice spacing approaches zero (in two or more dimensions). In this work we derive a new convergent RDME (CRDME) that eliminates this problem. The CRDME is obtained by finite volume discretization of a spatially-continuous stochastic reaction-diffusion model. We demonstrate the empirical numerical convergence of reaction time statistics associated with the CRDME. Although the reaction time statistics of the RDME diverge as the lattice spacing approaches zero, we show they approach those of the CRDME for sufficiently large lattice spacings or slow bimolecular reaction rates. As such, the RDME may be interpreted as an approximation to the CRDME in several asymptotic limits.

  15. On the study of nonlinear dynamics of complex chemical reaction systems

    Institute of Scientific and Technical Information of China (English)

    XIN; Houwen; HOU; Zhonghuai

    2006-01-01

    With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.

  16. Molecular dynamics study of phase separation in fluids with chemical reactions

    Science.gov (United States)

    Krishnan, Raishma; Puri, Sanjay

    2015-11-01

    We present results from the first d =3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A ⇌B ). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓeq) in the steady state suggests a power-law dependence on the reaction rate ɛ :ℓeq˜ɛ-θ with θ ≃1.0 .

  17. Molecular dynamics simulations of the reaction mechanism in Ni/Al reactive intermetallics

    International Nuclear Information System (INIS)

    We present an atomistic level description of the reaction mechanisms in thermally ignited samples of reactive core/shell Ni/Al wires. The combination of very long simulation times (up to 0.1 μs) and very reactive core/shell nanostructures enables ignition at unprecedentedly low temperatures for molecular dynamics simulations. Samples ignited at low temperatures (900 K or less) follow a multi-stage reaction process involving solid-phase diffusion and the formation of the B2 NiAl phase, while samples ignited at higher temperatures, follow a direct reaction path with accelerated diffusion of Ni into molten Al, leading to a completely molten final state. Interestingly, NiAl nucleates and grows under a significant concentration gradient, which may explain the absence of other phases like AlNi3. The formation of the B2 intermetallic slows atomic diffusion and consequently the reaction rates

  18. 7Be- and 8B-reaction dynamics at Coulomb barrier energies

    Science.gov (United States)

    Mazzocco, M.; Boiano, A.; Boiano, C.; La Commara, M.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Strano, E.; Torresi, D.; Yamaguchi, H.; Kahl, D.; Acosta, L.; Di Meo, P.; Fernandez-Garcia, J. P.; Glodariu, T.; Grebosz, J.; Guglielmetti, A.; Imai, N.; Hirayama, Y.; Ishiyama, H.; Iwasa, N.; Jeong, S. C.; Jia, H. M.; Keeley, N.; Kim, Y. H.; Kimura, S.; Kubono, S.; Lay, J. A.; Lin, C. J.; Marquinez-Duran, G.; Martel, I.; Miyatake, H.; Mukai, M.; Nakao, T.; Nicoletto, M.; Pakou, A.; Rusek, K.; Sakaguchi, Y.; Sánchez-Benítez, A. M.; Sava, T.; Sgouros, O.; Stefanini, C.; Soramel, F.; Soukeras, V.; Stiliaris, E.; Stroe, L.; Teranishi, T.; Toniolo, N.; Wakabayashi, Y.; Watanabe, Y. X.; Yang, L.; Yang, Y. Y.

    2016-05-01

    We investigated the reaction dynamics induced by the Radioactive Ion Beams 7Be and 8B on a 208Pb target at energies around the Coulomb barrier. The two measurements are strongly interconnected, being 7Be (Sα = 1.586 MeV) the loosely bound core of the even more exotic 8B (Sp = 0.1375 MeV) nucleus. Here we summarize the present status of the data analysis for the measurement of the elastic scattering process for both reactions and the preliminary results for the optical model analysis of the collected data.

  19. Spin distribution as a probe to investigate the dynamical effects in fusion reactions

    Directory of Open Access Journals (Sweden)

    Kaur Maninder

    2015-01-01

    Full Text Available The spin distributions are measured for the compound nucleus 80Sr populated in the reactions 16O+64Zn and 32S+48Ti. The comparison of the experimental results for both the systems shows that the mean γ-ray multiplicity values for the system 32S+48Ti are lower than those for 16O+64Zn. The spin distribution of the compound nucleus populated through the symmetric channel is also found to be lower than the asymmetric channel. Present investigation directly shows the effect of entrance channel mass asymmetry on the reaction dynamics.

  20. 7Be- and 8B-reaction dynamics at Coulomb barrier energies

    Directory of Open Access Journals (Sweden)

    Mazzocco M.

    2016-01-01

    Full Text Available We investigated the reaction dynamics induced by the Radioactive Ion Beams 7Be and 8B on a 208Pb target at energies around the Coulomb barrier. The two measurements are strongly interconnected, being 7Be (Sα = 1.586 MeV the loosely bound core of the even more exotic 8B (Sp = 0.1375 MeV nucleus. Here we summarize the present status of the data analysis for the measurement of the elastic scattering process for both reactions and the preliminary results for the optical model analysis of the collected data.

  1. Dynamics of Surface Exchange Reactions Between Au and Pt for HER and HOR

    DEFF Research Database (Denmark)

    Abrams, Billie; Vesborg, Peter Christian Kjærgaard; Bonde, Jacob Lindner;

    2009-01-01

    Cyclic voltammetric analysis of the Pt-on-Au system for hydrogen evolution and oxidation reactions (HER/HOR) indicates that dynamic surface exchange reactions occur between Pt and Au. HER/HOR activities depend on the dominant surface species present, which is controllable by the potential applied...... electrode, NHE, at pH 0). Following deactivation, the system can be reactivated by cycling above this potential, giving an activation potential of ~+1.0 V vs NHE. This deactivation/reactivation can be cycled repeatedly and occurs for various forms of the Pt-on-Au system. This potential-dependent surface...

  2. 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...... rate coefficients, identified by mathematical optimization, were 4.65(±0.74) hrs- and 2.98(± 0.48) hrs- for struvite and amorphous calcium phosphate (ACP), respectively. The joint parameter confidence regions found were highly nonlinear and asymmetric, indicating that the model was more tolerant...

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

    International Nuclear Information System (INIS)

    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: NH3+ + D2, and electron and proton transfer reactions of anions. 9 refs

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

    OpenAIRE

    Takayoshi Kobayashi; Atsushi Yabushita; Shigehiko Hayashi; Izumi Iwakura; Yu Kaneko

    2013-01-01

    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-m...

  5. Plane wave density functional molecular dynamics study of exothermic reactions of Al/CuO thermites

    Science.gov (United States)

    Oloriegbe, Suleiman; Sewell, Thomas; Chen, Zhen; Jiang, Shan; Gan, Yong

    2014-03-01

    Exothermic reactions between nanosize aluminum (Al) and copper oxide (CuO) structures are of current interest because of their high reaction enthalpy and energy density which exceed those of traditional monomolecular energetic compounds such as TNT, RDX, and HMX. In this work, molecular dynamics simulations with forces obtained from plane wave density functional theory are used to investigate the atomic-scale and electronic processes that occur during the fast thermite reactions between Al and CuO nanostructures under adiabatic conditions. Aluminum surfaces in contact with O-exposed and Cu-exposed CuO surfaces are studied. Starting from initial temperature T = 800 K, we have observed: faster chemical reaction at the oxygen-rich interface during the initial 0.5 ps, linear temperature rise, and fast oxygen diffusion into the Al region with the rate 1.87 X 10-3 cm2/s. The density-derived electrostatic and chemical method is used to evaluate the net atomic charges and charge transfer during the important redox processes. High charge density around the oxygen-exposed interface may be responsible for the faster initial reactions at that interface. The overall reaction rate, determined using the time evolution of Cu-O charge orbital overlap population, is approximately first order.

  6. Introduction to dynamic spin chemistry magnetic field effects on chemical and biochemical reactions

    CERN Document Server

    Hayashi, Hisaharu

    2004-01-01

    This book presents a detailed account of one of the most mysterious problems in science - whether ordinary magnetic fields can exert an appreciable influence on chemical and biochemical reactions. The first aim of the book is to introduce this research, through theoretical and dynamic spin chemistry, to graduate students and researchers, by means of detailed theoretical and experimental descriptions. The second aim is to review typical recent investigations, which will stimulate new interest and applications in the 21st century. Because dynamic spin chemistry is based on established science, i

  7. Nonadiabatic dynamics in the CH3+HCl→CH4+Cl(2PJ) reaction

    International Nuclear Information System (INIS)

    Nonadiabatic dynamics in the title reaction have been investigated by 2+1 REMPI detection of the Cl(2P3/2) and Cl*(2P1/2) products. Reaction was initiated by photodissociation of CH3I at 266 nm within a single expansion of a dilute mixture of CH3I and HCl in argon, giving a mean collision energy of 7800 cm-1 in the center-of-mass frame. Significant production of Cl* was observed, with careful checks made to ensure that no additional photochemical or inelastic scattering sources of Cl* perturbed the measurements. The fraction of the total yield of Cl(2PJ) atoms formed in the J=(1/2) level at this collision energy was 0.150±0.024, and must arise from nonadiabatic dynamics because the ground potential energy surface correlates to CH4+Cl(2P3/2) products

  8. Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.

    Science.gov (United States)

    Raff, L. M.; Thompson, D. L.; Sims, L. B.; Porter, R. N.

    1972-01-01

    The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.

  9. Nonadiabatic quantum wave packet dynamics of the H + H2 reaction including the coriolis coupling

    Indian Academy of Sciences (India)

    B Jayachander Rao; S Mahapatra

    2009-09-01

    The effect of coriolis coupling on the dynamics of H + H2 reaction is examined by calculating the initial state-selected and energy resolved reaction probabilities on the coupled manifold of its degenerate 2 (') ground electronic state. H3 in this state is prone to the Jahn-Teller (JT) instability and consequently the degeneracy is split upon distortion from its 3ℎ equilibrium geometry. The orbital degeneracy is, however, restored along the 3ℎ symmetry configuration and it results into conical intersections of the two JT split component states. The energetically lower adiabatic component of latter is repulsive, and mainly (`rather solely’) drive the H + H2 reaction dynamics. On the otherhand, the upper adiabatic component is of bound type and can only impart non-adiabaticity on the dynamics of lower state. Comparison calculations are therefore also carried out on the uncoupled lower adiabatic sheet to assess the nonadiabatic effect. Exact quantum scattering calculations are performed by a chebyshev polynomial propagator and employing the double many body expansion potential energy surface of the electronic ground state of H3. Reaction probabilities are reported up to a total energy of ∼ 3.0 eV, slightly above the energetic minimum of the seam of conical intersections at ∼ 2.74 eV. Reaction probabilities are calculated up to the total angular momentum, = 20 and for each value of , the projection quantum number is varied from 0 to min (, max), with max = 4. Probability results are compared and discussed with those obtained without the coriolis coupling.

  10. Phase-space geometry and reaction dynamics near index 2 saddles

    International Nuclear Information System (INIS)

    We study the phase-space geometry associated with index 2 saddles of a potential energy surface and its influence on reaction dynamics for n degree-of-freedom (DoF) Hamiltonian systems. In recent years, similar studies have been carried out for index 1 saddles of potential energy surfaces, and the phase-space geometry associated with classical transition state theory has been elucidated. In this case, the existence of a normally hyperbolic invariant manifold (NHIM) of saddle stability type has been shown, where the NHIM serves as the 'anchor' for the construction of dividing surfaces having the no-recrossing property and minimal flux. For the index 1 saddle case, the stable and unstable manifolds of the NHIM are co-dimension 1 in the energy surface and have the structure of spherical cylinders, and thus act as the conduits for reacting trajectories in phase space. The situation for index 2 saddles is quite different, and their relevance for reaction dynamics has not previously been fully recognized. We show that NHIMs with their stable and unstable manifolds still exist, but that these manifolds by themselves lack sufficient dimension to act as barriers in the energy surface in order to constrain reactions. Rather, in the index 2 case there are different types of invariant manifolds, containing the NHIM and its stable and unstable manifolds, that act as co-dimension 1 barriers in the energy surface. These barriers divide the energy surface in the vicinity of the index 2 saddle into regions of qualitatively different trajectories exhibiting a wider variety of dynamical behavior than for the case of index 1 saddles. In particular, we can identify a class of trajectories, which we refer to as 'roaming trajectories', which are not associated with reaction along the classical minimum energy path (MEP). We illustrate the significance of our analysis of the index 2 saddle for reaction dynamics with two examples. The first involves isomerization on a potential energy

  11. Neutron evaporation as a probe for dynamical effects in heavy ion fusion reactions

    International Nuclear Information System (INIS)

    The compound nucleus 76Kr* was populated at the excitation energy of 75 MeV and angular momentum of 39 (ℎ/2π) in fusion reactions with two complementary, mass-symmetric (31P+45Sc) and mass asymmetric (12C+64Zn) entrance channels. The neutron evaporation spectra were measured and compared with the predictions of the statistical model calculations. The results for the mass-asymmetric reaction are found to be consistent with the predictions of the statistical model calculations. However, for the mass-symmetric reaction (31P+45Sc), the experimental spectra are found to be harder than the theoretical neutron spectra. The dynamical model calculations of Feldmeier show that the formation time for the compound nucleus for the symmetric system is relatively larger as compared to the asymmetric system

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

    Science.gov (United States)

    Zobač, Vladmír; Lewis, James P.; Jelínek, Pavel

    2016-07-01

    We report non-adiabatic molecular dynamic simulations of the ring opening reaction of diarylethene (DAE) derivative molecules, both free standing and embedded between gold electrodes. Simulations are performed by the surface hopping method employing density functional theory. Typically, the free-standing molecules exhibit large quantum yields to open and close; however the process is quenched for the molecules embedded between electrodes. Our simulations reveal the importance of the DAE side chemical groups, which explain the efficiency of the quenching process. Namely, delocalization of the LUMO state contributes to electronic coupling between the molecule and electrodes, suppressing or enhancing the reaction process. The simulations indicate that a proper choice of the chemical side group, which provides the strong localization of the LUMO state, can substantially diminish the quenching mechanism. Additionally, we analyze a strong dependency of the quantum yield of the opening reaction coming from the mechanical strength of the molecules.

  13. Pion-photon reactions and chiral dynamics in Primakoff processes at COMPASS

    Energy Technology Data Exchange (ETDEWEB)

    Friedrich, Jan Michael [Physik-Department, Technische Universität München (Germany)

    2016-01-22

    With the COMPASS experiment at CERN, pion-photon reactions are investigated via the Primakoff effect, implying that high-energetic pions react with the quasi-real photon field surrounding the target nuclei. The production of a single hard photon in such a pion scattering at lowest momentum transfer to the nucleus is related to pion Compton scattering. From the measured cross-section shape, the pion polarisability is determined. The COMPASS measurement is in contradiction to the earlier dedicated measurements, and rather in agreement with the theoretical expectation from chiral perturbation theory. In the same data taking, reactions with neutral and charged pions in the final state are measured and analyzed. At low energy in the pion-photon centre-of-momentum system, these reactions are governed by chiral dynamics and contain information relevant for chiral perturbation theory. At higher energies, resonances are produced and their radiative coupling is investigated.

  14. Back reaction effects on the dynamics of heavy probes in heavy quark cloud

    CERN Document Server

    Chakrabortty, Shankhadeep

    2016-01-01

    We holographically study the effect of back reaction on the hydrodynamical properties of $\\mathcal{N} = 4$ strongly coupled super Yang-Mills (SYM) thermal plasma. The back reaction we consider arises from the presence of static heavy quarks uniformly distributed over $\\mathcal{N} = 4$ SYM plasma. In order to study the hydrodynamical properties, we use heavy quark as well as heavy quark-antiquark bound state as probes and compute the jet quenching parameter, screening length and binding energy. We also consider the rotational dynamics of heavy probe quark in the back-reacted plasma and analyse associated energy loss. We observe that the presence of back reaction enhances the energy-loss in the thermal plasma. Finally, we show that there is no effect of angular drag on the rotational motion of quark-antiquark bound state probing the back reacted thermal plasma.

  15. Pion-photon reactions and chiral dynamics in Primakoff processes at COMPASS

    International Nuclear Information System (INIS)

    With the COMPASS experiment at CERN, pion-photon reactions are investigated via the Primakoff effect, implying that high-energetic pions react with the quasi-real photon field surrounding the target nuclei. The production of a single hard photon in such a pion scattering at lowest momentum transfer to the nucleus is related to pion Compton scattering. From the measured cross-section shape, the pion polarisability is determined. The COMPASS measurement is in contradiction to the earlier dedicated measurements, and rather in agreement with the theoretical expectation from chiral perturbation theory. In the same data taking, reactions with neutral and charged pions in the final state are measured and analyzed. At low energy in the pion-photon centre-of-momentum system, these reactions are governed by chiral dynamics and contain information relevant for chiral perturbation theory. At higher energies, resonances are produced and their radiative coupling is investigated

  16. Theoretical and Experimental Study of Proton Transfer Reaction Dynamics in Pyrrole 2-Caboxyldehyde

    CERN Document Server

    Chowdhury, Papia; Pathak, Anirban

    2009-01-01

    Photophysical and photochemical dynamics of ground state and excited state proton transfer reaction is reported for Pyrrole 2-Caboxyldehyde (PCL). Steady state absorption and emission measurements are conducted in this five member heterocyclic system (PCL). The theoretical investigation is done by using different quantum mechanical methods (e.g. Hartree Fock, DFT, MP2, CCSD etc.). The reaction pathway and two dimensional potential energy surfaces are computed in various level of theory. A transition state is also reported in gas phase and reaction filed calculation. It is established that PCL forms different emitting species in different media. A large Stokes shifted emission band, which is attributed to species undergoing excited state intramolecular proton transfer, is observed in hydrocarbon solvent. Intermolecular proton transfer is observed in hydroxylic polar solvent. Experimental observations yield all possible signatures of intramolecular and intermolecular proton transfer in excited state of PCL. The...

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

    CERN Document Server

    Saito, Seiki; Nakamura, Hiroaki

    2009-01-01

    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 $\\theta$ and azimuthal angle $\\phi$ of the incident hydrogen. From the simulation results, it is found that the reaction rates strongly depend on polar angle $\\theta$. Reflection rate becomes larger with increasing $\\theta$, and the $\\theta$ dependence of adsorption rate is also found. The $\\theta$ dependence is caused by three dimensional structure of the small potential barrier which covers adsorption sites. $\\phi$ dependence of penetration rate is also found for large $\\theta$.

  18. Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications

    CERN Document Server

    Suleimanov, Yury V; Guo, Hua

    2016-01-01

    This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze theory and its connection to quantum transition state theory. We then focus on its practical application to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rates in multifarious cases. This review serves as an important checkpoint in RPMD rate theory development, which shows that RPMD is shifting from being just one of recent novel ideas to a well-established and validated alternative to conventional techniques for calculating thermal chemical rates. We also hope it will motivate further applications of RPMD to various chemical reactions.

  19. Microscopic dynamics simulations of heavy-ion fusion reactions induced by neutron-rich nuclei

    CERN Document Server

    Wang, Ning; Zhang, Yingxun; Li, Zhuxia

    2014-01-01

    The heavy-ion fusion reactions induced by neutron-rich nuclei are investigated with the improved quantum molecular dynamics (ImQMD) model. With a subtle consideration of the neutron skin thickness of nuclei and the symmetry potential, the stability of nuclei and the fusion excitation functions of heavy-ion fusion reactions $^{16}$O+$^{76}$Ge, $^{16}$O+$^{154}$Sm, $^{40}$Ca+$^{96}$Zr and $^{132}$Sn+$^{40}$Ca are systematically studied. The fusion cross sections of these reactions at energies around the Coulomb barrier can be well reproduced by using the ImQMD model. The corresponding slope parameter of the symmetry energy adopted in the calculations is $L \\approx 78$ MeV and the surface energy coefficient is $g_{\\rm sur}=18\\pm 1.5$ MeVfm$^2$. In addition, it is found that the surface-symmetry term significantly influences the fusion cross sections of neutron-rich fusion systems. For sub-barrier fusion, the dynamical fluctuations in the densities of the reaction partners and the enhanced surface diffuseness at ...

  20. 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.

  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

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

    International Nuclear Information System (INIS)

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (Hen, 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 He4 and He5 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

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

    Science.gov (United States)

    Hu, Lin; Hammond, Karl D.; Wirth, Brian D.; Maroudas, Dimitrios

    2015-10-01

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (Hen, 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 He4 and He5 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.

  5. 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 ostatní: 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

  6. Cluster fragmentation and cluster beam steering studied by dynamic reaction coordinate and molecular dynamics calculations

    International Nuclear Information System (INIS)

    In this study either cluster fragmentation, using a time-dependent Hartree-Fock formulation, or cluster deposition, based on classical molecular dynamics, have been studied. An exhaustive analysis has been performed on the many parameters acting on the two processes. Fragmentation calculations show a primary dependence on the input energy whereas the interatomic forces play a primary role in deposition. However the central result of this study is the essential agreement between the classical and quantum mechanical calculation

  7. Bimolecular Fluorescence Complementation to Assay the Interactions of Ubiquitylation Enzymes in Living Yeast Cells.

    Science.gov (United States)

    Blaszczak, Ewa; Prigent, Claude; Rabut, Gwenaël

    2016-01-01

    Ubiquitylation is a versatile posttranslational protein modification catalyzed through the concerted action of ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). These enzymes form transient complexes with each other and their modification substrates and determine the nature of the ubiquitin signals attached to their substrates. One challenge in the field of protein ubiquitylation is thus to identify the E2-E3 pairs that function in the cell. In this chapter, we describe the use of bimolecular fluorescence complementation to assay E2-E3 interactions in living cells, using budding yeast as a model organism. PMID:27613039

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

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-21

    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. PMID:26090617

  9. Role of Long-Range Protein Dynamics in Different Thymidylate Synthase Catalyzed Reactions

    Directory of Open Access Journals (Sweden)

    Thelma Abeysinghe

    2015-04-01

    Full Text Available Recent studies of Escherichia coli thymidylate synthase (ecTSase showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-mono­phosphate (dUMP, its altered dynamics is more pronounced on the binding of the remote cofactor, (6R-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate, revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function.

  10. 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.

  11. Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics

    Science.gov (United States)

    Naruemon, Rueangkham; Charin, Modchang

    2016-04-01

    Most biochemical processes in cells are usually modeled by reaction–diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.

  12. A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

    International Nuclear Information System (INIS)

    In order to investigate proton transfer reaction in solution, mixed quantum-classical molecular dynamics calculations have been carried out based on our previously proposed quantum equation of motion for the reacting system [A. Yamada and S. Okazaki, J. Chem. Phys. 128, 044507 (2008)]. Surface hopping method was applied to describe forces acting on the solvent classical degrees of freedom. In a series of our studies, quantum and solvent effects on the reaction dynamics in solutions have been analysed in detail. Here, we report our mixed quantum-classical molecular dynamics calculations for intramolecular proton transfer of malonaldehyde in water. Thermally activated proton transfer process, i.e., vibrational excitation in the reactant state followed by transition to the product state and vibrational relaxation in the product state, as well as tunneling reaction can be described by solving the equation of motion. Zero point energy is, of course, included, too. The quantum simulation in water has been compared with the fully classical one and the wave packet calculation in vacuum. The calculated quantum reaction rate in water was 0.70 ps−1, which is about 2.5 times faster than that in vacuum, 0.27 ps−1. This indicates that the solvent water accelerates the reaction. Further, the quantum calculation resulted in the reaction rate about 2 times faster than the fully classical calculation, which indicates that quantum effect enhances the reaction rate, too. Contribution from three reaction mechanisms, i.e., tunneling, thermal activation, and barrier vanishing reactions, is 33:46:21 in the mixed quantum-classical calculations. This clearly shows that the tunneling effect is important in the reaction

  13. An ab initio molecular dynamics study of the roaming mechanism of the H{sub 2}+HOC{sup +} reaction

    Energy Technology Data Exchange (ETDEWEB)

    Yu Huagen, E-mail: hgy@bnl.gov [Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2011-08-01

    We report here a direct ab initio molecular dynamics study of the p-/o-H{sub 2}+HOC{sup +} reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H{sub 2}+HOC{sup +} reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.

  14. 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.

  15. A new intermediate in the Prins reaction

    Directory of Open Access Journals (Sweden)

    Shinichi Yamabe

    2013-03-01

    Full Text Available Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O13 + (H2C=O2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1. TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2 leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R–CH2–CH2–OH. This intermediate undergoes ring closure (TS4, affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them.

  16. Kinetically constrained ring-polymer molecular dynamics for non-adiabatic chemical reactions

    International Nuclear Information System (INIS)

    We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral representation in the set of nuclear coordinates and electronic states to provide continuous equations of motion that describe the quantized, electronically non-adiabatic dynamics of the system. KC-RPMD preserves the favorable properties of the usual RPMD formulation in the position representation, including rigorous detailed balance, time-reversal symmetry, and invariance of reaction rate calculations to the choice of dividing surface. However, the new method overcomes significant shortcomings of position-representation RPMD by enabling the description of non-adiabatic transitions between states associated with general, many-electron wavefunctions and by accurately describing deep-tunneling processes across asymmetric barriers. We demonstrate that KC-RPMD yields excellent numerical results for a range of model systems, including a simple avoided-crossing reaction and condensed-phase electron-transfer reactions across multiple regimes for the electronic coupling and thermodynamic driving force

  17. Kinetically constrained ring-polymer molecular dynamics for non-adiabatic chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Menzeleev, Artur R.; Bell, Franziska; Miller, Thomas F., E-mail: tfm@caltech.edu [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125 (United States)

    2014-02-14

    We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral representation in the set of nuclear coordinates and electronic states to provide continuous equations of motion that describe the quantized, electronically non-adiabatic dynamics of the system. KC-RPMD preserves the favorable properties of the usual RPMD formulation in the position representation, including rigorous detailed balance, time-reversal symmetry, and invariance of reaction rate calculations to the choice of dividing surface. However, the new method overcomes significant shortcomings of position-representation RPMD by enabling the description of non-adiabatic transitions between states associated with general, many-electron wavefunctions and by accurately describing deep-tunneling processes across asymmetric barriers. We demonstrate that KC-RPMD yields excellent numerical results for a range of model systems, including a simple avoided-crossing reaction and condensed-phase electron-transfer reactions across multiple regimes for the electronic coupling and thermodynamic driving force.

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

    Energy Technology Data Exchange (ETDEWEB)

    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/sub 2//sup +/ + H/sub 2/ systems. Charge and proton transfer cross sections are presented for the reactions of H/sub 2//sup +/ and D/sub 2//sup +/ with Ar, N/sub 2/, CO, and O/sub 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/sub 2//sup +/ + Ar, N/sub 2/). Oscillatory structure is observed in the collision energy dependence of the endoergic H/sub 2//sup +/ (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.

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

    International Nuclear Information System (INIS)

    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 H2+ + H2 systems. Charge and proton transfer cross sections are presented for the reactions of H2+ and D2+ with Ar, N2, CO, and O2. 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 (H2+ + Ar, N2). Oscillatory structure is observed in the collision energy dependence of the endoergic H2+ (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

  20. Amoeba-Inspired Heuristic Search Dynamics for Exploring Chemical Reaction Paths.

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

    We propose a nature-inspired model for simulating chemical reactions in a computationally resource-saving manner. The model was developed by extending our previously proposed heuristic search algorithm, called "AmoebaSAT [Aono et al. 2013]," which was inspired by the spatiotemporal dynamics of a single-celled amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment efficiently [Zhu et al. 2013]. AmoebaSAT is used for solving an NP-complete combinatorial optimization problem [Garey and Johnson 1979], "the satisfiability problem," and finds a constraint-satisfying solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods [Iwama and Tamaki 2004] for a class of randomly generated problem instances [ http://www.cs.ubc.ca/~hoos/5/benchm.html ]. In cases where the problem has more than one solution, AmoebaSAT exhibits dynamic transition behavior among a variety of the solutions. Inheriting these features of AmoebaSAT, we formulate "AmoebaChem," which explores a variety of metastable molecules in which several constraints determined by input atoms are satisfied and generates dynamic transition processes among the metastable molecules. AmoebaChem and its developed forms will be applied to the study of the origins of life, to discover reaction paths for which expected or unexpected organic compounds may be formed via unknown unstable intermediates and to estimate the likelihood of each of the discovered paths. PMID:26129639

  1. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

    International Nuclear Information System (INIS)

    This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate

  2. Dynamic quenching as a simple test for the mechanism of excited-state reaction

    International Nuclear Information System (INIS)

    We report on comparative studies of dynamic fluorescence quenching of 3-hydroxyflavone (3HF) and of its novel analogs by nitric oxide spin compound TEMPO. These dyes exhibit the excited-state intramolecular proton transfer (ESIPT) reaction that allows observation of two separate bands in fluorescence emission - of initially excited form and of the product of ESIPT reaction. In the frame of two-state excited-state reaction formalism, we develop the theory predicting different dependence of intensities at two bands in steady-state spectra in the cases of thermodynamic and kinetic control of ESIPT. In line with these predictions, the quenching changes strongly the distribution of intensities between these bands for 3HF but does not change it for the novel compounds whose excited states exhibit strong charge transfer character. Based on these findings, we suggest that the quenching of fluorescence by an efficient collisional quencher can be a simple and convenient method using only the steady-state experiment for distinguishing the excited-state reactions occurring under thermodynamic or under kinetic controls. This method can be used for large-scale screening of a series of compounds - potential candidates for application in fluorescence sensor and biosensor technologies

  3. Communication: Mode specific quantum dynamics of the F + CHD3 → HF + CD3 reaction

    Science.gov (United States)

    Qi, Ji; Song, Hongwei; Yang, Minghui; Palma, Juliana; Manthe, Uwe; Guo, Hua

    2016-05-01

    The mode specific reactivity of the F + CHD3 → HF + CD3 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 CD3 umbrella mode has a relatively small impact on reactivity. On the other hand, the excitation of the C-H vibration (v1) in CHD3 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.

  4. Molecular-beam studies of the dynamics of organic electron transfer reactions

    International Nuclear Information System (INIS)

    Using crossed molecular beams we have studied the dynamics of several electron transfer reactions, A+B→A++B-, where A is an organic base and B is SnCl4, SbF5, or TiCl4. We propose a simple, modified stripping model whereby the electron jumps at the point where the ionic and covalent surfaces cross to form a pair of ions produced by a vertical, Franck--Condon transition. All initial energy in excess of this vertical threshold appears in the translational energy of the products. This model is verified in one case where the vertical ionization potential and electron affinity are known and is then used to obtain a rough vertical electron affinity of SbF5. Except at the lowest energies all the reactions follow this modified stripping mechanism

  5. A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

    CERN Document Server

    Harris, L A; Clancy, Paulette; Harris, Leonard A.

    2006-01-01

    We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single *partitioned leaping* algorithmic framework. Distinguishing characteristics of the method include automatic, dynamic and theoretically justifiable time step determination and timescale separation procedures that utilize concepts underlying the tau-leap approach [D.T. Gillespie, J. Chem. Phys. 115, 1716 (2001); D.T. Gillespie and L.R. Petzold, J. Chem. Phys. 119, 8229 (2003)] and require the definition of only three model-independent parameters. Both procedures are based on an individual (but not independent) consideration of reactions, a subtle yet significant ideological concept used in the development of previous exact-stochastic simulation methods [D.T. Gillespie, J. Comput. Phys. 22, 403 (1976); M.A. Gibson and J. Bruck, J. Phys. Chem. A 104, 1876 (2000)]. The result is a method that correctly accounts for ...

  6. Parity violation and dynamical relativistic effects in $(\\vec{e},e'N)$ reactions

    CERN Document Server

    González-Jiménez, R; Donnelly, T W

    2015-01-01

    It is well known that coincidence quasielastic $(\\vec{e},e'N)$ reactions are not appropriate to analyze effects linked to parity violation due the presence of the fifth electromagnetic (EM) response $R^{TL'}$. Nevertheless, in this work we develop a fully relativistic approach to be applied to parity-violating (PV) quasielastic $(\\vec{e},e'N)$ processes. This is of importance as a preliminary step in the subsequent study of inclusive quasielastic PV $(\\vec{e},e')$ reactions. Moreover, our present analysis allows us to disentangle effects associated with the off-shell character of nucleons in nuclei, gauge ambiguities and the role played by the lower components in the nucleon wave functions, i.e., dynamical relativistic effects. This study can help in getting clear information on PV effects. Particular attention is paid to the relativistic plane-wave impulse approximation where the explicit expressions for the PV single-nucleon responses are shown for the first time.

  7. Static and dynamical critical behavior of the monomer-monomer reaction model with desorption

    Science.gov (United States)

    da Costa, E. C.; Rusch, Flávio Roberto

    2016-06-01

    We studied in this work the monomer-monomer reaction model on a linear chain. The model is described by the following reaction: A + B → AB, where A and B are two monomers that arrive at the surface with probabilities yA and yB, respectively, and we have considered desorption of the monomer B with probability α. The model is studied in the adsorption controlled limit where the reaction rate is infinitely larger than the adsorption rate. We employ site and pair mean-field approximations as well as static and dynamical Monte Carlo simulations. We show that the model exhibits a continuous phase transition between an active steady state and an A-absorbing state, when the parameter yA is varied through a critical value, which depends on the value of α. Monte Carlo simulations and finite-size scaling analysis near the critical point are used to determine the static critical exponents β and ν⊥ and the dynamical critical exponents ν∥ and z. The results found for the monomer-monomer reaction model with B desorption, in the linear chain, are different from those found by E. V. Albano (Albano, 1992) and are in accordance with the values obtained by Jun Zhuo and Sidney Redner (Zhuo and Redner, 1993), and endorse the conjecture of Grassberger, which states that any system undergoing a continuous phase transition from an active steady state to a single absorbing state, exhibits the same critical behavior of the directed percolation universality class.

  8. Entrance Channel Dynamics of Hot and Cold Fusion Reactions Leading to Superheavy Elements

    CERN Document Server

    Umar, A S; Maruhn, J A; Reinhard, P -G

    2010-01-01

    We investigate the entrance channel dynamics for the reactions $\\mathrm{^{70}Zn}+\\mathrm{^{208}Pb}$ and $\\mathrm{^{48}Ca}+\\mathrm{^{238}U}$ using the fully microscopic time-dependent Hartree-Fock (TDHF) theory coupled with a density constraint. We calculate excitation energies and capture cross-sections relevant for the study of superheavy formations. We discuss the deformation dependence of the ion-ion potential for the $\\mathrm{^{48}Ca}+\\mathrm{^{238}U}$ system and perform an alignment angle averaging for the calculation of the capture cross-section. The results show that this parameter-free approach can generate results in good agreement with experiment and other theories.

  9. Reaction dynamics of the D+ + H2 system. A comparison of theoretical approaches

    OpenAIRE

    Jambrina, P. G.; Alvariño, José M.; Aoiz, F. Javier; Herrero, Víctor J.; Sáez Rábanos, Vicente

    2010-01-01

    The dynamics of the deuteron-proton exchange D+ + H2 → HD + H+ reaction on its ground 11A′ potential energy surface has been the subject of a theoretical study for collision energies below 1.5 eV. The results obtained with three theoretical approaches: quasi-classical trajectory (QCT), statistical quasi-classical trajectory (SQCT), and accurate time-independent quantum mechanical (QM) calculations are compared in the range of collision energies from 5 meV to 0.2 eV. The QM calculations includ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Awes, T.C.

    1997-12-01

    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.

  11. Improved Quantum Molecular Dynamics Model and its Application to Fusion Reaction Near Barrier

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An improved quantum molecular dynamics model is proposed. By using this model, the properties of ground state of nuclei from 6Li to 208Pb can be described very well with one set of parameters. The fusion reactions for 40Ca+90Zr, 40Ca+96Zr and 48Ca+90Zr at the energy near the barrier are studied by this model. The experimental data of the fusion cross sections for 40Ca+90,96Zr at the energy near the barrier can be reproduced remarkably well without introducing any new parameters. The mechanism

  12. Energy momentum pseudo-tensor of high frequency gravitational waves and their dynamical back-reaction

    Institute of Scientific and Technical Information of China (English)

    LI Jian-jie; LAN Ming-jian; LI Fang-yu

    2008-01-01

    To describe properties of the high frequency gravitational wave (HFGW) propagating through the vacuum gravitational field in Robertson-Walker background space-time, we calculated its energy momentum pseudo-tensor (EMPT) in the limit of short wavelengths by taking the Brill-Hartle average on the second order perturbation of the Einstein tensor over several wavelengths. By rewriting the EMPT as a form of perfect fluid, the dynamical back-reaction of HFGW on the background space-time was discussed. The result shows that the energy density of HFGW, which is in the gauge we chose, is positive definite. The HFGW serves as a source for curving the background space-time and affects the dynamical evolution and time evolution of the scale factor of the Robertson-Walker metric.

  13. The dynamics of nonlinear reaction-diffusion equations with small Lévy noise

    CERN Document Server

    Debussche, Arnaud; Imkeller, Peter

    2013-01-01

    This work considers a small random perturbation of alpha-stable jump type nonlinear reaction-diffusion equations with Dirichlet boundary conditions over an interval. It has two stable points whose domains of attraction meet in a separating manifold with several saddle points. Extending a method developed by Imkeller and Pavlyukevich it proves that in contrast to a Gaussian perturbation, the expected exit and transition times between the domains of attraction depend polynomially on the noise intensity in the small intensity limit. Moreover the solution exhibits metastable behavior: there is a polynomial time scale along which the solution dynamics correspond asymptotically to the dynamic behavior of a finite-state Markov chain switching between the stable states.

  14. Dynamical Effects of Orientations on reaction 238U+238U near Coulomb Barrier

    International Nuclear Information System (INIS)

    The dynamical effects of three orientations (nose-nose, nose-side, and side-side) on reaction 238U+238U have been investigated by using Improved Quantum Molecular Dynamics(ImQMD) model. Due to Coulomb repulsive interaction, the change of the deformations or orientations of colliding nuclei is found even before touching configuration, especially for nose-nose. The average lifetime of the giant system and the probability producing super-heavy fragments (SHF) with Z>110 are found to be dependent on the orientations of two nuclei. At the time of 1000fm/c after re-separation of giant system, side-side orientation provide a larger probability of producing SHF than nose-nose case. And the maximum value of the probability locates a smaller incident energy for side-side orientation compared with nose-nose.

  15. Neutrino-nucleus reactions and their role for supernova dynamics and nucleosynthesis

    Science.gov (United States)

    Balasi, K. G.; Langanke, K.; Martínez-Pinedo, G.

    2015-11-01

    The description of nuclear reactions induced by supernova neutrinos has witnessed significant progress during the recent years. On one hand this progress is due to experimental data which serve as important constraints to model calculations, on the other hand it is related to advances in nuclear modeling itself and in computer hardware. At the energies and momentum transfers relevant for supernova neutrinos, neutrino-nucleus cross sections are dominated by allowed transitions, however, often with non-negligible contributions from (first) forbidden transitions. For several nuclei, allowed Gamow-Teller strength distributions have been derived from charge-exchange reactions and from inelastic electron scattering data. Importantly the diagonalization shell model has been proven to accurately reproduce these data and hence became the appropriate tool to calculate the allowed contributions to neutrino-nucleus cross sections for supernova neutrinos. Higher multipole contributions are usually calculated within the framework of the Quasiparticle Random Phase Approximation, which describes the total strength and the position of the giant resonances quite well. Both are the relevant quantities for a reliable calculation of the forbidden contributions to the cross sections. The current manuscript reviews the recent progress achieved in calculating supernova-relevant neutrino-nucleus cross sections and discusses its verification by data. Moreover, the review summarizes also the impact which neutrino-nucleus reactions have on the dynamics of supernovae and on the associated nucleosynthesis. With relevance to the supernova dynamics, these include the absorption of neutrinos by nuclei (the inverse of nuclear electron capture which is the dominating weak-interaction process during collapse), inelastic neutrino-nucleus scattering and nuclear de-excitation by neutrino-pair emission. For supernova nucleosynthesis we discuss the role of neutrino-induced reactions for the recently

  16. Isospin in Reaction Dynamics. The Case of Dissipative Collisions at Fermi Energies

    CERN Document Server

    Di Toro, M

    2005-01-01

    A key question in the physics of unstable nuclei is the knowledge of the $EOS$ for asymmetric nuclear matter ($ANM$) away from normal conditions. We recall that the symmetry energy at low densities has important effects on the neutron skin structure, while the knowledge in high densities region is crucial for supernovae dynamics and neutron star properties. The $only$ way to probe such region of the isovector $EOS$ in terrestrial laboratories is through very dissipative collisions of asymmetric (up to exotic) heavy ions from low to relativistic energies. A general introduction to the topic is firstly presented. We pass then to a detailed discussion on the $neck-fragmentation$ process as the main dissipative mechanism at the Fermi energies and to the related isospin dynamics. From Stochastic Mean Field simulations the isospin effects on all the phases of the reaction dynamics are thoroughly analysed, from the fast nucleon emission to the mid-rapidity fragment formation up to the dynamical fission of the $spect...

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

    International Nuclear Information System (INIS)

    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 Zn. 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 Rn 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)

  18. Adiabatic and nonadiabatic dynamics in the CH3(CD3)+HCl reaction

    International Nuclear Information System (INIS)

    The scattering dynamics leading to the formation of Cl (2P3/2) and Cl* (2P1/2) products of the CH3+HCl reaction (at a mean collision energy coll>=22.3 kcal mol-1) and the Cl (2P3/2) products of the CD3+HCl reaction (at coll>=19.4 kcal mol-1) have been investigated by using photodissociation of CH3I and CD3I as sources of translationally hot methyl radicals and velocity map imaging of the Cl atom products. Image analysis with a Legendre moment fitting procedure demonstrates that, in all three reactions, the Cl/Cl* products are mostly forward scattered with respect to the HCl in the center-of-mass (c.m.) frame but with a backward scattered component. The distributions of the fraction of the available energy released as translation peak at ft=0.31-0.33 for all the reactions, with average values that lie in the range t>=0.42-0.47. The detailed analysis indicates the importance of collision energy in facilitating the nonadiabatic transitions that lead to Cl* production. The similarities between the c.m.-frame scattering and kinetic energy release distributions for Cl and Cl* channels suggest that the nonadiabatic transitions to a low-lying excited potential energy surface (PES) correlating to Cl* products occur after passage through the transition state region on the ground-state PES. Branching fractions for Cl* are determined to be 0.14±0.02 for the CH3+HCl reaction and 0.20±0.03 for the CD3+HCl reaction. The difference cannot be accounted for by changes in collision energy, mass effects, or vibrational excitation of the photolytically generated methyl radical reagents and instead suggests that the low-frequency bending modes of the CD3H or CH4 coproduct are important mediators of the nonadiabatic couplings occurring in this reaction system

  19. Hydrated electron production by reaction of hydrogen atoms with hydroxide ions: A first-principles molecular dynamics study

    International Nuclear Information System (INIS)

    The solvated electron production by reaction between the H atom and the hydroxide anion was studied using Density Functional Theory based first-principles molecular dynamics. The simulation reveals a complex mechanism, controlled by proton transfers in the coordination sphere of the hydroxide and by the diffusion of the H atom in its solvent cavity. We formulate the hypothesis, based on a coupling between classical and first-principles molecular dynamics, that these two processes give rise to a lag time for the reaction that would explain the H atom extremely small reactivity compared to other radical species. Furthermore, the reaction observed gives an original insight in excess electron solvation. (authors)

  20. The reaction of the building structure with window unit to the explosiveimpact on the basis of dynamic equation solution

    Directory of Open Access Journals (Sweden)

    Doronin Fedor Leonidovich

    2014-01-01

    Full Text Available When designing residential buildings, additional measures for increasing the strength at dynamic effects indoors are not foreseen. The walls of the structure fixed in the framework are not designed for shock wave caused by explosion of utility gas. When designing a building, the task of the special dynamic load is often reduced to the calculation of the safe shock pressure, exceeding of which leads to the destruction of the structures. The wall with the window area under dynamic effects is a blast relief panel, which reduces the excess pressure inside the room. The proposed method of calculating a design with a window unit allows determining the dynamic reaction of the wall on explosive pulse. The proposed calculation technique of the constructions at shock loads allows tracing the changes of the inertial forces and displacements at any stage of dynamic response. The reaction to dynamic loads can be also set for non-monolithic structures, consisting of different materials with different conditions of fastening. Elastoplastic reaction of a brick wall with glass units was determined using step-by-step method of linear acceleration. The calculation of stress-strain state of brick walls with window panes determined the strength properties of the structures close to the monolithic version. The proposed technique of numerical solution of dynamic equations is applied only in the analysis of elastic systems, in which the dynamic characteristics remain unchanged throughout the reaction process.

  1. Determination of trace elements in serum by dynamic reaction cell inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    D' Ilio, S. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy)]. E-mail: sdilio@iss.it; Violante, N. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy); Caimi, S. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy); Di Gregorio, M. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy); Petrucci, F. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy); Senofonte, O. [Department of Environment and Primary Prevention, Istituto Superiore di Sanita, Viale Regina Elena 299, 00161 Rome (Italy)

    2006-07-28

    An inductively coupled plasma mass spectrometer (ICP-MS), equipped with a dynamic reaction cell (DRC) and coupled with a desolvating nebulizing system (Apex-ACM) to reduce the oxide formation, was used in the determination of Al, Co, Cr, Mn, Ni and Se in serum samples. The effect of the operating conditions of the DRC system was studied to get the best signal-to-background (S/B) ratio. The potentially interfering molecular ions at the masses m/z {sup 27}Al, {sup 59}Co, {sup 52}Cr, {sup 55}Mn, {sup 60}Ni and {sup 78}Se, were significantly reduced in intensity by using NH{sub 3} and H{sub 2}, as the reaction cell gases in the DRC, while a proper Dynamic Bandpass Tuning parameter q (RPq) value was optimized. The detection limits for {sup 27}Al, {sup 59}Co, {sup 52}Cr, {sup 55}Mn, {sup 60}Ni and {sup 78}Se, estimated with 3-{sigma} method, resulted to be 0.14, 0.003, 0.002, 0.01, 0.01 and 1.8 {mu}g L{sup -1}, respectively. This analytical method was developed on both a human serum certified reference material and a lyophilized animal serum produced and proposed in an intercomparison study. The results obtained for the reference samples agreed satisfactorily with the certified values. Precision (expressed as CV%) between sample replicates was better than 10% for elements determination, with the only exception of aluminium (14%)

  2. Determination of trace elements in serum by dynamic reaction cell inductively coupled plasma mass spectrometry

    International Nuclear Information System (INIS)

    An inductively coupled plasma mass spectrometer (ICP-MS), equipped with a dynamic reaction cell (DRC) and coupled with a desolvating nebulizing system (Apex-ACM) to reduce the oxide formation, was used in the determination of Al, Co, Cr, Mn, Ni and Se in serum samples. The effect of the operating conditions of the DRC system was studied to get the best signal-to-background (S/B) ratio. The potentially interfering molecular ions at the masses m/z 27Al, 59Co, 52Cr, 55Mn, 60Ni and 78Se, were significantly reduced in intensity by using NH3 and H2, as the reaction cell gases in the DRC, while a proper Dynamic Bandpass Tuning parameter q (RPq) value was optimized. The detection limits for 27Al, 59Co, 52Cr, 55Mn, 60Ni and 78Se, estimated with 3-σ method, resulted to be 0.14, 0.003, 0.002, 0.01, 0.01 and 1.8 μg L-1, respectively. This analytical method was developed on both a human serum certified reference material and a lyophilized animal serum produced and proposed in an intercomparison study. The results obtained for the reference samples agreed satisfactorily with the certified values. Precision (expressed as CV%) between sample replicates was better than 10% for elements determination, with the only exception of aluminium (14%)

  3. Crystalline-state photochromism of rhodium dinuclear complexes having a dithionite group and its reaction dynamics

    International Nuclear Information System (INIS)

    The compounds that undergo photochromic reaction in the crystalline-state are rare and their reaction dynamics are not well characterized as a result of the low degree of interconversion ratios and/or instability of the photo-generated isomers in the solid phase. We have recently found that a rhodium dinuclear complex [(RhCp*)2(μ-CH2)2(μ-O2SSO2)] (Cp*=η5-C5Me5) having a photo-responsive dithionite group (μ-O2SSO2) undergoes an essentially 100% reversible crystalline-state photochromism upon interconversion to [(RhCp*)2(μ-CH2)2(μ-O2SOSO)]. Taking an advantage of this unique full reversibility, we have investigated the dynamics of the system by using stepwise single crystal diffraction and variable-temperature solid-state NMR technique. The stereospecific oxygen-atom rearrangement process of the dithionite ligand and reorientational motion of the Cp* ligands, which are coupled to the photochromism, are presented. (author)

  4. Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions

    CERN Document Server

    Oberhofer, H

    2009-01-01

    We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following earlier work of Wu et al. Phys. Rev. A 72, 024502 (2005), the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born-Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge, and present expressions for the constraint forces. The method is applied to the Ru2+-Ru3+ electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories, and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1-0.2 eV lower than a previous estimate based on a continuum model for solvation. smaller value for re...

  5. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, B.J.

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in {approximately}240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH{sub 2}I{sub 2} and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a {approximately}350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  6. Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction

    Science.gov (United States)

    Wang, Dunyou

    2003-01-01

    A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

  7. Particle emission before equilibrium during heavy ion reactions: a dynamical approach

    International Nuclear Information System (INIS)

    The de-excitation mode, accompanying heavy-ion reaction, is investigated namely the particle emission during the interaction. The particle emission is analysed in term of sequential process. In the framework, it is possible to reproduce the total production of particles. Then, the characteristics of such a process are shown. Two different approaches are involved: the analyse of light particles energy spectrum, the analyse of residues speed distributions. The light particles have a large average energy, they are emitted in the forward direction, they induce a reduction of the linear momentum of the system. In other words, they are emitted prior the thermal equilibration of the system. A quantitative estimation of the ''preequilibrium'' emission is obtained using the two analyses. The reaction 14N+27Al Esub(lab)=11 MeV/u.m.a. is studied. Then, a phenomenologic approach to this process is proposed. Two aspects of the problem are treated: the dynamic of the reaction and the ''preequilibrium'' emission. The equation are solved for different systems, the quantitative estimation of the ''preequilibrium'' process are obtained. The investigation concern incident energies between 10 and 40 MeV/u.m.a

  8. N-dimensional switch function for energy conservation in multiprocess reaction dynamics.

    Science.gov (United States)

    Mogo, César; Brandão, João

    2016-06-15

    The MReaDy program was designed for studying Multiprocess Reactive Dynamic systems, that is, complex chemical systems involving different and concurrent reactions. It builds a global potential energy surface integrating a variety of potential energy surfaces, each one of them representing an elementary reaction expected to play a role in the chemical process. For each elementary reaction, energy continuity problems may happen in the transition between potential energy surfaces due to differences in the functional form for each of the fragments, especially if built by different authors. A N-dimensional switch function is introduced in MReaDy in order to overcome such a problem. As an example, results of a collision trajectory calculation for H2  + OH → H3 O are presented, showing smooth transition in the potential energy, leading to conservation in the total energy. Calculations for a hydrogen combustion system from 1000 K up to 4000 K shows a variation of 0.012% when compared to the total energy of the system. © 2016 Wiley Periodicals, Inc. PMID:26992438

  9. Activation energies of photoinduced unimolecular, bimolecular and termolecular processes on silica gel surfaces.

    Science.gov (United States)

    Williams, Siân L; Worrall, David R; Kirkpatrick, Iain; Vancea, Anisoara; Pan, Jiawei

    2011-01-01

    Activation energies for energy and electron transfer have been measured in various systems on silica gel. In the case of ion-electron recombination, a facile technique involving fluorescence recovery is described which complements diffuse reflectance spectroscopy in the study of these systems. In bimolecular anthracene/azulene systems, activation energies have been shown to be independent of pre-treatment temperature in the range 25-210 °C, demonstrating that physisorbed water plays little role in determining diffusion rates on silica gel. In a ternary anthracene/azulene/perylene system, we have for the first time presented comparative activation energies for the diffusion of azulene and its radical cation, and have shown a greater activation energy for diffusion of the latter species. PMID:20978659

  10. Nonequilibrium inflaton dynamics and reheating: Back reaction of parametric particle creation and curved spacetime effects

    International Nuclear Information System (INIS)

    We present a detailed and systematic analysis of the nonperturbative, nonequilibrium dynamics of a quantum field in the reheating phase of inflationary cosmology, including full back reactions of the quantum field on the curved spacetime, as well as the fluctuations on the mean field. We use the O(N) field theory with unbroken symmetry in a spatially flat Friedmann-Robertson-Walker (FRW) universe to study the dynamics of the inflaton in the post-inflation, preheating stage. Oscillations of the inflaton close-quote s zero mode induce parametric amplification of quantum fluctuations, resulting in a rapid transfer of energy to the inhomogeneous modes of the inflaton field. The large-amplitude oscillations of the mean field, as well as stimulated emission effects require a nonperturbative formulation of the quantum dynamics, while the nonequilibrium evolution requires a statistical field theory treatment. We adopt the coupled nonperturbative equations for the mean field and variance derived in a preceding paper [S. A. Ramsey and B. L. Hu, this issue, Phys. Rev. D 56, 661 (1997)] by means of a two-particle-irreducible (2PI), closed-time-path (CTP) effective action for curved spacetimes while specialized to a dynamical FRW background, up to leading order in the 1/N expansion. Adiabatic regularization is employed to yield a covariantly conserved, renormalized energy-momentum tensor. The renormalized dynamical equations are evolved numerically from initial data which are generic to the end state of slow roll in many inflationary cosmological scenarios. The initial conditions consist of a large-amplitude, quasiclassical, oscillating mean field left-angle Φ right-angle with variance left-angle Φ2 right-angle -left-angle Φ right-angle 2 around the de Sitter-invariant vacuum. (Abstract Truncated)

  11. Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes.

    Science.gov (United States)

    Nilsen, Ian A; Osborne, Derek G; White, Aaron M; Anna, Jessica M; Kubarych, Kevin J

    2014-10-01

    Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy. PMID:25296812

  12. Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes

    International Nuclear Information System (INIS)

    Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C6H6Cr(CO)3, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of kBT. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 kBT above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy

  13. Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

    Energy Technology Data Exchange (ETDEWEB)

    Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

    2015-07-07

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  14. 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

  15. Quantum dynamics study of the X + F2 and F + XF (X = Mu, H, and D) reactions

    International Nuclear Information System (INIS)

    Graphical abstract: Quantum reactive scattering calculations have been performed for the X + F2 and FX + F′ (X = Mu, H and D) reactions on the accurate ab initio potential energy surface. Highlights: ► Reaction dynamics for X + F2 and FX + F′ (X = Mu, H and D) reactions were studied. ► Tunneling is very important for the Mu + F2 and F + MuF′ reactions. ► Reaction probability for F + MuF′ is enhanced around the reaction threshold. - Abstract: Quantum reactive scattering calculations for the X + F2 → XF + F (X = Mu, H and D) and F + XF → FX + F (X = Mu and H) reactions were performed on a global potential energy surface developed at an ab initio multi-reference configuration interaction level. Rate constants for the former reaction were estimated with the J-shifting approximation and compared to previous experimental measurements. A strongly curved behavior observed in the experimental Arrhenius plot was reproduced by the present quantum calculation at a fairly good level. The calculated reaction probabilities for the Mu-exchange reaction show sharp resonance structures around the asymptotic levels. It has been found that the observed resonances are mainly associated with the F⋯MuF complex. Due to the strong coupling between resonance effects and tunneling effects in this heavy–light–heavy system, it is found that the reaction probability is significantly enhanced around the threshold energy.

  16. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

    Science.gov (United States)

    Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-07-01

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  17. The power-law reaction rate coefficient for barrierless reactions

    International Nuclear Information System (INIS)

    We study the power-law reaction rate coefficient for barrierless reactions, when the reactions take place in systems with power-law distributions, and derive a generalized rate formula for the barrierless reactions in the Gorin model. We show that, unlike those for bimolecular and unimolcular reactions, due to the lack of barriers, the power-law rate coefficient for barrierless reactions does not have a power-law function, and thus is not very strongly dependent on the ν-parameter. Four barrierless reactions are taken as application examples to calculate the new rate coefficients, which with larger fitting ν-parameters can be exactly in agreement with measurements in the experimental studies. (paper)

  18. Interior dynamics in the unified connected reaction theory of Polyzou and Redish

    International Nuclear Information System (INIS)

    We discuss the unified reaction theory of Polyzou and Redish [Ann. Phys. (N.Y.) 119, 1(1979)] with regard to the freedom to perturb the approximate Hamiltonian by a connected operator. A proper treatment of this freedom is crucial for a good treatment of the dynamics. We show how to construct an effective N-body force so the approximate Hamiltonian is a projection of the exact Hamiltonian on an appropriate infinite dimensional subspace. Because this operator is connected it should not alter the unitarity considerations in the above paper. The methods used in constructing this effective interaction can also be used to reformulate the scattering integral equations as equivalent equations with noncompact contractive kennels. This reduces the scattering problem to uniformly convergent perturbation theory

  19. Dynamics of the induced acrosome reaction in boar sperm evaluated by flow cytometry

    DEFF Research Database (Denmark)

    Birck, Anders; Labouriau, Rodrigo; Christensen, Preben

    2009-01-01

    The present study investigated the dynamics of the in vitro induced acrosome reaction (AR) in boar sperm in response to medium composition, incubation time and ionophore concentration. The AR is a prerequisite for normal sperm fertilizing capability and can be studied in vitro following induction...... information on sperm viability and acrosomal status. The ionophore induced AR was dependent on extracellular Ca2+, but could be easily induced in boar sperm without capacitation. Capacitation-associated plasma membrane phospholipid scrambling was assessed and a medium specific ability to induce these membrane...... changes was observed. Both sperm viability and the induced AR were significantly affected by sperm capacitation, incubation time and ionophore concentration. The results lead to suggestions for an optimized AR induction protocol that takes both sperm viability and the effectiveness of AR induction...

  20. Dynamics aspect of subbarrier fusion reaction in light heavy ion systems

    CERN Document Server

    Huang, M; Wada, R; Liu, X; Lin, W; Zhao, M; Wang, J; Chen, Z; Ma, C; Yang, Y; Wang, Q; Ma, J; Han, J; Ma, P; Jin, S; Bai, Z; Hu, Q; Jin, L; Chen, J; Su, Y; Li, Y

    2012-01-01

    Subbarrier fusion of the 7Li + 12C reaction is studied using an antisymmetrized molecular dynamics model (AMD) with an after burner, GEMINI. In AMD, 7Li shows an \\alpha + t structure at its ground state and it is significantly deformed. Simulations are made near the Coulomb barrier energies, i.e., E_{cm} = 3 - 8 MeV. The total fusion cross section of the AMD + GEMINI calculations as a function of incident energy is compared to the experimental results and both are in good agreement at E_{cm} > 3 MeV. The cross section for the different residue channels of the AMD + GEMINI at E_{cm} = 5 MeV is also compared to the experimental results.

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

    Directory of Open Access Journals (Sweden)

    Ciepał I.

    2014-03-01

    $$\\overrightarrow d$ , ppn 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.

  2. Adaptive coarse-grained Monte Carlo simulation of reaction and diffusion dynamics in heterogeneous plasma membranes

    Directory of Open Access Journals (Sweden)

    Stamatakis Michail

    2010-04-01

    Full Text Available Abstract Background An adaptive coarse-grained (kinetic Monte Carlo (ACGMC simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime. Results Coarse-graining of dimerization, rather than of diffusion, may lead to computational error. It is shown that the ACGMC method is an effective technique to minimize error in diffusion-reaction processes and is superior to the microscopic kinetic Monte Carlo simulation in terms of computational cost while retaining accuracy. The low computational cost enables sensitivity analysis calculations. Sensitivity analysis indicates that it may be possible to retain clusters of receptors over the time scale of minutes under suitable conditions and the cluster lifetime may depend on both receptor density and cluster size. Conclusions The ACGMC method is an ideal platform to resolve large length and time scales in heterogeneous biological systems well beyond the plasma membrane and the EGFR system studied here. Our results demonstrate that cluster size must be considered in conjunction with receptor density, as they synergistically affect EGFR cluster lifetime. Further, the cluster lifetime being of the order of several seconds suggests that any mechanisms responsible for EGFR aggregation must operate on shorter timescales (at most a fraction of a second, to overcome dissipation and produce stable clusters observed experimentally.

  3. Effect of reaction-step-size noise on the switching dynamics of stochastic populations

    Science.gov (United States)

    Be'er, Shay; Heller-Algazi, Metar; Assaf, Michael

    2016-05-01

    In genetic circuits, when the messenger RNA lifetime is short compared to the cell cycle, proteins are produced in geometrically distributed bursts, which greatly affects the cellular switching dynamics between different metastable phenotypic states. Motivated by this scenario, we study a general problem of switching or escape in stochastic populations, where influx of particles occurs in groups or bursts, sampled from an arbitrary distribution. The fact that the step size of the influx reaction is a priori unknown and, in general, may fluctuate in time with a given correlation time and statistics, introduces an additional nondemographic reaction-step-size noise into the system. Employing the probability-generating function technique in conjunction with Hamiltonian formulation, we are able to map the problem in the leading order onto solving a stationary Hamilton-Jacobi equation. We show that compared to the "usual case" of single-step influx, bursty influx exponentially decreases the population's mean escape time from its long-lived metastable state. In particular, close to bifurcation we find a simple analytical expression for the mean escape time which solely depends on the mean and variance of the burst-size distribution. Our results are demonstrated on several realistic distributions and compare well with numerical Monte Carlo simulations.

  4. Dynamic NMR study of ligand exchange reactions in U(VI)-phosphonic acid systems

    International Nuclear Information System (INIS)

    The rates of hydrogen ion exchange on phosphonic acid ligands and that of phosphonate ligand exchange on selected uranyl-phosphonate complexes have been investigated by dynamic NMR spectroscopy. The spin-spin relaxation time (ln(1/T2)) for H+ exchange on the fee ligands exhibits a parabolic dependence on reciprocal temperature (1/T (K-1)). The empirical fit parameters are correlated with the activation parameters (ΔH*, ΔS*, ΔCp*) by adapting the statistical mechanical framework developed by Braibanti et al. to the Eyring activated complex theory. The correlation of the apparent activation enthalpy with temperature indicates that 6--11 water molecules participate in the transition from reactants to activated complex for ligand proton exchange reactions, depending on the ligand. Mechanistic details of ligand exchange reactions of phosphonic acid complexants onto the corresponding uranium(VI) complexes are not fully developed, but the negative values for ΔS* imply increased order in the transition to the activated complex. Though ΔH* for ligand exchange covers a range of 15 kJ/mol, the free energy of activation (ΔG*) is nearly constant for the series of ligands, implying substantial entropy compensation in the activation process. Application of the Marcus relationship defines a correlation between ΔG* and the thermodynamic stability (ΔG degree) for the 1:2 uranyl complexes with methanediphosphonic acid and 1-hydroxyethane-1,1-diphosphonic acid

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

    Science.gov (United States)

    Lespade, Laure

    2016-08-01

    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.

  6. Heavy-ion induced reactions: Dynamical aspects of fusion-like processes

    International Nuclear Information System (INIS)

    In this thesis dynamical processes in the heavy ion reactions 40Ar+181Ta as well as 40Ar+165Ho are studied by means of nuclear-chemical off-line measuring methods. For this fission products arising in the reaction are captured by catcher foils and by gamma-radiation measurement and subsequent decay-curve analysis determined for charge and mass. The measurement of the anisotropy An=W(180deg, 0deg)/W(90deg) in dependence on the exit-channel mass asymmetry α in the angular distributions of all systems shows for the 40Ar+181Ta system and the 40Ar+165Ho a distinctly weaker dependence of the anisotropy than the 40Ar+197Au system. The increasement of the anisotropy with increasing vertical strokeαvertical stroke seems also to be connected with the onset of the asymmetric component in the angular distribution. This region begins in all systems nearly equally at vertical strokeαvertical stroke ≅ 0.12. (orig./HSI)

  7. Closed, heated reaction chamber design for dynamic high-temperature x-ray-diffraction analyses of gas/solid displacement reactions

    International Nuclear Information System (INIS)

    A closed, x-ray transparent chamber for containing a hot reactive gas (generated from an internal condensed source) has been designed and evaluated for use in dynamic x-ray-diffraction analysis of a gas/solid displacement reaction. The chamber consisted of a square-bottom base and lid machined from dense pyrolytic graphite. The base contained a flat pedestal, upon which SiO2 microshells (the reactant oxide) were placed, raised above adjacent cavities holding Mg flakes (the condensed precursor to the reactive gas). Upon heating to 650 deg. C, the Mg evaporated and reacted with the SiO2 inside the sealed chamber. By passing incident and diffracted x rays through the vertical side walls of the chamber and by blocking undesired graphite-diffracted x rays with platinum, the Mg(g)/SiO2(s) displacement reaction could be tracked with time. This is the first use of dynamic high-temperature x-ray diffraction analysis to monitor the progress of a displacement reaction involving a reactant gas that was generated and confined within a closed reaction chamber

  8. Complementarity between Quantum and Classical Mechanics in Chemical Modeling. The H + HeH+ → H2 + + He Reaction: A Rigourous Test for Reaction Dynamics Methods.

    Science.gov (United States)

    Esposito, Fabrizio; Coppola, Carla Maria; De Fazio, Dario

    2015-12-24

    In this work we present a dynamical study of the H + HeH+ → H2+ + He reaction in a collision energy range from 0.1 meV to 10 eV, suitable to be used in applicative models. The paper extends and complements a recent work [ Phys. Chem. Chem. Phys. 2014, 16, 11662] devoted to the characterization of the reactivity from the ultracold regime up to the three-body dissociation breakup. In particular, the accuracy of the quasi-classical trajectory method below the three-body dissociation threshold has been assessed by a detailed comparison with previous calculations performed with different reaction dynamics methods, whereas the reliability of the results in the high energy range has been checked by a direct comparison with the available experimental data. Integral cross sections for several HeH+ roto-vibrational states have been analyzed and used to understand the extent of quantum effects in the reaction dynamics. By using the quasi-classical trajectory method and quantum mechanical close coupling data, respectively, in the high and low collision energy ranges, we obtain highly accurate thermal rate costants until 15 000 K including all (178) the roto-vibrational bound and quasi-bound states of HeH+. The role of the collision-induced dissociation is also discussed and explicitly calculated for the ground roto-vibrational state of HeH+. PMID:26583384

  9. 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. PMID:21229990

  10. Modeling of advection-diffusion-reaction processes using transport dissipative particle dynamics

    Science.gov (United States)

    Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-11-01

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. In particular, the transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of Lagrangian particles. To validate the proposed tDPD model and the boundary conditions, three benchmark simulations of one-dimensional diffusion with different boundary conditions are performed, and the results show excellent agreement with the theoretical solutions. Also, two-dimensional simulations of ADR systems are performed and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, an application of tDPD to the spatio-temporal dynamics of blood coagulation involving twenty-five reacting species is performed to demonstrate the promising biological applications of the tDPD model. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.

  11. Role of radiation reaction forces in the dynamics of centrifugally accelerated particles

    International Nuclear Information System (INIS)

    In this paper we study the influence of radiation reaction (RR) forces on the dynamics of centrifugally accelerated particles. It is assumed that the particles move along magnetic field lines anchored in the rotating central object. The common 'bead-on-the-wire' approximation is used. The solutions are found and analyzed for cases when the form of the prescribed trajectory (rigidly rotating field line) is approximated by: (a) straight line, and (b) Archimedes spiral. Dynamics of neutral and charged particles are compared with the emphasis on the role of RR forces in the latter case. It is shown that for charged particles there exist locations of stable equilibrium. It is demonstrated that for particular initial conditions RR forces cause centripetal motion of the particles: their 'falling' on the central rotating object. It is found that in the case of Archimedes spiral both neutral and charged particles can reach infinity where their motion has asymptotically force-free character. The possible importance of these processes for the acceleration of relativistic, charged particles by rotating magnetospheres in the context of the generation of nonthermal, high-energy emission of AGN and pulsars is discussed

  12. Infrared driven CO oxidation reactions on isolated platinum cluster oxides, PtnOm+

    NARCIS (Netherlands)

    Hermes, A. C.; Hamilton, S. M.; Cooper, G. A.; Kerpal, C.; Harding, D. J.; Meijer, G.; Fielicke, A.; Mackenzie, S. R.

    2012-01-01

    This collaboration has recently shown that infrared excitation can drive decomposition reactions of molecules on the surface of gas-phase transition metal clusters. We describe here a significant extension of this work to the study of bimolecular reactions initiated in a similar manner. Specifically

  13. Monitoring equilibrium reaction dynamics of a nearly barrierless molecular rotor using ultrafast vibrational echoes

    Energy Technology Data Exchange (ETDEWEB)

    Nilsen, Ian A.; Osborne, Derek G.; White, Aaron M.; Anna, Jessica M.; Kubarych, Kevin J., E-mail: kubarych@umich.edu [Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109 (United States)

    2014-10-07

    Using rapidly acquired spectral diffusion, a recently developed variation of heterodyne detected infrared photon echo spectroscopy, we observe ∼3 ps solvent independent spectral diffusion of benzene chromium tricarbonyl (C{sub 6}H{sub 6}Cr(CO){sub 3}, BCT) in a series of nonpolar linear alkane solvents. The spectral dynamics is attributed to low-barrier internal torsional motion. This tripod complex has two stable minima corresponding to staggered and eclipsed conformations, which differ in energy by roughly half of k{sub B}T. The solvent independence is due to the relative size of the rotor compared with the solvent molecules, which create a solvent cage in which torsional motion occurs largely free from solvent damping. Since the one-dimensional transition state is computed to be only 0.03 k{sub B}T above the higher energy eclipsed conformation, this model system offers an unusual, nearly barrierless reaction, which nevertheless is characterized by torsional coordinate dependent vibrational frequencies. Hence, by studying the spectral diffusion of the tripod carbonyls, it is possible to gain insight into the fundamental dynamics of internal rotational motion, and we find some evidence for the importance of non-diffusive ballistic motion even in the room-temperature liquid environment. Using several different approaches to describe equilibrium kinetics, as well as the influence of reactive dynamics on spectroscopic observables, we provide evidence that the low-barrier torsional motion of BCT provides an excellent test case for detailed studies of the links between chemical exchange and linear and nonlinear vibrational spectroscopy.

  14. The functional role of protein dynamics in photosynthetic reaction centers investigated by elastic and quasielastic neutron scattering

    International Nuclear Information System (INIS)

    This short review summarizes our current knowledge about the functional relevance of protein dynamics in photosynthetic reaction centers. The essential processes of photosynthetic water splitting take place in a membrane-bound protein assembly denoted as Photosystem II (PS II). In the case of PS II membrane fragments, elastic and quasielastic neutron scattering experiments reveal a dynamical transition at about 240 K corresponding to the activation of picosecond molecular motions. Likewise, a 'freezing' of molecular dynamics is observed upon dehydration. Intriguingly, these effects correlate with the pronounced temperature- and hydration-dependence of specific electron transfer steps in PS II indicating that molecular dynamics is an indispensable prerequisite for its function. Thus, electron transfer in PS II appears to be a prototypical example for a dynamics-function correlation. Finally, the laser-neutron pump-probe technique is shown to permit in-situ monitoring of molecular dynamics in specific functional states of a protein in real time

  15. The functional role of protein dynamics in photosynthetic reaction centers investigated by elastic and quasielastic neutron scattering

    Directory of Open Access Journals (Sweden)

    Pieper Jörg

    2015-01-01

    Full Text Available This short review summarizes our current knowledge about the functional relevance of protein dynamics in photosynthetic reaction centers. In the case of Photosystem II membrane fragments, elastic and quasielastic neutron scattering experiments reveal a dynamical transition at about 240 K corresponding to the activation of picosecond molecular motions. Likewise, a “freezing” of molecular dynamics is observed upon dehydration. Intriguingly, these effects correlate with the pronounced temperature- and hydration-dependence of specific electron transfer steps in Photosystem II indicating that molecular dynamics is an indispensable prerequisite for its function. Thus, electron transfer in Photosystem II appears to be a prototypical example for a dynamics-function correlation. Finally, the laser-neutron pump-probe technique is shown to permit in-situ monitoring of molecular dynamics in specific functional states of a protein in real time.

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

    KAUST Repository

    Alsam, Amani A.

    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.

  17. An improved bimolecular fluorescence complementation tool based on superfolder green fluorescent protein

    Institute of Scientific and Technical Information of China (English)

    Jun Zhou; Jian Lin; Cuihong Zhou; Xiaoyan Deng; Bin Xia

    2011-01-01

    Bimolecular fluorescence complementation (BiFC) has been widely used in the analysis of protein-protein interactions (PPIs) in recent years. There are many notable advantages of BiFC such as convenience and direct visualization of PPI in cells. However, BiFC has one common limitation: the separated non-fluorescent fragments can be spontaneously self-assembled into an intact protein,which leads to false-positive results. In this study, a pair of complementary fragments (sfGFPN and sfGFPC) was constructed by splitting superfolder GFP (sfGFP) between the 214 and 215 amino acid residue, and sfGFPC was mutated by site-directed gene mutagenesis to decrease the signal of negative control. Our results showed that mutations in sfGFPC (sfGFPC(m12)) can effectively decrease the signal of negative control. Thus, we provide an improved BiFC tool for the analysis of PPI. Further,since the self-assembly problem is a common shortcoming for application of BiFC, our research provides a feasible strategy for other BiFC candidate proteins with the same problem.

  18. Analysis of the papillomavirus E2 and bromodomain protein Brd4 interaction using bimolecular fluorescence complementation.

    Directory of Open Access Journals (Sweden)

    Christine M Helfer

    Full Text Available The human papillomavirus (HPV vaccines effectively protect against new infections of up to four HPV subtypes. However, these vaccines are not protective against many other clinically relevant HPV subtypes and are ineffective at treating established HPV infections. There is therefore a significant need for antiviral treatments for persistent HPV infections. A promising anti-HPV drug target is the interaction between the HPV E2 protein and cellular bromodomain-containing protein 4 (Brd4 since this protein complex mediates several processes important for the viral life cycle including viral genome maintenance, replication, and transcription. Using bimolecular fluorescence complementation (BiFC technology, we demonstrate the E2 and Brd4 interaction on both interphase chromatin and mitotic chromosomes throughout mitosis. The E2-Brd4 BiFC was significantly diminished by mutating the Brd4 binding sites in E2 or by a dominant negative inhibitor of the E2-Brd4 interaction, demonstrating the potential of BiFC for identifying inhibitors of this important virus-host interaction. Importantly, when Brd4 was released from chromatin using the bromodomain inhibitor JQ1(+, the E2-Brd4 interacting complex relocated into foci that no longer associate with mitotic chromosomes, pointing to JQ1(+ as a promising antiviral inhibitor of HPV genome maintenance during HPV persistent infection.

  19. Studies of solvent effects on reaction dynamics using ultrafast transient absorption spectroscopy

    Science.gov (United States)

    Harris, Don Ahmasi

    Ultrafast transient absorption spectroscopy was used to investigate the solvent dependent reaction dynamics of two prototypical chemical systems: (1) The ring-opening reaction of 1,3-cyclohexadiene, the isolated chromophore in Provitamin D, and (2) The photolysis of various Vitamin B12 cofactors. We investigated the influence of solvent polarity on the ground state conformational relaxation of 1,3,5-cis hexatriene subsequent to the ring opening of 1,3-cyclohexadiene in methanol and 1-propanol solvents. Comparisons to the conformational relaxation in alkane solvents studied earlier demonstrated a surprising influence of solvent polarity on single bond isomerization. Temperature dependent transient absorption measurements were performed on 1,3,5-cis hexatriene in cyclohexane and 1-propanol to determine the effect of solvent polarity on the activation energy barrier for ground state single bond isomerization. These measurements conclude that the polar solvent lowers the energy barrier for single bond isomerization allowing conformational relaxation to proceed faster in alcohol solvents compared to alkane solvents. With no perceived polar transition state for single bond isomerization, this result disagrees with the conventional view of solvation and differentiates the single bond isomerization dynamics of polyenes from alkanes. Transient absorption spectroscopy was also utilized to study the solvent effects in the photolysis of various B12 cofactors in different environments. We investigated the solvent dependent photolysis of adenosylcobalamin, methylcobalamin, and cyanocobalamin in water and ethylene glycol as a function of solvent temperature. In comparing the radical cage escape of adenosylcobalamin and cyanocobalamin, we determined a larger than expected hydrodynamic radii for the diffusing radicals in water compared to ethylene glycol, thus making necessary a revised perspective of solvent interaction with the diffusing radical. In addition, we investigated the

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

    International Nuclear Information System (INIS)

    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 MoS2 tribofilm on iron surface. The initially amorphous MoS2 layer self-organized its structure as result of the tribochemical reactions and formed layered MoS2 tribofilm. The friction coefficient significantly decreased as the MoS2 tribofilm was formed. Besides, sliding was observed between sulfur layers of MoS2 tribofilms which occurred due to repulsive Coulombic interaction forces between sulfur atoms. This indicates that the formation of the layered MoS2 tribofilm is important to achieve better lubrication properties

  1. Influence of Soil Reaction on Phosphorus, Potassium, Calcium and Magnesium Dynamics in Grapevine (Vitis vinifera L.

    Directory of Open Access Journals (Sweden)

    Lepomir Čoga

    2009-03-01

    Full Text Available Influence of soil reaction on phosphorus, potassium, calcium and magnesium dynamics in grapevine was studied on the variety Sauvignon Blanc in 2007, in the Plešivica wine-growing region. Investigations were conducted on three vitisol subtypes: dystric cambisol (pHKCl 3.73-3.76, pseudogley (pHKCl 4.67-4.69 and rendzina on marl (pHKCl 7.21-7.27. To establish the amount and dynamics of P, K, Ca and Mg in plant material, leaf samples were taken three times during the growing period: at the flowering and veraison stages and at the end of the growing period. At all sampling times, significantly higher leaf contents of P, Ca and Mg were found on alkaline soil compared to acid soils, while differences in K levels were not statistically significant. Differences in P contents may be explained by better solubility and thereby better availability of P from Ca-phosphates compared to Al, Mn and Fe-phosphates in acid soils. In addition, the cation ratio K/(Ca+Mg that has a significant influence on grape quality, was also determined in leaves. Compared to optimal values (0.30–0.40, the least favourable ratio K/ (Ca+Mg was recorded at flowering on acid soils (0.38–0.77 and at harvest on calcareous soil (0.12–0.27. Differences in the content of sugar and total acids in must indicate a positive correlation between leaf contents of P, Ca and Mg and sugar content of must, and a negative correlation between leaf contents of P, Ca and Mg and the total acid content of must.

  2. Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

    International Nuclear Information System (INIS)

    A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact that accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S(1D) + HD → SH + D, S(1D) + DH → SD + H, N(2D) +H2 → NH + H, and H+ + D2 → HD + D+. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H2 → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions

  3. Reactive strip method for mixing and reaction in two dimensions

    CERN Document Server

    Bandopadhyay, Aditya; Méheust, Yves

    2016-01-01

    A numerical method to efficiently solve for mixing and reaction of scalars in a two-dimensional flow field at large P\\'eclet numbers but otherwise arbitrary Damk\\"ohler numbers is reported. We consider a strip of one reactant in a pool of another reactant, both of which are advected with the known velocity field. We first establish that the system evolution for such a system under certain conditions is described by a locally one-dimensional reaction-diffusion problem. The approximation of a locally one-dimensional dynamics is true for cases where the strip thickness is smaller than the local radius of curvature and also when the strip thickness is smaller than the distance between adjacent strips. We first demonstrate the method for the transport of a conservative scalar under a linear shear flow, point vortex and a chaotic sine flow. We then proceed to consider the situation with a simple bimolecular reaction between two reactants to yield a single product. The methodology presented herewith essentially gene...

  4. Probing Single-Molecule Dissociations from a Bimolecular Complex NO-Co-Porphyrin.

    Science.gov (United States)

    Kim, Howon; Chang, Yun Hee; Jang, Won-Jun; Lee, Eui-Sup; Kim, Yong-Hyun; Kahng, Se-Jong

    2015-07-28

    Axial coordinations of diatomic NO molecules to metalloporphyrins play key roles in dynamic processes of biological functions such as blood pressure control and immune response. Probing such reactions at the single molecule level is essential to understand their physical mechanisms but has been rarely performed. Here we report on our single molecule dissociation experiments of diatomic NO from NO-Co-porphyrin complexes describing its dissociation mechanisms. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses gave rise to dissociations of NO with threshold voltages, +0.68 and -0.74 V at 0.1 nA tunneling current on Au(111). From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances by stochastically tunneling electrons, which is supported with our density functional theory calculations. Our study shows that single molecule dissociation experiments can be used to probe reaction mechanisms in a variety of axial coordinations between small molecules and metalloporphyrins. PMID:26172541

  5. Fragment production in 16O + 80Br reaction within dynamical microscopic theory

    Indian Academy of Sciences (India)

    Rajeev K Puri; Jaivir Singh; Suneel Kumar

    2002-07-01

    We analyze the formation of fragments in O+Br reaction at different incident energies between / = 50 MeV and 200 MeV. This study is carried out within the quantum molecular dynamics (QMD) model coupled with recently advanced simulated annealing clusterization algorithm (SACA). For comparison, we also use the conventional minimum spanning tree (MST) method. Our detailed study shows that the SACA can detect the final stable fragment configuration as early as 60 fm/c which is marked by a dip in the heaviest fragment. On the other hand, the MST method needs several hundred fm/c to identify the final stable distribution. A comparison of the charge distribution with experimental data shows that the SACA is able to reproduce the data very nicely whereas (as reported earlier) the MST method fails to break the spectator matter into intermediate mass fragments. Furthermore, our results with SACA method indicate the onset of multi-fragmentation around 75 MeV/A which is again in good agreement with experimental findings.

  6. Universality in the cold and ultracold dynamics of the barrierless D$^{+}$+ H$_2$ reaction

    CERN Document Server

    Lara, Manuel; Aoiz, F J; Launay, J -M

    2014-01-01

    We have calculated quantum reactive and elastic cross-sections for D^{+}+ para-H2(v=0,j=0) $\\rightarrow$ H$^+$ + HD collisons using the hyperspherical quantum reactive scattering method [Chem. Phys. Lett. 1990,169, 473]. The H$_{3}^{+}$ system is the prototype of barrierless ion-molecule reactions, apart from its relevance in astrochemistry. The considered collision energy ranges from the ultracold regime, where only one partial wave is open, up to the Langevin regime, where many of them contribute. At very low kinetic energies, both an accurate description of the long-range (LR) region in the potential energy surface (PES), and long dynamical propagations, up to distances of 10$^{5}$ a0, are required. Accordingly, calculations have been carried out on the PES by Velilla et al. [J. Chem. Phys. 2008, 129,084307] which accurately reproduces the LR interactions. Hyperspherical methodology was recently modified in order to allow the accurate inclusion of LR interactions while minimizing the computational expense....

  7. The dynamics of localized spot patterns for reaction-diffusion systems on the sphere

    Science.gov (United States)

    Trinh, Philippe H.; Ward, Michael J.

    2016-03-01

    In the singularly perturbed limit corresponding to a large diffusivity ratio between two components in a reaction-diffusion (RD) system, quasi-equilibrium spot patterns are often admitted, producing a solution that concentrates at a discrete set of points in the domain. In this paper, we derive and study the differential algebraic equation (DAE) that characterizes the slow dynamics for such spot patterns for the Brusselator RD model on the surface of a sphere. Asymptotic and numerical solutions are presented for the system governing the spot strengths, and we describe the complex bifurcation structure and demonstrate the occurrence of imperfection sensitivity due to higher order effects. Localized spot patterns can undergo a fast time instability and we derive the conditions for this phenomena, which depend on the spatial configuration of the spots and the parameters in the system. In the absence of these instabilities, our numerical solutions of the DAE system for N  =  2 to N  =  8 spots suggest a large basin of attraction to a small set of possible steady-state configurations. We discuss the connections between our results and the study of point vortices on the sphere, as well as the problem of determining a set of elliptic Fekete points, which correspond to globally minimizing the discrete logarithmic energy for N points on the sphere.

  8. 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.

  9. Effects of isospin dynamics on neck fragmentation in isotopic nuclear reactions

    Science.gov (United States)

    Feng, Zhao-Qing

    2016-07-01

    The neck dynamics in Fermi-energy heavy-ion collisions, to probe the nuclear symmetry energy in the domain of subsaturation densities, is investigated within an isospin-dependent transport model. The single and double ratios of neutrons to protons from free nucleons and light clusters (complex particles) in the isotopic reactions are analyzed systematically. Isospin effects of particles produced from the neck fragmentations are explored. It is found that the ratios of the energetic isospin particles strongly depend on the stiffness of the nuclear symmetry energy and the effects increase with softening of the symmetry energy, which would be a nice probe for extracting the symmetry energy below the normal density in experiments. A flat structure appears at the tail spectra from the double ratio distributions. The neutron to proton ratio of light intermediate-mass fragments with charge number Z ≤8 is related to the density dependence of the symmetry energy with less sensitivity in comparison to the isospin ratios of nucleons and light particles.

  10. Progress of a new instrument to study molecular dynamics of interstellar ion-neutral reactions

    Science.gov (United States)

    Perera, Manori; Roenitz, Kevin; Lamm, Ben; Rudd, Lydia; Justl, Andrew; Landeweer, Steven; Roadman, Danny; Koscielniak, Justyna; Sonnenberger, Andrew

    2016-06-01

    Astrochemistry, a relatively young field of research, addresses a gap in our understanding of molecular evolution in space. With many space missions gathering data, the number of unresolved spectral lines is growing rapidly. Each year there are about three new molecules that are identified in the interstellar medium (ISM). However, our understanding of molecular processes, branching ratios, and rates are at a beginner level. For instance, we do not yet understand the chemical processes associated with the creation and evolution of even the most basic prebiotic molecules such as water and methanol in space. One of the important steps toward understanding the chemistry of the ISM is to identify, through laboratory and theoretical work, a list of potential target molecules that are likely to exist in the ISM. This work describes experimental progress towards building a spectrometer that is able to produce complex cold ions that will react with cooled neutral molecules under conditions similar to those in space. I plan to present the instrumental progress and how astronomical reaction dynamic needs will be met using the instrument, and the present status of the instrument and measurements in my lab.

  11. A diabatic representation including both valence nonadiabatic interactions and spin-orbit effects for reaction dynamics.

    Science.gov (United States)

    Valero, Rosendo; Truhlar, Donald G

    2007-09-01

    A diabatic representation is convenient in the study of electronically nonadiabatic chemical reactions because the diabatic energies and couplings are smooth functions of the nuclear coordinates and the couplings are scalar quantities. A method called the fourfold way was devised in our group to generate diabatic representations for spin-free electronic states. One drawback of diabatic states computed from the spin-free Hamiltonian, called a valence diabatic representation, for systems in which spin-orbit coupling cannot be ignored is that the couplings between the states are not zero in asymptotic regions, leading to difficulties in the calculation of reaction probabilities and other properties by semiclassical dynamics methods. Here we report an extension of the fourfold way to construct diabatic representations suitable for spin-coupled systems. In this article we formulate the method for the case of even-electron systems that yield pairs of fragments with doublet spin multiplicity. For this type of system, we introduce the further simplification of calculating the triplet diabatic energies in terms of the singlet diabatic energies via Slater's rules and assuming constant ratios of Coulomb to exchange integrals. Furthermore, the valence diabatic couplings in the triplet manifold are taken equal to the singlet ones. An important feature of the method is the introduction of scaling functions, as they allow one to deal with multibond reactions without having to include high-energy diabatic states. The global transformation matrix to the new diabatic representation, called the spin-valence diabatic representation, is constructed as the product of channel-specific transformation matrices, each one taken as the product of an asymptotic transformation matrix and a scaling function that depends on ratios of the spin-orbit splitting and the valence splittings. Thus the underlying basis functions are recoupled into suitable diabatic basis functions in a manner that

  12. Proton and charge transfer reactions dynamics of a hydroxyflavone derivative in a polar solvent and in a cyclodextrin nanocavity

    International Nuclear Information System (INIS)

    In this work, we report on the observation of ultrafast intramolecular charge- and proton-transfer reactions of 4'-dimethylaminoflavonol (DMAF) in N,N-dimethyl formamide and in γ-cyclodextrin (γ-CD) solution. Upon femtosecond excitation an intramolecular charge transfer (ICT) reaction takes place to produce an ICT structure in ∼200 fs. This structure may undergo a proton transfer reaction to generate a zwitterionic (Z) form in 2-3 ps, or relaxes in its potential energy well, to later equilibrate with that of Z in hundreds of ps. Addition of γ-CD does not significantly affect the fast dynamics of the formed anion. The fs-emission signals of the parent molecule, 3-hydroxyflavone, indicate that the dimethyl amino group in DMAF enhances the rate constant of intermolecular proton-transfer and intramolecular charge-transfer reactions

  13. Fusion and quasifission dynamics in the reactions $^{48}$Ca+$^{249}$Bk and $^{50}$Ti+$^{249}$Bk using TDHF

    CERN Document Server

    Umar, A S; Simenel, C

    2016-01-01

    Background: Synthesis of superheavy elements (SHE) with fusion-evaporation reactions is strongly hindered by the quasifission (QF) mechanism which prevents the formation of an equilibrated compound nucleus and which depends on the structure of the reactants. New SHE have been recently produced with doubly-magic $^{48}$Ca beams. However, SHE synthesis experiments with single-magic $^{50}$Ti beams have so far been unsuccessful. Purpose: In connection with experimental searches for $Z=117,119$ superheavy elements, we perform a theoretical study of fusion and quasifission mechanisms in $^{48}$Ca,$^{50}$Ti+$^{249}$Bk reactions in order to investigate possible differences in reaction mechanisms induced by these two projectiles. Methods: The collision dynamics and the outcome of the reactions are studied using unrestricted time-dependent Hartree-Fock (TDHF) calculations as well as the density-constrained TDHF method to extract the nucleus-nucleus potentials and the excitation energy in each fragment. Results: Nucleu...

  14. Ionization dynamics of water dimer on ice surface

    Science.gov (United States)

    Tachikawa, Hiroto

    2016-05-01

    The solid surface provides an effective two-dimensional reaction field because the surface increases the encounter probability of bi-molecular collision reactions. Also, the solid surface stabilizes a reaction intermediate because the excess energy generated by the reaction dissipates into the bath modes of surface. The ice surface in the universe is one of the two dimensional reaction fields. However, it is still unknown how the ice surface affects to the reaction mechanism. In the present study, to elucidate the specific property of the ice surface reaction, ionization dynamics of water dimer adsorbed on the ice surface was theoretically investigated by means of direct ab-initio molecular dynamics (AIMD) method combined with ONIOM (our own n-layered integrated molecular orbital and molecular mechanics) technique, and the result was compared with that of gas phase reaction. It was found that a proton is transferred from H2O+ to H2O within the dimer and the intermediate complex H3O+(OH) is formed in both cases. However, the dynamic features were different from each other. The reaction rate of the proton transfer on the ice surface was three times faster than that in the gas phase. The intermediate complex H3O+(OH) was easily dissociated to H3O+ and OH radical on the ice surface, and the lifetime of the complex was significantly shorter than that of gas phase (100 fs vs. infinite). The reason why the ice surface accelerates the reaction was discussed in the present study.

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

    International Nuclear Information System (INIS)

    Dynamic X-ray Diffraction (DXRD) has been to used to identify and quantify the solid state reactions that take place between sodium nickel ferrocyanide, Na2NiFe(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

  16. Dynamic Linkages between Denitrification Functional Genes/Enzymes and Biogeochemical Reaction Rates of Nitrate and Its Reduction Products

    Science.gov (United States)

    Li, M.; Shi, L.; Qian, W.; Gao, Y.; Liu, Y.; Liu, C.

    2015-12-01

    Denitrification is a respiratory process in which oxidized nitrogen compounds are used as alternative electron acceptors for energy production when oxygen is limited. Denitrification is an important process that not only accounts for the significant loss of nitrogen fertilizers from soils but also leads to NO, N2O and CO2 emissions, which are important greenhouse gas species. In this study, denitrification was investigated in Columbia River sediments, focusing on the dynamic linkages between functional genes/enzymes and biogeochemical reaction rates of nitrate and its reduction products. NO3-, NO2- and N2O were assayed in different incubation time. DNA was extracted from the sediments and functional genes were quantified as a function of time during the denitrification. Functional enzymes were extracted from the sediments and measured using a newly developed, targeted protein method. The biogeochemical, functional gene, and enzyme data were collectively used to establish the dynamic correlation of functional genes/enzymes and biogeochemical reaction rates. The results provide fundamental insights regarding the dynamic regulation of functional genes and enzymes in the processes of denitrification and greenhouse gas production, and also provide experimental data critical for the development of biogeochemical reaction models that incorporate genome-scale insights and describe macroscopic biogeochemical reaction rates in ecosystems.

  17. Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + Cl2 based on the GHNS potential energy surface with total angular momentum J = 0. The effects of the translational, vibrational and rotational excitation of Cl2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.

  18. Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl

    Institute of Scientific and Technical Information of China (English)

    王胜龙; 赵新生

    2001-01-01

    We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + CI2 based on the GHNS potential energy surface with total angular momentum J= 0. The effects of the translational, vibrational and rotational excitation of CI2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.

  19. Viral bimolecular fluorescence complementation: a novel tool to study intracellular vesicular trafficking pathways.

    Directory of Open Access Journals (Sweden)

    Brennan S Dirk

    Full Text Available The Human Immunodeficiency Virus type 1 (HIV-1 accessory protein Nef interacts with a multitude of cellular proteins, manipulating the host membrane trafficking machinery to evade immune surveillance. Nef interactions have been analyzed using various in vitro assays, co-immunoprecipitation studies, and more recently mass spectrometry. However, these methods do not evaluate Nef interactions in the context of viral infection nor do they define the sub-cellular location of these interactions. In this report, we describe a novel bimolecular fluorescence complementation (BiFC lentiviral expression tool, termed viral BiFC, to study Nef interactions with host cellular proteins in the context of viral infection. Using the F2A cleavage site from the foot and mouth disease virus we generated a viral BiFC expression vector capable of concurrent expression of Nef and host cellular proteins; PACS-1, MHC-I and SNX18. Our studies confirmed the interaction between Nef and PACS-1, a host membrane trafficking protein involved in Nef-mediated immune evasion, and demonstrated co-localization of this complex with LAMP-1 positive endolysosomal vesicles. Furthermore, we utilized viral BiFC to localize the Nef/MHC-I interaction to an AP-1 positive endosomal compartment. Finally, viral BiFC was observed between Nef and the membrane trafficking regulator SNX18. This novel demonstration of an association between Nef and SNX18 was localized to AP-1 positive vesicles. In summary, viral BiFC is a unique tool designed to analyze the interaction between Nef and host cellular proteins by mapping the sub-cellular locations of their interactions during viral infection.

  20. Identifying Enclosed Chemical Reaction and Dynamics at the Molecular Level Using Shell-Isolated Miniaturized Plasmonic Liquid Marble.

    Science.gov (United States)

    Han, Xuemei; Lee, Hiang Kwee; Lee, Yih Hong; Hao, Wei; Liu, Yejing; Phang, In Yee; Li, Shuzhou; Ling, Xing Yi

    2016-04-21

    Current microscale tracking of chemical kinetics is limited to destructive ex situ methods. Here we utilize Ag nanocube-based plasmonic liquid marble (PLM) microreactor for in situ molecular-level identification of reaction dynamics. We exploit the ultrasensitive surface-enhanced Raman scattering (SERS) capability imparted by the plasmonic shell to unravel the mechanism and kinetics of aryl-diazonium surface grafting reaction in situ, using just a 2-μL reaction droplet. This reaction is a robust approach to generate covalently functionalized metallic surfaces, yet its kinetics remain unknown to date. Experiments and simulations jointly uncover a two-step sequential grafting process. An initial Langmuir chemisorption of sulfonicbenzene diazonium (dSB) salt onto Ag surfaces forms an intermediate sulfonicbenzene monolayer (Ag-SB), followed by subsequent autocatalytic multilayer growth of Ag-SB3. Kinetic rate constants reveal 19-fold faster chemisorption than multilayer growth. Our ability to precisely decipher molecular-level reaction dynamics creates opportunities to develop more efficient processes in synthetic chemistry and nanotechnology. PMID:27050645

  1. Reaction dynamics induced by the radioactive ion beam 7Be on medium-mass and heavy targets

    Science.gov (United States)

    Mazzocco, M.; Boiano, A.; Boiano, C.; La Commara, M.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Stefanini, C.; Strano, E.; Torresi, D.; Acosta, L.; Di Meo, P.; Fernandez-Garcia, J. P.; Glodariu, T.; Grebosz, J.; Guglielmetti, A.; Keeley, N.; Lay, J. A.; Marquinez-Duran, G.; Martel, I.; Mazzocchi, C.; Molini, P.; Nicoletto, M.; Pakou, A.; Parkar, V. V.; Rusek, K.; Sánchez-Benítez, A. M.; Sandoli, M.; Sava, T.; Sgouros, O.; Signorini, C.; Silvestri, R.; Soramel, F.; Soukeras, V.; Stiliaris, E.; Stroe, L.; Toniolo, N.; Zerva, K.

    2015-10-01

    We studied the reaction dynamics induced at Coulomb barrier energies by the weakly-bound Radioactive Ion Beam 7Be (Sα = 1.586 MeV) on medium-mass (58Ni) and heavy (208Pb) targets. The experiments were performed at INFN-LNL (Italy), where a 2-3×105 pps 7Be secondary beam was produced with the RIB in-flight facility EXOTIC. Charged reaction products were detected by means of high-granularity silicon detectors in rather wide angular ranges. The contribution presents an up-to-date status of the data analysis and theoretical interpretation for both systems.

  2. Reaction dynamics induced by the radioactive ion beam 7Be on medium-mass and heavy targets

    International Nuclear Information System (INIS)

    We studied the reaction dynamics induced at Coulomb barrier energies by the weakly-bound Radioactive Ion Beam 7Be (Sα = 1.586 MeV) on medium-mass (58Ni) and heavy (208Pb) targets. The experiments were performed at INFN-LNL (Italy), where a 2-3×105 pps 7Be secondary beam was produced with the RIB in-flight facility EXOTIC. Charged reaction products were detected by means of high-granularity silicon detectors in rather wide angular ranges. The contribution presents an up-to-date status of the data analysis and theoretical interpretation for both systems

  3. Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

    International Nuclear Information System (INIS)

    The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

  4. Photo-induced isomerization and chemical reaction dynamics in superfluid helium droplets

    Science.gov (United States)

    Merritt, Jeremy; Douberly, Gary; Miller, Roger

    2008-03-01

    Near threshold photo-induced isomerization and photo-induced chemical reactions have long been sough after as sensitive probes of the underlying potential energy surface. One of the most important questions asked is how the initially bright quantum state couples to the reaction coordinate, and thus relates to energy transfer in general. Helium droplets have now allowed us to stabilize entrance channel clusters behind very small reaction barriers such that vibrational excitation may result in reaction. Through two examples, namely the isomerization of the 2 binary complexes of HF-HCN Douberly et al. PCCP 2005, 7,463, and the induced reaction of the gallium-HCN complex Merritt et al. JPCA 2007, DOI:10.1021/jp074981e we will show how the branching ratios for reaction and predissociation can determined and the influence of the superfluid He solvent.

  5. Distribution of energy in bimolecular chemiluminescent reactions involving hydrogen atoms. Final report, May 1, 1978-April 30, 1979

    International Nuclear Information System (INIS)

    Analysis of spectroscopic observations of the production of visible and ultraviolet photons from the collision of approx. 5-eV H atoms with a Li/Li2 crossed beam and with 02 and H2O crossed beams is described. Complementary theoretical and nonbeam spectroscopic work related to the Li2H system is also noted. 5 figures, 1 table

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

    International Nuclear Information System (INIS)

    A method of dynamic elution of recoiled 51Cr+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)

  7. Production of cold formaldehyde molecules for study and control of chemical reaction dynamics with hydroxyl radicals

    OpenAIRE

    Hudson, Eric R.; Ticknor, Christopher; Sawyer, Brian C.; Taatjes, Craig A.; Lewandowski, H. J.; Bochinski, J. R.; Bohn, John L.; Ye, Jun

    2005-01-01

    We propose a method for controlling a class of low temperature chemical reactions. Specifically, we show the hydrogen abstraction channel in the reaction of formaldehyde (H$_{2}$CO) and the hydroxyl radical (OH) can be controlled through either the molecular state or an external electric field. We also outline experiments for investigating and demonstrating control over this important reaction. To this end, we report the first Stark deceleration of the H$_{2}$CO molecule. We have decelerated ...

  8. 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.

  9. Anomalous reaction-transport processes: the dynamics beyond the Mass Action Law

    OpenAIRE

    Campos Moreno, Daniel; Fedotov, Sergei; Méndez López, Vicenç

    2008-01-01

    In this paper we reconsider the Mass Action Law (MAL) for the anomalous reversible reaction $A\\rightleftarrows B$ with diffusion. We provide a mesoscopic description of this reaction when the transitions between two states $A$ and $B$ are governed by anomalous (heavy-tailed) waiting-time distributions. We derive the set of mesoscopic integro-differential equations for the mean densities of reacting and diffusing particles in both states. We show that the effective reaction rate memory kernels...

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

    International Nuclear Information System (INIS)

    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

  11. 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)

    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 H2 stretching and CH3 umbrella modes, along with the translational energy, strongly promote the reactivity, while the CH3 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

  12. 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.

  13. 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

    Energy Technology Data Exchange (ETDEWEB)

    Kojima, H.; Yamada, A.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)

    2015-05-07

    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.

  14. Population–reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems

    OpenAIRE

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka

    2016-01-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism lev...

  15. Reaction dynamics following electron capture of chlorofluorocarbon adsorbed on water cluster : a direct density functional theory molecular dynamics study

    OpenAIRE

    Tachikawa, Hiroto; ABE, Shigeaki

    2007-01-01

    The electron capture dynamics of halocarbon and its water complex have been investigated by means of the full dimensional direct density functional theory molecular dynamics method in order to shed light on the mechanism of electron capture of a halocarbon adsorbed on the ice surface. The CF2Cl2 molecule and a cyclic water trimer (H2O)3 were used as halocarbon and water cluster, respectively. The dynamics calculation of CF2Cl2 showed that both C–Cl bonds are largely elongated after the electr...

  16. A Coupled Dynamical Model of Redox Flow Battery Based on Chemical Reaction, Fluid Flow, and Electrical Circuit

    OpenAIRE

    Li, Minghua; Hikihara, Takashi

    2008-01-01

    The redox (Reduction-Oxidation) flow battery is one of the most promising rechargeable batteries due to its ability to average loads and output of power sources. The transient characteristics are well known as the remarkable feature of the battery. Then it can also compensate for a sudden voltage drop. The dynamics are governed by the chemical reactions, fluid flow, and electrical circuit of its structure. This causes the difficulty of the analysis at transient state. This paper discusses the...

  17. 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.

  18. Stereo-dynamics of the exchange reaction Ha+LiHb→LiHa+Hb and its isotopic variants

    Institute of Scientific and Technical Information of China (English)

    Zhai Hong-Sheng; Yin Shu-Hui

    2012-01-01

    The quasi-classical trajectory (QCT) method is used to calculate the stereo-dynamics of the exchange reaction Ha+LiHb→LiHa+Hb and its isotopic variants based on an accurate potential energy surface reported by Prudente et al.[Prudente F V,Marques J M C and Maniero A M 2009 Chem.Phys.Lett.474 18].The reactive probability of the title reaction is computed.The vector correlations and four polarization-dependent generalized differential cross sections (PDDCSs) at different collision energies are presented.The influences of the collision energy and the reagent rotation on the product polarization are studied in the present work.The results indicate that the product rotational angular momentum j' is not only aligned,but also oriented along the direction perpendicular to the scattering plane.The product polarization distributions of the title reaction and its isotopic variants exhibit distinct differences which may arise from different mass combinations.

  19. 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.

  20. Charge carrier concentration dependence of encounter-limited bimolecular recombination in phase-separated organic semiconductor blends

    Science.gov (United States)

    Heiber, Michael C.; Nguyen, Thuc-Quyen; Deibel, Carsten

    2016-05-01

    Understanding how the complex intermolecular configurations and nanostructure present in organic semiconductor donor-acceptor blends impacts charge carrier motion, interactions, and recombination behavior is a critical fundamental issue with a particularly major impact on organic photovoltaic applications. In this study, kinetic Monte Carlo (KMC) simulations are used to numerically quantify the complex bimolecular charge carrier recombination behavior in idealized phase-separated blends. Recent KMC simulations have identified how the encounter-limited bimolecular recombination rate in these blends deviates from the often used Langevin model and have been used to construct the new power mean mobility model. Here, we make a challenging but crucial expansion to this work by determining the charge carrier concentration dependence of the encounter-limited bimolecular recombination coefficient. In doing so, we find that an accurate treatment of the long-range electrostatic interactions between charge carriers is critical, and we further argue that many previous KMC simulation studies have used a Coulomb cutoff radius that is too small, which causes a significant overestimation of the recombination rate. To shed more light on this issue, we determine the minimum cutoff radius required to reach an accuracy of less than ±10 % as a function of the domain size and the charge carrier concentration and then use this knowledge to accurately quantify the charge carrier concentration dependence of the recombination rate. Using these rigorous methods, we finally show that the parameters of the power mean mobility model are determined by a newly identified dimensionless ratio of the domain size to the average charge carrier separation distance.

  1. Effect of CH stretching excitation on the reaction dynamics of F + CHD3 → DF + CHD2

    International Nuclear Information System (INIS)

    The vibrationally excited reaction of F + CHD3(ν1 = 1) → DF + CHD2 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 CHD3 reagent in the crossed-beam region. It is found that all vibrational states of the CHD2 products observed in the ground-state reaction, which mainly involve the excitation of the umbrella mode of the CHD2 products, are severely suppressed by the CH stretching excitation. However, there are four additional vibrational states of the CHD2 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 CHD2 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

  2. DYNAMIC MATHEMATICAL MODELLING OF REACTION KINETICS FOR CYCLODEXTRINS PRODUCTION FROM DIFFERENT STARCH SOURCES USING BACILLUS MACERANS CYCLODEXTRIN GLUCANOTRANSFERASE

    Directory of Open Access Journals (Sweden)

    Syahinaz Shahrazi

    2013-01-01

    Full Text Available This study relates to the mathematical modelling of enzymatic production of Cyclodextrins (CDs by Cyclodextrin Glucanotransferase (CGTase from Bacillus macerans. The experiments were carried out in batch mode using different starch sources and the results were used to estimate unknown parameters using linearization and dynamic simulation methods. α- and β-CD produced from tapioca were found to give the highest Michaelis-Menten constant, KM,i of 58.23 and 54.07 g L-1, respectively and maximum velocity, Vmax,i of 3.45 and 2.76 g L-1.min, respectively, while sago resulted in the highest KM,i and Vmax,i values of 342.35 g L-1 and 5.97 g L-1.min, respectively, for γ-CD obtained by the linearization method. Value of product inhibition, K1,i and CD degradation coefficient rate, δCD,i, were estimated using dynamic simulation, indicating that exponential reaction kinetics could be fitted better with the experimental data. Sensitivity analysis revealed that the product inhibition parameter in the exponential reaction kinetic equation is more significant in the process. For validation, the production of CDs by fed batch method was undertaken and starch and enzyme were added into the reaction medium. Then, the predicted profiles generated by simulation were compared with the experimental values. The proposed exponential reaction kinetics shows good fitting with the experimental data.

  3. Study of fusion-fission dynamics in 19F+238U reaction

    Science.gov (United States)

    Dubey, R.; Sugathan, P.; Jhingan, A.; Kaur, Gurpreet; Mukul, Ish; Siwal, Davinder; Saneesh, N.; Banerjee, Tathagata; Yadav, Abhishek; Thakur, Meenu; Mahajan, Ruchi; Chaterjee, M. B.

    2016-05-01

    Mass angle distribution measurements for 19F+238U reaction were carried out around the sub barrier energies. Mass angle correlation has not been observed at above and below the fusion barrier in present reaction. This infer the minimal presence of non compound like events at these bombarding energies range.

  4. 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.

  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. QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels-Alder Reaction.

    Science.gov (United States)

    Yang, Zhongyue; Doubleday, Charles; Houk, K N

    2015-12-01

    We describe a solvent-perturbed transition state (SPTS) sampling scheme for simulating chemical reaction dynamics in condensed phase. The method, adapted from Truhlar and Gao's ensemble-averaged variational transition state theory, includes the effect of instantaneous solvent configuration on the potential energy surface of the reacting system (RS) and allows initial conditions for the RS to be sampled quasiclassically by TS normal mode sampling. We use a QM/MM model with direct dynamics, in which QM forces of the RS are computed at each trajectory point. The SPTS scheme is applied to the acceleration of the Diels-Alder reaction of cyclopentadiene (CP) + methyl vinyl ketone (MVK) in water. We explored the effect of the number of SPTS and of solvent box size on the distribution of bond lengths in the TS. Statistical sampling of the sampling was achieved when distribution of forming bond lengths converged. We describe the region enclosing the partial bond lengths as the transition zone. Transition zones in the gas phase, SMD implicit solvent, QM/MM, and QM/MM+QM (3 water molecules treated by QM) vary according to the ability of the medium to stabilize zwitterionic structures. Mean time gaps between formation of C-C bonds vary from 11 fs for gas phase to 25 fs for QM/MM+QM. Mean H-bond lengths to O(carbonyl) in QM/MM+QM are 0.14 Å smaller at the TS than in MVK reactant, and the mean O(carbonyl)-H(water)-O(water) angle of H-bonds at the TS is 10° larger than in MVK reactant. PMID:26588803

  7. Ab Initio Molecular Dynamics with Explicit Solvent Reveals a Two-Step Pathway in the Frustrated Lewis Pair Reaction.

    Science.gov (United States)

    Pu, Maoping; Privalov, Timofei

    2015-12-01

    The role solvent plays in reactions involving frustrated Lewis pairs (FLPs)-for example, the stoichiometric mixture of a bulky Lewis acid and a bulky Lewis base-still remains largely unexplored at the molecular level. For a reaction of the phosphorus/boron FLP and dissolved CO2 gas, first principles (Born-Oppenheimer) molecular dynamics with explicit solvent reveals a hitherto unknown two-step reaction pathway-one that complements the concerted (one-step) mechanism known from the minimum-energy-path calculations. The rationalization of the discovered reaction pathway-that is, the stepwise formation of PC and OB bonds-is that the environment (typical organic solvents) stabilizes an intermediate which results from nucleophilic attack of the phosphorus Lewis base on CO2 . This finding is significant because presently the concerted reaction-path paradigm predominates in the rationalization of FLP reactivity. Herein we point out how to attain experimental proof of our results. PMID:26524999

  8. Study of viscosity on the fission dynamics of the excited nuclei 228U produced in 19F + 209Bi reactions

    International Nuclear Information System (INIS)

    A two-dimensional (2D) dynamical model based on Langevin equations was applied to study the fission dynamics of the compound nuclei 228U produced in 19F + 209Bi reactions at intermediate excitation energies. The distance between the centers of masses of the future fission fragments was used as the first dimension and the projection of the total spin of the compound nucleus onto the symmetry axis, K, was considered as the second dimension in Langevin dynamical calculations. The magnitude of post-saddle friction strength was inferred by fitting measured data on the average pre-scission neutron multiplicity for 228U. It was shown that the results of calculations are in good agreement with the experimental data by using values of the post-saddle friction equal to 6–8 × 1021s-1. (author)

  9. Dynamic Multiscaling of the Reaction-Diffusion Front for mA+nB ->0

    OpenAIRE

    CORNELL, Stephen; Koza, Zbigniew; Droz, Michel

    1994-01-01

    We consider the reaction zone that grows between separated regions of diffusing species $A$ and $B$ that react according to $mA+nB\\to 0$, within the framework of the mean-fieldlike reaction-diffusion equations. For distances from the centre of the reaction zone much smaller than the diffusion length $X_D\\equiv \\sqrt{Dt}$, the particle density profiles are described by the scaling forms predicted by a quasistatic approximation, whereas they have a diffusive cutoff at a distance of order $X_D$....

  10. Dynamical birth and thermal death of angular momentum in heavy ion reactions

    International Nuclear Information System (INIS)

    Dynamical and equilibrium angular momentum fractionation as well as equilibrium angular momentum distributions associated with a variety of collective modes of the intermediate complex are described. (orig.)

  11. Effects of chemical reactions on the performance of gas dynamic lasers

    Energy Technology Data Exchange (ETDEWEB)

    Rom, J.; Stricker, J.

    1974-01-01

    It is shown that chemical reactions in the stagnation region of a gasdynamic laser in the shock tube may not be completed during the available test time. Therefore, analysis of data obtained in the shock tube must account for the instantaneous composition which may be effected by chemical reactions. A CO/sub 2/--N/sub 2/ gasdynamic laser experimental program in the shock tube including addition of H/sub 2/ into the system is described. This experiment involves reasonably complicated chemical reactions. These chemical reactions result in H/sub 2/O production under certain conditions. The comparison of the experimental results with the calculated results shows that such measurements can also be used to evaluate the energy transfer rates. The small-signal gain measurements indicate that the hydrogen is much more effective in depopulating the ..nu.. sub 3 level to ..nu.. sub 2 than previously assumed.

  12. Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

    International Nuclear Information System (INIS)

    We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtained with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation

  13. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach

    Science.gov (United States)

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid “2D/1D model”, i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  14. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach.

    Science.gov (United States)

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  15. Dynamic modelling of the effects of ion diffusion and side reactions on the capacity loss for vanadium redox flow battery

    Science.gov (United States)

    Tang, Ao; Bao, Jie; Skyllas-Kazacos, Maria

    The diffusion of vanadium ions across the membrane along with side reactions can have a significant impact on the capacity of the vanadium redox flow battery (VFB) over long-term charge-discharge cycling. Differential rates of diffusion of the vanadium ions from one half-cell into the other will facilitate self-discharge reactions, leading to an imbalance between the state-of-charge of the two half-cell electrolytes and a subsequent drop in capacity. Meanwhile side reactions as a result of evolution of hydrogen or air oxidation of V 2+ can further affect the capacity of the VFB. In this paper, a dynamic model is developed based on mass balances for each of the four vanadium ions in the VFB electrolytes in conjunction with the Nernst Equation. This model can predict the capacity as a function of time and thus can be used to determine when periodic electrolyte remixing or rebalancing should take place to restore cell capacity. Furthermore, the dynamic model can be potentially incorporated in the control system of the VFB to achieve long term optimal operation. The performance of three different types of membranes is studied on the basis of the above model and the simulation results together with potential operational issues are analysed and discussed.

  16. Production of cold formaldehyde molecules for study and control of chemical reaction dynamics with hydroxyl radicals

    CERN Document Server

    Hudson, E R; Sawyer, B C; Taatjes, C A; Lewandowski, H J; Bochinski, J R; Bohn, J L; Ye, J; Hudson, Eric R.; Ticknor, Christopher; Sawyer, Brian C.; Taatjes, Craig A.; Bohn, John L.; Ye, Jun

    2005-01-01

    We propose a method for controlling a class of low temperature chemical reactions. Specifically, we show the hydrogen abstraction channel in the reaction of formaldehyde (H$_{2}$CO) and the hydroxyl radical (OH) can be controlled through either the molecular state or an external electric field. We also outline experiments for investigating and demonstrating control over this important reaction. To this end, we report the first Stark deceleration of the H$_{2}$CO molecule. We have decelerated a molecular beam of H$_{2}$CO essentially to rest, producing cold molecule packets at a temperature of 100 mK with a few million molecules in the packet at a density of $\\sim10^{6}$ cm$^{-3}$.

  17. Quantum dynamics of the Cl+H2 reaction at ultracold temperatures

    Indian Academy of Sciences (India)

    N Balakrishnan

    2012-01-01

    Quantum calculations are reported for the reaction between vibrationally excited H2 molecules and Cl atoms at energies ranging from the ultracold to thermal regimes. It is found that chemical reaction leading to vibrationally excited HCl molecules dominates over non-reactive vibrational quenching. The product HCl molecule is found to be formed predominantly in the = 1 vibrational level with appreciable rotational excitation. A spin-orbit uncorrected value of 1.86 × 10−12 cm3 molecule-1 s-1 is predicted for the rate coefficient in the zero-temperature limit, which is about two orders of magnitude larger than the thermal rate coefficient of the Cl+H2 reaction at 300 K.

  18. An eight-dimensional quantum dynamics study of the Cl + CH4→ HCl + CH3 reaction

    International Nuclear Information System (INIS)

    In this work, the later-barrier reaction Cl + CH4 → HCl + CH3 is investigated with an eight-dimensional quantum dynamics method [R. Liu et al., J. Chem. Phys. 137, 174113 (2012)] on the ab initio potential energy surface of Czakó and Bowman [J. Chem. Phys. 136, 044307 (2012)]. The reaction probabilities with CH4 initially in its ground and vibrationally excited states are calculated with a time-dependent wavepacket method. The theoretical integral cross sections (ICSs) are extensively compared with the available experimental measurements. For the ground state reaction, the theoretical ICSs excellently agree with the experimental ones. The good agreements are also achieved for ratios between ICSs of excited reactions. For ICS ratios between various states, the theoretical values are also consistent with the experimental observations. The rate constants over 200-2000 K are calculated and the non-Arrhenius effect has been observed which is coincident with the previous experimental observations and theoretical calculations

  19. Reaction dynamics induced by the radioactive ion beam {sup 7}Be on medium-mass and heavy targets

    Energy Technology Data Exchange (ETDEWEB)

    Mazzocco, M., E-mail: marco.mazzocco@pd.infn.it; Stefanini, C.; Strano, E.; Torresi, D.; Lay, J. A.; Molini, P.; Soramel, F. [Dipartimento di Fisica e Astronomia, Università di Padova, via F. Marzolo 8, I-35131 Padova (Italy); INFN-Sezione di Padova, via F. Marzolo 8, I-35131 Padova (Italy); Boiano, A.; Parascandolo, C.; Pierroutsakou, D.; Di Meo, P. [INFN-Sezione di Napoli, via Cintia, I-80126, Napoli (Italy); Boiano, C. [INFN-Sezione di Milano, via Celoria 16, I-20133, Napoli (Italy); La Commara, M.; Sandoli, M.; Silvestri, R. [INFN-Sezione di Napoli, via Cintia, I-80126, Napoli (Italy); Dipartimento di Fisica, Università di Napoli “Federico II”, via Cintia, I-80126, Napoli (Italy); Manea, C.; Nicoletto, M. [INFN-Sezione di Padova, via F. Marzolo 8, I-35131 Padova (Italy); Acosta, L. [Departamento de Fìsica Aplicada, Universidad de Huelva, Campus de El Carmen, E-21071 Huelva (Spain); INFN-Sezione di Catania, via Santa Sofia 64, I-95123, Catania (Italy); Fernandez-Garcia, J. P. [INFN-Sezione di Catania, via Santa Sofia 64, I-95123, Catania (Italy); Glodariu, T. [National Institute for Physics and Nuclear Engineering (NIPNE), 30 Reactorului St., 077125 Magurele (Romania); and others

    2015-10-15

    We studied the reaction dynamics induced at Coulomb barrier energies by the weakly-bound Radioactive Ion Beam {sup 7}Be (S{sub α} = 1.586 MeV) on medium-mass ({sup 58}Ni) and heavy ({sup 208}Pb) targets. The experiments were performed at INFN-LNL (Italy), where a 2-3×10{sup 5} pps {sup 7}Be secondary beam was produced with the RIB in-flight facility EXOTIC. Charged reaction products were detected by means of high-granularity silicon detectors in rather wide angular ranges. The contribution presents an up-to-date status of the data analysis and theoretical interpretation for both systems.

  20. On the dynamics of immobilized enzyme kinetics in a microreactor: A study of AP-catalyzed reactions

    Directory of Open Access Journals (Sweden)

    Pratap R Patnaik

    2011-11-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin-top:0in; mso-para-margin-right:0in; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0in; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} The kinetics of immobilized enzyme-catalyzed reactions in microreactors differ from those in macro-scale reactors. Recognizing this, a recent study (Patnaik 2011 based on a new interpretation of the kinetics of AP-catalyzed reactions showed that dynamic behavior is feasible only certain loci relating key kinetic parameters. That work has been extended here, and the kinetic parameters have now been related to bulk phase concentrations, thereby providing a link with the reaction system per se. It has also been shown that under certain conditions the reaction may become self-quenching but either monotonically or as damped oscillations. These two studies thus establish the importance of understanding kinetic dynamics in microreactors and in selecting feasible operating conditions.

  1. 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.

  2. 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

  3. Dynamics of reactions O((1)D)+C(6)H(6) and C(6)D(6).

    Science.gov (United States)

    Chen, Hui-Fen; Liang, Chi-Wei; Lin, Jim J; Lee, Yuan-Pern; Ogilvie, J F; Xu, Z F; Lin, M C

    2008-11-01

    The reaction between O((1)D) and C(6)H(6) (or C(6)D(6)) was investigated with crossed-molecular-beam reactive scattering and time-resolved Fourier-transform infrared spectroscopy. From the crossed-molecular-beam experiments, four product channels were identified. The major channel is the formation of three fragments CO+C(5)H(5)+H; the channels for formation of C(5)H(6)+CO and C(6)H(5)O+H from O((1)D)+C(6)H(6) and OD+C(6)D(5) from O((1)D)+C(6)D(6) are minor. The angular distributions for the formation of CO and H indicate a mechanism involving a long-lived collision complex. Rotationally resolved infrared emission spectra of CO (1ratio of [CO]/[OH]=2.1+/-0.4 for O((1)D)+C(6)H(6) and [CO]/[OD]>2.9 for O((1)D)+C(6)D(6) is consistent with the expectation for an abstraction reaction. The mechanism of the reaction may be understood from considering the energetics of the intermediate species and transition states calculated at the G2M(CC5) level of theory for the O((1)D)+C(6)H(6) reaction. The experimentally observed branching ratios and deuterium isotope effect are consistent with those predicted from calculations. PMID:19045343

  4. Quantum dynamics of insertion reactions involving metastable atoms and H2

    Science.gov (United States)

    Honvault, Pascal; Launay, Jean-Michel

    2004-05-01

    Using a time-independent method with body-frame democratic hyperspherical coordinates, we have performed quantum reactive scattering calculations on recent ab initio potential energy surfaces for the O(1D), N(2D), C(1D) and S(1D) + H2 reactions [1]. We have found that these reactions present common features (decrease of the vibrational distribution with the final vibrational state v', forward-backward symmetry in center-of-mass differential cross sections,...). However some features are specific for each reaction : for O(1D) + H2, important role of the first excited potential energy surface for energies larger than 100 meV; tunneling effect in the initial arrangement for N(2D) + H2; dense resonance structures in reaction probabilities for C(1D) and S(1D) + H2. [1] F.J. Aoiz et al., Phys. Rev. Lett., 86, 1729 (2001); N. Balucani et al., Phys. Rev. Lett., 89, 013201 (2002); L. Banares, F.J. Aoiz, P. Honvault, B. Bussery-Honvault, J.-M. Launay, J. Chem. Phys., 118, 565 (2003); P. Honvault, J.-M. Launay, Chem. Phys. Lett., 370, 371 (2003).

  5. Reaction dynamics of 34-38Mg projectile with carbon target using Glauber model

    International Nuclear Information System (INIS)

    We have studied nuclear reaction cross-sections for 34-38Mg isotopes as projectile with 12C 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 37Mg is also investigated

  6. In pursuit of eternal beauty in the very instantaneous——A glance at molecular reaction dynamics research at DICP

    Institute of Scientific and Technical Information of China (English)

    SONG Jianlan

    2009-01-01

    @@ Enchanted by the glamour of the fascinating effects resulting from the collisions between the molecules of hydrogen, deuteride and fluorine, Prof. YANG Xueming never expects to attract too many spotlights. However, over the past few years after his returning to the Dalian Institute of Chemical Physics (DICP), CAS, his team was frequently caught by the media on the center stage. Discoveries made by his team ranked top 10 S&T advancements of China consecutively in 2006 and 2007. Significant progress was also made in 2008 by this group in the research field of molecular reaction dynamics, and he himself has won a number of important awards and prizes.

  7. Rate Coefficients of the HCl + OH → Cl + H2O Reaction from Ring Polymer Molecular Dynamics.

    Science.gov (United States)

    Zuo, Junxiang; Li, Yongle; Guo, Hua; Xie, Daiqian

    2016-05-26

    Thermal rate coefficients at temperatures between 200 and 1000 K are calculated for the HCl + OH → Cl + H2O reaction on a recently developed permutation invariant potential energy surface, using ring polymer molecular dynamics (RPMD). Large deviations from the Arrhenius limit are found at low temperatures, suggesting significant quantum tunneling. Agreement with available experimental rate coefficients is generally satisfactory, although the deviation becomes larger at lower temperatures. The theory-experiment discrepancy is attributed to the remaining errors in the potential energy surface, which is known to slightly overestimate the barrier. In the deep tunneling region, RPMD performs better than traditional transition-state theory with semiclassical tunneling corrections. PMID:27149243

  8. Role of the BO bond in the reaction dynamics of BO+H 2→HBO+H

    Science.gov (United States)

    Sogas, J.; Albertí, M.; Giménez, X.; Aguilar, A.

    2001-10-01

    An extensive quasiclassical trajectory study of the dynamics of the title reaction has been carried out on a six-dimensional, analytical potential energy surface, with the goal of understanding the role of the BO bond. For this purpose, trajectories for different hypothetical isotopes of the BO molecule have been calculated, for selected rovibrational levels of the reactants, at low and moderate collision energies. For all these cases, a clear departure from the BO bond spectator behaviour, as well as an unexpected role of hindered rotation normal modes at the transition state, is found.

  9. Probing Reaction Dynamics of Transition-Metal Complexes in Solution via Time-Resolved X-ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Huse, Nils; Khalil, Munira; Kim, Tae Kyu; Smeigh, Amanda L.; Jamula, Lindsey; McCusker, James K.; Schoenlein, Robert W.

    2009-05-24

    We report measurements of the photo-induced Fe(II) spin crossover reaction dynamics in solution via time-resolved x-ray absorption spectroscopy. EXAFS measurements reveal that the iron?nitrogen bond lengthens by 0.21+-0.03 Angstrom in the high-spin transient excited state relative to the ground state. XANES measurements at the Fe L-edge show directly the influence of the structural change on the ligand-field splitting of the Fe(II) 3d orbitals associated with the spin transition.

  10. Probing reaction dynamics of transition-metal complexes in solution via time-resolved X-ray spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Huse, Nils [Chemical Sciences Division, Lawrence Berkeley National Laboratory, 1Cyclotron Road, Berkeley, CA 94720 (United States); Khalil, Munira [Department of Chemistry, University of Washington, Seattle, WA 98195 (United States); Kim, Tae Kyu [Department of Chemistry, Pusan National University, Busan 609-735 (Korea, Republic of); Smeigh, Amanda L; Jamula, Lindsey; McCusker, James K [Department of Chemistry, Michigan State University, East Lansing, MI 48824 (United States); Schoenlein, Robert W, E-mail: nhuse@lbl.go, E-mail: rwschoenlein@lbl.go [Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA (United States)

    2009-02-01

    We report measurements of the photoinduced Fe{sup II} spin crossover reaction dynamics in solution via time-resolved x-ray absorption spectroscopy. EXAFS measurements reveal that the iron-nitrogen bond lengthens by 0.21+-0.03 A in the high-spin transient excited state relative to the ground state. XANES measurements at the Fe L-edge show directly the influence of the structural change on the ligand-field splitting of the Fe{sup II} 3d orbitals associated with the spin transition.

  11. Quantum molecular dynamics approach to estimate spallation yield from + 208Pb reaction at 800 MeV

    Indian Academy of Sciences (India)

    P K Sarkar; Maitreyee Nandy

    2003-10-01

    The spallation yield of neutrons and other mass fragments produced in 800 MeV proton induced reaction on 208Pb have been calculated in the framework of quantum molecular dynamics (QMD) model. The energy spectra and angular distribution have been calculated. Also, multiplicity distributions of the emitted neutrons and kinetic energy carried away by them have been estimated and compared with the available experimental data. The agreement is satisfactory. A major contribution to the neutron emission comes from statistical decay of the fragments. For mass and charge distributions of spallation productsthe QMD process gives rise to target-like and projectile-like fragments only.

  12. A comprehensive study of in-complete fusion reaction dynamics in 16O + 181Ta system at 4-7 MeV/nucleon

    International Nuclear Information System (INIS)

    For the better understanding of ICF reaction dynamics, system 16O + 181Ta has been studied where, excitation functions (EFs) and recoil range distributions (RRDs) for a large number of reaction products have been measured, thus having a complementary as well as comprehensive study of this system

  13. Probing dynamics of fusion reactions through cross-section and spin distribution measurement

    Directory of Open Access Journals (Sweden)

    Kaur Maninder

    2016-01-01

    Full Text Available Present work aims to explicate the effect of entrance channel mass asymmetry on fusion dynamics for the Compound Nucleus 80Sr populated through two different channels, 16O+64Zn and 32S+48Ti, using cross-section and spin distribution measurements as probes. The evaporation spectra studies for these systems, reported earlier indicate the presence of dynamical effects for mass symmetric 32S+48Ti system.The CCDEF and TDHF calculations have been performed for both the systems and an attempt has been made to explain the reported deviations in the α-particle spectrum for the mass symmetric system.

  14. Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

    International Nuclear Information System (INIS)

    In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency

  15. Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca [Department of Mathematics, Ryerson University, Toronto, Ontario M5B 2K3 (Canada)

    2015-12-21

    In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

  16. Vector meson-baryon dynamics in photoproduction reactions around 2 GeV

    Directory of Open Access Journals (Sweden)

    Ramos A.

    2014-01-01

    Full Text Available We investigate the role of vector mesons and coupled-channel unitarization on photoproduction reactions o_ the proton at energies around 2 GeV. We explain the sudden drop on the γp → K0Σ+ cross section, observed recently by the CBELSA/TAPS collaboration, by a delicate interference between amplitudes having K*Λ and K*Σ intermediate states modulated by the presence of a nearby N* resonance produced by our model, a feature that we have employed to predict its properties. We also show the importance of coupled-channel unitarization in the γp → K*0Σ+ reaction, measured recently by CBELSA/TAPS and CLAS with conflicting results.

  17. Fast dynamic neutron sources based on the (γ,n) reactions

    International Nuclear Information System (INIS)

    Highly monoenergetic photon beams in the energy range 5 to 10 MeV obtained from thermal neutron capture on metallic elements such as iron, chromium, nickel, manganese, and copper are used for generating monoenergetic fast neutrons from the (γ,n) reactions on various elements. The later are resonance reactions based on a chance overlap between a γ line of the photon source and a nuclear level in the target. Both the incident γ lines and the nuclear levels are Doppler broadened where the broadening is caused by thermal motion and by the strong binding forces of the metallic state and is of the order of 10 eV for energies of around 8 MeV. (authors). 3 refs., 1 tab

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

    International Nuclear Information System (INIS)

    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 16O + 169Tm 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

  19. Understanding of the Effects of Ionic Strength on the Bimolecular Rate Constant between Structurally Identified Redox Enzymes and Charged Substrates Using Numerical Simulations on the Basis of the Poisson-Boltzmann Equation.

    Science.gov (United States)

    Sugimoto, Yu; Kitazumi, Yuki; Shirai, Osamu; Yamamoto, Masahiro; Kano, Kenji

    2016-03-31

    To understand electrostatic interactions in biomolecules, the bimolecular rate constants (k) between redox enzymes and charged substrates (in this study, redox mediators in the electrode reaction) were evaluated at various ionic strengths (I) for the mediated bioelectrocatalytic reaction. The k value between bilirubin oxidase (BOD) and positively charged mediators increased with I, while that between BOD and negatively charged mediators decreased with I. The opposite trend was observed for the reaction of glucose oxidase (GOD). In the case of noncharged mediators, the k value was independent of I for both BOD and GOD. These results reflect the electrostatic interactions between the enzymes and the mediators. Furthermore, we estimated k/k° (k° being the thermodynamic rate constant) by numerical simulation (finite element method) based on the Poisson-Boltzmann (PB) equation. By considering the charges of individual atoms involved in the amino acids around the substrate binding sites in the enzymes, the simulated k/k° values well reproduced the experimental data. In conclusion, k/k° can be predicted by PB-based simulation as long as the crystal structure of the enzyme and the substrate binding site are known. PMID:26956542

  20. 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

    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...

  1. Role of diffuseness coefficient in reaction dynamics using collective clusterization method

    International Nuclear Information System (INIS)

    In the present work, the decay of compound nucleus 112Xe* is studied using the dynamical cluster decay model (DCM) over a wide range of energies. The issue of fusion hindrance is addressed within DCM in terms of its inbuilt property of barrier lowering which helps to account for the data at sub barrier region

  2. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation. [Spiropyrans

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, B.J.

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in [approximately]240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH[sub 2]I[sub 2] and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a [approximately]350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  3. Preface to the Special Issue: International Workshop on Nuclear Dynamics in Heavy-Ion Reactions and Neutron Stars

    International Nuclear Information System (INIS)

    The International Workshop on Nuclear Dynamics in Heavy-Ion Reactions and Neutron Stars was held from 9-14 July 2007 in Beijing. This workshop was organized by Beijing Normal University, Shanghai Institute of Applied Physics of the Chinese Academy of Sciences, Shanghai Jiatong University, Huzhou Teachers' College, Institute of High Energy Physics of the Chinese Academy of Sciences, Laboratori Nazionali del Sud (LNS) of Istituto Nazionale di Fisica Nucleare (INFN), University of Catania, and Texas A & M University-Commerce. More than 60 physicists, from local and abroad, participated in the workshop and more than 35 of them presented talks. The workshop covered a great variety of hot topics, including nuclear reaction dynamics and isospin effects in heavy-ion collisions, EOS of nuclear matter and neutron stars, phase transitions of nuclear matter (liquid-to-gas in low energy HIC, QGP in high energy HIC, color superconductivity), exotic nuclei and structure of hadronic matter in the high density regime (neutron star inner core).

  4. REACTION CHEMISTRY RELATED TO FCC GASOLINE QUALITY

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    About 80% of the gasoline pool as a whole in China for supplying the domestic market at current stage directly originates from FCC units. Obviously, FCC gasoline quality is critical for refiners to meet the nations more and more stringent gasoline specifications. FCC process is expected to produce gasoline with reduced contents of olefins, aromatics, benzene, sulfur, and, contradictorily, still with high octane number.   Catalytic cracking process involves a series of acid catalyzed reactions. Bronsted acid sites dominate the surface of the catalyst used for FCC process. All the reactions of hydrocarbons in FCC process are based on carbonium ions of penta-coordinated, or carbenium ions of tri-coordinated. The monomolecular beta scission mechanism for alkane cracking explains that the cracking of carbon-carbon bonding occurs at the beta position to the carbon atom bearing positive charge, and hence forms two small hydrocarbon molecules: one alkane molecule and one olefin molecule. The molar ratio of alkane to olefin for the primary cracking product will be 1 and it will be less than 1 if the cracking reaction proceeds.   However, it is proved that bimolecular reaction pathways exist between surface carbenium ions and the feed molecules. The products of this bimolecular disproportionation reaction could be an alkane molecule and a newly formed carbenium ion. The better understanding of the reaction chemistry of FCC process based on monomolecular pathways and bimolecular pathways should be the basis for searching approaches to the improvement of FCC gasoline quality. In the complicated reaction scheme of the FCC process, the isomerization reaction leading to the formation of iso-alkanes is obviously a target reaction, which favors both olefin reduction and octane enhancement.   The cracking of small paraffin molecules, due to its limited number of reaction pathways and products, has been used to investigate cracking mechanism. In the present work the

  5. Bimolecular Fluorescence Complementation (BiFC) Analysis of Protein-Protein Interactions and Assessment of Subcellular Localization in Live Cells.

    Science.gov (United States)

    Pratt, Evan P S; Owens, Jake L; Hockerman, Gregory H; Hu, Chang-Deng

    2016-01-01

    Bimolecular fluorescence complementation (BiFC) is a fluorescence imaging technique used to visualize protein-protein interactions (PPIs) in live cells and animals. One unique application of BiFC is to reveal subcellular localization of PPIs. The superior signal-to-noise ratio of BiFC in comparison with fluorescence resonance energy transfer or bioluminescence resonance energy transfer enables its wide applications. Here, we describe how confocal microscopy can be used to detect and quantify PPIs and their subcellular localization. We use basic leucine zipper transcription factor proteins as an example to provide a step-by-step BiFC protocol using a Nikon A1 confocal microscope and NIS-Elements imaging software. The protocol given below can be readily adapted for use with other confocal microscopes or imaging software. PMID:27515079

  6. Unusual charge transport and reduced bimolecular recombination in PDTSiTzTz:PC71BM bulk heterojunction blend

    International Nuclear Information System (INIS)

    Solar cells with bulk heterojunction active layers containing donor-acceptor copolymer PDTSiTzTz exhibit persistent high fill factors with thicknesses up to 400 nm. Transport and recombination in a blend of PDTSiTzTz and fullerene derivative PC71BM is studied using lateral organic photovoltaic structures. This material system is characterized by carrier-concentration-dependent charge carrier mobilities, a strongly reduced bimolecular recombination factor, and a negative Poole–Frenkel coefficient. The analysis provides an explanation for the relatively thickness-independent fill factor behaviour seen in solar cells using the copolymer PDTSiTzTz. Cumulative insights from this copolymer can be employed for future organic photovoltaic material development, study of existing high performance bulk heterojunciton blends, and improved solar cell design. (paper)

  7. Lighting the Way to Protein-Protein Interactions: Recommendations on Best Practices for Bimolecular Fluorescence Complementation Analyses[OPEN

    Science.gov (United States)

    Kudla, Jörg

    2016-01-01

    Techniques to detect and verify interactions between proteins in vivo have become invaluable tools in functional genomic research. While many of the initially developed interaction assays (e.g., yeast two-hybrid system and split-ubiquitin assay) usually are conducted in heterologous systems, assays relying on bimolecular fluorescence complementation (BiFC; also referred to as split-YFP assays) are applicable to the analysis of protein-protein interactions in most native systems, including plant cells. Like all protein-protein interaction assays, BiFC can produce false positive and false negative results. The purpose of this commentary is to (1) highlight shortcomings of and potential pitfalls in BiFC assays, (2) provide guidelines for avoiding artifactual interactions, and (3) suggest suitable approaches to scrutinize potential interactions and validate them by independent methods. PMID:27099259

  8. 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)

    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

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

    International Nuclear Information System (INIS)

    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 CH3CO+ and CH4, and C-O bond cleavagto C3H5+ (presumably to allyl cation) and H2O. The CH3CO+ 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 C3H5+ 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

  10. The pp->p Lambda K+ and pp->p Sigma0 K+ reactions with chiral dynamics

    CERN Document Server

    Xie, Ju-Jun; Oset, E

    2011-01-01

    We report on a theoretical study of the pp->p Lambda K+ and pp->p Sigma0 K+ reactions near threshold using a chiral dynamical approach. The production process is described by single-pion and single-kaon exchange. The final state interactions of nucleon-hyperon, K-hyperon and K-nucleon systems are also taken into account. We show that our model leads to a fair description of the experimental data on the total cross section of the pp->p Lambda K+ and pp->p Sigma0 K+ reactions. We find that the experimental observed strong suppression of Sigma0 production compared to Lambda production at the same excess energy can be explained. However, ignorance of phases between some amplitudes does not allow to properly account for the nucleon-hyperon final state interaction for the pp->p Sigma0 K+ reaction. We also demonstrate that the invariant mass distribution and the Dalitz plot provide direct information about the Lambda and Sigma0 production mechanism, and can be tested by experiments at COSY or HIRFL-CSR.

  11. Dynamic Solvent Control of a Reaction in Ionic Deep Eutectic Solvents: Time-Resolved Fluorescence Measurements of Reactive and Nonreactive Dynamics in (Choline Chloride + Urea) Melts.

    Science.gov (United States)

    Das, Anuradha; Biswas, Ranjit

    2015-08-01

    Dynamic fluorescence anisotropy and Stokes shift measurements of [f choline chloride + (1 - f) urea)] deep eutectic solvents at f = 0.33 and 0.40 have been carried out using a dipolar solute, coumarin 153 (C153), in the temperature range 298 ≤ T ≤ 333 K. Subsequently, measured time-dependent solvent response is utilized to investigate the dynamic solvent control on the measured rates of photoexcited intramolecular charge transfer (ICT) reactions of two molecules, 4-(1-azetidinyl)benzonitrile (P4C) and 4-(1-pyrrolidinyl)benzonitrile (P5C), occurring in these media. Measured average reaction time scales (⟨τ(rxn)⟩) exhibit the following dependence on average solvation times scales (⟨τ(s)⟩): ⟨τ(rxn)⟩ ∝ ⟨τ(s)⟩(α) with α = 0.5 and 0.35 for P4C and P5C, respectively. Such a strong dynamic solvent control of ⟨τ(rxn)⟩, particularly for P4C, is different from earlier observations with these ICT molecules in conventional molecular solvents. Excitation wavelength-dependent fluorescence emissions of C153 and trans-2-[4-(dimethylamino)styryl]-benzothiazole (DMASBT), which differ widely in average fluorescence lifetimes (⟨τ(life)⟩), suggest the presence of substantial spatial heterogeneity in these systems. Dynamic heterogeneity is reflected via the following fractional viscosity (η) dependences of ⟨τ(s)⟩ and ⟨τ(r)⟩ (⟨τ(r)⟩ being solute's average rotation time): ⟨τx⟩ ∝ (η/T)(p) with 0.7 ≤ p ≤ 0.9. Different correlations between ⟨τ(s)⟩ and ⟨τ(r)⟩ emerge at different temperature regimes, indicating variable frictional coupling at low and high temperatures. Estimated dynamic Stokes shifts in these media vary between ∼1200 and ∼1600 cm(-1), more than 50% of which possess a time scale much faster than the temporal resolution (∼75 ps) employed in these measurements. Estimated activation energy for η is closer to that for ⟨τ(r)⟩ than that for ⟨τ(s)⟩, suggesting ⟨τ(s)⟩ being more decoupled

  12. A ``partitioned leaping'' approach for multiscale modeling of chemical reaction dynamics

    Science.gov (United States)

    Harris, Leonard A.; Clancy, Paulette

    2006-10-01

    We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single partitioned leaping algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters, and is particularly well suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation, and demonstrate the utility of the method via illustrative examples.

  13. Intramolecular dynamics and unimolecular reaction. A case study of state-selectively excited nitrogen dioxide

    International Nuclear Information System (INIS)

    Quantum levels of the quasibound dissociating NO2 were observed by introduction of PHOFEX spectroscopy in which a yield of photofragment molecules in a specific quantum level is detected as a function of the photolysis energy. Thus, the unimolecular rate constant specific to each quantum level of excited NO2 was determined which shows a stepwise increase when a new product state channel opens. This is a direct experimental proof of the statistical theory of the unimolecular reaction process. Furthermore, the product state distribution indicated quantum fluctuations associated with the individual quasibound eigenstates. (author)

  14. 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

    toward the S1 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 S1 minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics...

  15. Dynamics study on effect of temperature to Nitrous nitrification reaction of coking wastewater

    Institute of Scientific and Technical Information of China (English)

    SHAN Ming-jun; ZHANG Hai-ling; LU Yan-li

    2007-01-01

    Dynamic effects of NO2 - - N accumulation were discussed owing to temperature. In different temperature, a series ofvmax and Ks were found considering the relation between the temperature and rate of ammonia nitrogen transforming into NO2 - - N. The kinetics models, which reflected the conditions of ammonia nitrogen transforming into NO2 - - N in the treatment process of the coking wastewater, were built up. The characteristic coefficient temperature was determined according to Arrhenius.

  16. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

    OpenAIRE

    Bauler, Patricia; Huber, Gary A.; McCammon, J. Andrew

    2012-01-01

    Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetri...

  17. Dissolution Dynamic Nuclear Polarization Instrumentation for Real-time Enzymatic Reaction Rate Measurements by NMR.

    Science.gov (United States)

    Balzan, Riccardo; Fernandes, Laetitia; Comment, Arnaud; Pidial, Laetitia; Tavitian, Bertrand; Vasos, Paul R

    2016-01-01

    The main limitation of NMR-based investigations is low sensitivity. This prompts for long acquisition times, thus preventing real-time NMR measurements of metabolic transformations. Hyperpolarization via dissolution DNP circumvents part of the sensitivity issues thanks to the large out-of-equilibrium nuclear magnetization stemming from the electron-to-nucleus spin polarization transfer. The high NMR signal obtained can be used to monitor chemical reactions in real time. The downside of hyperpolarized NMR resides in the limited time window available for signal acquisition, which is usually on the order of the nuclear spin longitudinal relaxation time constant, T1, or, in favorable cases, on the order of the relaxation time constant associated with the singlet-state of coupled nuclei, TLLS. Cellular uptake of endogenous molecules and metabolic rates can provide essential information on tumor development and drug response. Numerous previous hyperpolarized NMR studies have demonstrated the relevancy of pyruvate as a metabolic substrate for monitoring enzymatic activity in vivo. This work provides a detailed description of the experimental setup and methods required for the study of enzymatic reactions, in particular the pyruvate-to-lactate conversion rate in presence of lactate dehydrogenase (LDH), by hyperpolarized NMR. PMID:26967906

  18. Investigation of dynamics of fusion reactions through cross-section and spin distribution measurements

    International Nuclear Information System (INIS)

    The CN populated at high excitation energy and angular momentum in fusion reactions can undergo decay through fission or emission of different light particles (α-particles, neutrons and protons). The statistical model has been extensively used to explain the evaporation spectra of these light particles and to extract important information about the properties of the CN. However, many of the evaporation studies show anomalous results from the statistical model predictions, for the mass symmetric systems. With this motivation we have performed the ER-gated spin distribution and the cross-section measurements for two systems 16O + 64Zn (mass asymmetric) and 32S + 48Ti (mass symmetric) populating the same CN (80Sr) for which the evaporation spectra studies have reported the existence of deviations for the symmetric system. Present measurements have been performed using 15 UD Pelletron accelerator and Heavy Ion Reaction Analyzer (HIRA) facility at Inter University Accelerator Centre (IUAC), New Delhi. The details of these measurements and analysis procedure have been described elsewhere

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

    Institute of Scientific and Technical Information of China (English)

    Stephen Johnston; Zachary Gallaher; Krzysztof Czaja

    2012-01-01

    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-ΔΔCt 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.

  20. Geochemical reactions and dynamics during titration of a contaminated groundwater with high uranium, aluminum, and calcium

    Science.gov (United States)

    Gu, Baohua; Brooks, Scott C.; Roh, Yul; Jardine, Philip M.

    2003-08-01

    This study investigated possible geochemical reactions during titration of a contaminated groundwater with a low pH but high concentrations of aluminum, calcium, magnesium, manganese, and trace contaminant metals/radionuclides such as uranium, technetium, nickel, and cobalt. Both Na-carbonate and hydroxide were used as titrants, and a geochemical equilibrium reaction path model was employed to predict aqueous species and mineral precipitation during titration. Although the model appeared to be adequate to describe the concentration profiles of some metal cations, solution pH, and mineral precipitates, it failed to describe the concentrations of U during titration and its precipitation. Most U (as uranyl, UO 22+) as well as Tc (as pertechnetate, TcO 4-) were found to be sorbed and coprecipitated with amorphous Al and Fe oxyhydroxides at pH below ˜5.5, but slow desorption or dissolution of U and Tc occurred at higher pH values when Na 2CO 3 was used as the titrant. In general, the precipitation of major cationic species followed the order of Fe(OH) 3 and/or FeCo 0.1(OH) 3.2, Al 4(OH) 10SO 4, MnCO 3, CaCO 3, conversion of Al 4(OH) 10SO 4 to Al(OH) 3,am, Mn(OH) 2, Mg(OH) 2, MgCO 3, and Ca(OH) 2. The formation of mixed or double hydroxide phases of Ni and Co with Al and Fe oxyhydroxides was thought to be responsible for the removal of Ni and Co in solution. Results of this study indicate that, although the hydrolysis and precipitation of a single cation are known, complex reactions such as sorption/desorption, coprecipitation of mixed mineral phases, and their dissolution could occur simultaneously. These processes as well as the kinetic constraints must be considered in the design of the remediation strategies and modeling to better predict the activities of various metal species and solid precipitates during pre- and post-groundwater treatment practices.

  1. Dynamical Analysis of a Delayed Reaction-Diffusion Predator-Prey System

    Directory of Open Access Journals (Sweden)

    Yanuo Zhu

    2012-01-01

    Full Text Available This work deals with the analysis of a delayed diffusive predator-prey system under Neumann boundary conditions. The dynamics are investigated in terms of the stability of the nonnegative equilibria and the existence of Hopf bifurcation by analyzing the characteristic equations. The direction of Hopf bifurcation and the stability of bifurcating periodic solution are also discussed by employing the normal form theory and the center manifold reduction. Furthermore, we prove that the positive equilibrium is asymptotically stable when the delay is less than a certain critical value and unstable when the delay is greater than the critical value.

  2. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Science.gov (United States)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

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

    Science.gov (United States)

    Siaï, A.; Oueslati, I.; Kerkeni, Boutheïna

    2016-08-01

    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.

  4. On the dynamics of collective motion in heavy-ion reactions

    International Nuclear Information System (INIS)

    Collective transverse motion is heavy-ion reactions is studied in the frame of the Landau-Vlasov model, for a wide range of beam energies. Nuclear mean-field is given by different parametrizations of local and non-local effective forces which correctly reproduce cold nuclear matter properties. It is shown that in the case of non-local forces, they must also be constrained to reproduce basic experimental data concerning the real part of the optical potential, in the energy range of interest. Symmetric colliding systems at 400 MeV of incident energy per nucleon are simulated and compared with experimental data. In this range of energy, the calculated flow is shown to be sensitive to the incompressibility modulus, and its numerical value is discussed. (authors). 10 refs., 6 figs., 3 tabs

  5. Dynamics and structure of light nuclei through (e,e'p) reactions with high momentum

    International Nuclear Information System (INIS)

    The (e,e'p) reaction is an efficient and accurate means to probe nuclear structure because of its simplicity (in the case of light nuclei exact calculations can be made) and because the entire nuclear volume is probed. Now high energy electron beams are available which allows nuclear matter to be investigated on distances shorter than the nucleon diameter, and as a consequence the measurement of effects linked to the internal structure of the nucleon appears reachable. Recent experiments performed at the Jefferson Laboratory on deuterium and helium targets have shown that the cross-section (e,e'p) with high momentum missing is dominated by many-body processes involving the propagation of a nucleon in the nuclear matter. The importance of these re-diffusion mechanisms can be amplified or minimized by acting on the value of the missing momentum or on the angle of the recoil particle. These experiments highlight the sensitivity of the He3(e,e'p)pn reactions to nucleon-nucleon correlations and their importance at high momentum missing. Theoretical results predict a very narrow window in anti-parallel kinematics through which an important reduction of the many-body mechanism is expected. The study of the color transparency effect through quasi-elastic scattering in light nuclei uses the re-diffusion features to show the existence of a small spatial extension of the nucleon's wave function. Recent development in the formalism of generalized parton distributions open the way for a systematic and complete study of the internal structure of the nucleon. (A.C.)

  6. Molecular beams studies of the energetics and dynamics of elementary chemical reactions

    Energy Technology Data Exchange (ETDEWEB)

    Hayden, C.C.

    1982-05-01

    Quantum mechanical effects on the angular distribution of HF products from the F + H/sub 2/ reaction were studied using crossed atomic and molecular beams with a rotatable mass spectrometer detector and time-of-flight velocity analysis. Measurement of the singlet-triplet splitting of CH/sub 2/ from the recoil velocities of fragments from ketene photodissociation in a molecular beam is also reported. Partial center-of-mass angular distributions, and velocity flux contour maps have been derived for individual vibrational states of the HF product from the F + H/sub 2/ reaction at collision energies of 2 and 3 kcal/mole. The center-of-mass distributions were obtained by analysis of laboratory angular and time-of-flight measurements of the reactive scattering. The results are consistent with recent three dimensional quantum mechanical scattering calculations, which predict that resonance effects should appear in the product angular distributions in this energy range. The photofragmentation of ketene in a molecular beam was used to measure the singlet-triplet splitting in CH/sub 2/. A rare gas halide excimer laser operating at 351 nm (XeF) and 308 nm (XeCl) dissociated the ketene. Time-of-flight measurements of the fragment velocities allowed determination of the energetics of the dissociation. The /sup 1/A/sub 1/ - /sup 3/B/sub 1/ splitting in CH/sub 2/ was found to be 8.5 +- 0.8 kcal/mole. This agrees with many experimental results, but not with the value of 19.5 kcal/mole derived from recent photodetachment experiments on CH/sub 2//sup -/.

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

    International Nuclear Information System (INIS)

    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 + CH3F. 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 (X2Δ) 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-CH3 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 a3F → z3F in the metal. This transition is forbidden from the ground state a3F2 of zirconium but allowed from the a3F4 state. Complexation of the metal atom with a CH3F molecule allows coupling of these two states to occur which ensures the optical transition from the ground state of the complex. (author)

  8. Microscopic approaches for nuclear Many-Body dynamics: applications to nuclear reactions

    CERN Document Server

    Simenel, Cédric; Lacroix, Denis

    2008-01-01

    These lecture notes are addressed to PhD student and/or researchers who want a general overview of microscopic approaches based on mean-field and applied to nuclear dynamics. Our goal is to provide a good description of low energy heavy-ion collisions. We present both formal aspects and practical applications of the time-dependent Hartree-Fock (TDHF) theory. The TDHF approach gives a mean field dynamics of the system under the assumption that particles evolve independently in their self-consistent average field. As an example, we study the fusion of both spherical and deformed nuclei with TDHF. We also focus on nucleon transfer which may occur between nuclei below the barrier. These studies allow us to specify the range of applications of TDHF in one hand, and, on the other hand, its intrinsic limitations: absence of tunneling below the Coulomb barrier, missing dissipative effects and/or quantum fluctuations. Time-dependent mean-field theories should be improved to properly account for these effects. Several ...

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

    International Nuclear Information System (INIS)

    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

  10. 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

  11. Reactive scattering of carbon atoms: the reaction dynamics of C(3P, 1D) +C2H2 and C2H4

    International Nuclear Information System (INIS)

    The reaction dynamics of C(3P, 1D) with acetylene and ethylene have been investigated by using the crossed beam technique with mass spectrometric detection and time-of-flight (TOF) analysis. The novel capability of generating continuous supersonic beams of carbon atoms by a radio-frequency discharge beam source is exploited. From angular and velocity distribution measurements, the primary reaction products are identified, their relative importance assessed, and their dynamics of formation characterized. While the reaction C(3P) + C2H2(X1Σg+) has been found to lead to C3H + H and C3(X1Σg+) + H2(X1Σg+) in comparable amount, the reaction C(3P) + C2H4(X1At) has been found to lead, predominantly, to H + C3H3 (propargylene). The dynamics of the C(1D) reactions are also characterized. The spin-forbidden H2 elimination channel in the reaction C(3P) + C2H2 is attributed to the occurrence of inter-system-crossing between the triplet and singlet manifold of the C3H2 potential energy surfaces. Interestingly, these findings provide evidence that the C(3P) + C2H2 reaction maybe the source of both C3H and C3 species detected in the extreme environment of dense interstellar clouds and outflows of carbon stars, as well as in combustion systems. (author)

  12. Dynamics of One- and Two-dimensional Kinks in Bistable Reaction-Diffusion Equations with Quasi-Discrete Sources of Reaction

    OpenAIRE

    Rotstein, Horacio G.; Zhabotinsky, Anatol M; Epstein, Irving R.

    2000-01-01

    We study the evolution of fronts in a bistable reaction-diffusion system when the nonlinear reaction term is spatially non-homogeneous. This equation has been used to model wave propagation in various biological systems. Extending previous works on homogeneous reaction terms, we derive asymptotically an equation governing the front motion, which is strongly nonlinear and, for the two-dimensional case, generalizes the classical mean curvature flow equation. We study the motion of one- and two-...

  13. Complete and incomplete fusion cross sections for 6Li+209Bi reaction in multi-body classical molecular dynamical model

    International Nuclear Information System (INIS)

    Using the multi-body Classical Molecular Dynamics simulation of 6Li+209Bi reaction it is shown that: (i) the breakup of a projectile fragment near the barrier leads to substantial increase in the ICF probabilities; (ii) the expected increase in σCF on relaxation of the rigid-body (RB) constraint on the projectile is compensated by reduction in the flux leading to CF, due to ICF events; (iii) the breakup probability increases with ECM and, for given ECM it also increases as b increases and peaks around some b>0, while cross sections σCF and σTF were calculated for b=0 only Therefore, we present the results of σCF (Complete Fusion) and σTF (Total Fusion) calculations which are obtained at critical impact parameter, bcr, where many ICF channels open up and compare with the calculations performed at b=0 only, where only few ICF channels open up

  14. Dynamic detection of wake-sleep transition with reaction time-magnitude

    Institute of Scientific and Technical Information of China (English)

    Chuang Gao; Bin Chen; Wei Wei

    2009-01-01

    BACKGROUND: According to observable behaviors, sleep and wakefulness are two fundamentally different behavioral states. Although electroencephalogram (EEG) is traditionally used to define sleep stage, it is difficult to detect or to quantify microarousals or disruptions during sleep. In addition,initial sleep cannot be defined. It is thought that the wake-sleep transition cannot be defined by EEG patterns.OBJECTIVE: To observe the behavioral response magnitude during wake-sleep transition by EEG monitoring and to define the wake-sleep transition.DESIGN, TIME AND SE'n'ING: A behavioral and neural network study was performed at the Key Lab of Human Being Development and Mental Health of Central China Normal University, and Lab of Brain and Cognitive Science of South Central University for Nationalities, China in July 2007.PARTICIPANTS: A total of 30 healthy volunteers, of equal gender and aged (19.7+1.1) years, were recruited from the Central China Normal University, China for this study. None of the subjects had undergone EEG recording prior to this study or received any medication for sleep disturbances.METHODS: A novel adaptive approach was applied to detect wake-sleep transition, which avoided stimulus-induced waking. To test the difference between wake state and wake-sleep transition, the amount of self-information and mutual-information were effective parameters to analyze wake-sleep transition.MAIN OUTCOME MEASURES: The following parameters were measured: morphological changes in reaction time-magnitude, as well as correlation between phase changes and sleep, and wake and wake-sleep transition.RESULTS: There were three typical phases in morphological changes of reaction time-magnitude.With regard to the behavioral definition and criterion for sleep, the phase morphological characteristics displayed good correlation with behavioral states, such as sleep, wakefulness, and sleep onset. Entropy as an indicator of brain cognitive processes was introduced to test

  15. [Dynamics of the antismallpox antibodies detectable in the passive hemagglutination reaction with various animal immunization schemes].

    Science.gov (United States)

    Matsevich, G R; Shelukhina, E M; Konikova, R E; Marennikova, S S

    1975-10-01

    Dynamics of accumulation and preservation of antibodies detectable in the PHAT (PHAT-AT) was studied on rabbits and guinea pigs with the use of various doses of the living inactivated virus and their combination in comparison with the virus-neutralizing antibodies, antihemagglutinins and precipitins. Accumulation of the virus-neutralizing antibodies did not coincide in time with the curve of the PHAT-AT accumulation; the titres of the virus-neutralizing antibodies were higher than the PHAT-AT titres. At the same time the percentage of seroconversions determined by PHAT was equal to 100 and the PHAT-AT level directly depended on the immunizing dose, the time of administration and the type of the antigen. On the basis of the data obtained PHAT could be recommended as a test for the assessment of the immunological efficacy of the smallpox vaccinations. PMID:1082220

  16. Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics

    CERN Document Server

    Qian, Hong

    2016-01-01

    We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity, but population wise with statistical rate laws in their syntheses, degradations, spatial diffusion, individual state transitions, and interactions. Such a formal kinetic system in a small volume $V$, like a single cell, can be rigorously treated in terms of a Markov process describing its nonlinear kinetics as well as nonequilibrium thermodynamics at a mesoscopic scale. We introduce notions such as open, driven chemical systems, entropy production, free energy dissipation, etc. Then in the macroscopic limit, we illustrate how two new "laws", in terms of a generalized free energy of the mesoscopic stochastic dynamics, emerge. Detailed balance and complex balance are two special classes of "simple" nonlinear kinetics. Phase transition is intrinsically related to multi-stability...

  17. Dynamical approach to spectator fragmentation in Au+Au reactions at 35 MeV/A

    CERN Document Server

    Vermani, Yogesh K

    2010-01-01

    The characteristics of fragment emission in peripheral $^{197}$Au+$^{197}$Au collisions 35 MeV/A are studied using the two clusterization approaches within framework of \\emph{quantum molecular dynamics} model. Our model calculations using \\emph{minimum spanning tree} (MST) algorithm and advanced clusterization method namely \\emph{simulated annealing clusterization algorithm} (SACA) showed that fragment structure can be realized at an earlier time when spectators contribute significantly toward the fragment production even at such a low incident energy. Comparison of model predictions with experimental data reveals that SACA method can nicely reproduce the fragment charge yields and mean charge of the heaviest fragment. This reflects suitability of SACA method over conventional clusterization techniques to investigate spectator matter fragmentation in low energy domain.

  18. Reaction dynamics of Si(001) oxidation at room temperature induced by supersonic O2 molecular beams

    International Nuclear Information System (INIS)

    Potential energy barriers for dissociative chemisorption of O2 molecules on clean and H2O-preadsorbed Si(001) surfaces were verified using supersonic O2 molecular beams and synchrotron radiation photoemission spectroscopy. The saturated oxygen amount on both kinds of Si(001) surfaces were measured as a function of incident energy of O2 molecules. The saturated oxygen amount was dependent in both cases on the incident energy. Especially, two energy thresholds appeared in the H2O-preadsorbed Si(001) surface oxidation. An Si-2p photoemission spectrum for the oxygen-saturated Si(001) surface formed by O2 gas possessing incident energy below the first threshold on the clean surface revealed the oxygen insertion into backbond sites of Si dimers. The dimer backbonds, however, were not oxidized by O2 irradiation without incident energy larger than 1.0 eV in the H2O-preadsorbed surface. These facts indicate that a chemisorption reaction path of the oxygen insertion into dimer backbonds through bridge and dangling bond sites is open for the clean surface oxidation, and the path is cut by termination of dangling bonds by H and OH radicals. (author)

  19. Dynamics of eosinophil infiltration in the bronchial mucosa before and after the late asthmatic reaction.

    Science.gov (United States)

    Aalbers, R; de Monchy, J G; Kauffman, H F; Smith, M; Hoekstra, Y; Vrugt, B; Timens, W

    1993-06-01

    We wanted to determine whether changes in bronchial hyperresponsiveness (BHR) following allergen challenge show a time relationship with inflammatory events in the airways of allergic asthmatic subjects. Lavage was performed and endobronchial biopsies were taken via the fiberoptic bronchoscope, before, and 3 and 24 h after, allergen challenge, on separate occasions, in nine dual asthmatic responders. The numbers of activated eosinophils, identified by immunohistochemistry, using the monoclonal anti-eosinophil cationic protein antibody, EG2, were significantly increased both at 3 h and at 24 h in the submucosa and bronchial lavage. A significant negative correlation was found between the number of EG2+ cells in the submucosa and in the bronchial lavage 24 h after the allergen challenge (r = -0.70). At 24 h, the amount of eosinophil cationic protein (ECP) was increased in the bronchial lavage. A significant correlation was observed between the amount of ECP at 3 h and the log provocative dose of house dust mite producing a 20% fall in forced expiratory volume in one second (PD20 HDM) (r = -0.63). The results suggest a recruitment of activated eosinophils to the submucosa and, further, to the epithelial lining, followed by degranulation. This process has already started 3 h after allergen challenge, and lasts for at least 24 h, which may result in mucosal damage and subsequent allergen-induced increase in BHR, before and after the late asthmatic reaction. PMID:8339804

  20. Discrete infinite-dimensional type-K monotone dynamical systems and time-periodic reaction-diffusion systems

    Science.gov (United States)

    Liang, Xing; Jiang, Jifa

    The asymptotic behavior of discrete type-K monotone dynamical systems and reaction-diffusion equations is investigated. The studying content includes the index theory for fixed points, permanence, global stability, convergence everywhere and coexistence. It is shown that the system has a globally asymptotically stable fixed point if every fixed point is locally asymptotically stable with respect to the face it belongs to and at this point the principal eigenvalue of the diagonal partial derivative about any component not belonging to the face is not one. A nice result presented is the sufficient and necessary conditions for the system to have a globally asymptotically stable positive fixed point. It can be used to establish the sufficient conditions for the system to persist uniformly and the convergent result for all orbits. Applications are made to time-periodic Lotka-Volterra systems with diffusion, and sufficient conditions for such systems to have a unique positive periodic solution attracting all positive initial value functions are given. For more general time-periodic type-K monotone reaction-diffusion systems with spatial homogeneity, a simple condition is given to guarantee the convergence of all positive solutions.

  1. A dynamic model for power deposition in 3He lasers pumped by 3He(n,p) 3H reactions

    Science.gov (United States)

    Çetin, Füsun

    2004-07-01

    The coupled variation of power density with gas density in a nuclear-pumped laser, which is excited by 3He(n,p) 3H reaction products, is considered. In the literature, volumetric excitation by reaction products of 3He(n,p) 3H is only considered for the case in which gas density is uniform and does not change during the pumping. In this work, a time-dependent model describing the coupled fluid dynamic and particle transport behaviour of the gas has been developed. In modelling charge particle transport behaviour, a previously reported energy deposition model for a constant gas density is extended for a variable gas density by taking into account variations in the particle range, macroscopic cross sections and neutron flux depending on density field of the gas. The coupled equations, which are obtained by using the power deposition density expression obtained for variable gas density in the acoustically filtered equations of motion of the gas, are solved numerically. Spatial and temporal variations of power deposition density and gas density during the pumping pulse are determined for various operating pressures ranging from 0.5 to 10 atm. In the calculations, the characteristics of I.T.U TRIGA Mark-II Reactor are used and it is assumed that laser tube is placed in the centre of the reactor core. Obtained results are presented and examined.

  2. On the role of dynamical barriers in barrierless-reactions at low energies: S($^1$D) + H$_2$

    CERN Document Server

    Lara, Manuel; Varandas, A J C; Launay, J -M; Aoiz, F J

    2011-01-01

    Reaction probabilities as a function of total angular momentum and the resulting reaction cross-sections for the collision of open shell S($^1$D) atoms with para-hydrogen have been calculated in the kinetic energy range 0.09--10 meV (1--120 K). The quantum mechanical (QM) hyperspherical reactive scattering method and quasi--classical trajectory (QCT) and statistical quasiclassical trajectory (SQCT) approaches were used. Two different ab initio potential energy surfaces (PESs) have been considered. The widely used RKHS PES by Ho et al. (J. Chem. Phys. 116, 4124, 2002) and the recently published DMBE/CBS PES by Song and Varandas (J. Chem. Phys. 130, 134317, 2009). The calculations at low collision energies reveal very different dynamical behaviors on the two PESs. The reactivity on the RKHS PES is found to be considerably larger than that on the DMBE/CBS PES. The observed differences have their origin in two major distinct topography features. Although both PESs are essentially barrierless for equilibrium H--H ...

  3. Does the pressure dependence of kinetic isotope effects report usefully on dynamics in enzyme H-transfer reactions?

    Science.gov (United States)

    Hoeven, Robin; Heyes, Derren J; Hay, Sam; Scrutton, Nigel S

    2015-08-01

    The temperature dependence of kinetic isotope effects (KIEs) has emerged as the main experimental probe of enzymatic H-transfer by quantum tunnelling. Implicit in the interpretation is a presumed role for dynamic coupling of H-transfer chemistry to the protein environment, the so-called 'promoting motions/vibrations hypothesis'. This idea remains contentious, and others have questioned the importance and/or existence of promoting motions/vibrations. New experimental methods of addressing this problem are emerging, including use of mass-modulated enzymes and time-resolved spectroscopy. The pressure dependence of KIEs has been considered as a potential probe of quantum tunnelling reactions, because semi-classical KIEs, which are defined by differences in zero-point vibrational energy, are relatively insensitive to kbar changes in pressure. Reported combined pressure and temperature (p-T) dependence studies of H-transfer reactions are, however, limited. Here, we extend and review the available p-T studies that have utilized well-defined experimental systems in which quantum mechanical tunnelling is established. These include flavoproteins, quinoproteins, light-activated enzymes and chemical model systems. We show that there is no clear general trend between the p-T dependencies of the KIEs in these systems. Given the complex nature of p-T studies, we conclude that computational simulations using determined (e.g. X-ray) structures are also needed alongside experimental measurements of reaction rates/KIEs to guide the interpretation of p-T effects. In providing new insight into H-transfer/environmental coupling, combined approaches that unite both atomistic understanding with experimental rate measurements will require careful evaluation on a case-by-case basis. Although individually informative, we conclude that p-T studies do not provide the more generalized insight that has come from studies of the temperature dependence of KIEs. PMID:25581554

  4. Quantum Mechanical and Molecular Dynamics Studies of the Reaction Mechanism of the Nucleophilic Substitution at the Si Atom.

    Science.gov (United States)

    Matsubara, Toshiaki; Ito, Tomoyoshi

    2016-05-01

    The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans. PMID:27046773

  5. PLATYPUS: A code for reaction dynamics of weakly-bound nuclei at near-barrier energies within a classical dynamical model

    Science.gov (United States)

    Diaz-Torres, Alexis

    2011-04-01

    A self-contained Fortran-90 program based on a three-dimensional classical dynamical reaction model with stochastic breakup is presented, which is a useful tool for quantifying complete and incomplete fusion, and breakup in reactions induced by weakly-bound two-body projectiles near the Coulomb barrier. The code calculates (i) integrated complete and incomplete fusion cross sections and their angular momentum distribution, (ii) the excitation energy distribution of the primary incomplete-fusion products, (iii) the asymptotic angular distribution of the incomplete-fusion products and the surviving breakup fragments, and (iv) breakup observables, such as angle, kinetic energy and relative energy distributions. Program summaryProgram title: PLATYPUS Catalogue identifier: AEIG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 332 342 No. of bytes in distributed program, including test data, etc.: 344 124 Distribution format: tar.gz Programming language: Fortran-90 Computer: Any Unix/Linux workstation or PC with a Fortran-90 compiler Operating system: Linux or Unix RAM: 10 MB Classification: 16.9, 17.7, 17.8, 17.11 Nature of problem: The program calculates a wide range of observables in reactions induced by weakly-bound two-body nuclei near the Coulomb barrier. These include integrated complete and incomplete fusion cross sections and their spin distribution, as well as breakup observables (e.g. the angle, kinetic energy, and relative energy distributions of the fragments). Solution method: All the observables are calculated using a three-dimensional classical dynamical model combined with the Monte Carlo sampling of probability-density distributions. See Refs. [1,2] for further details. Restrictions: The

  6. 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%.

  7. Picosecond dynamics of reactions in the liquid phase: studies of iodine photodissociation and development of new laser techniques

    International Nuclear Information System (INIS)

    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

  8. Picosecond dynamics of reactions in the liquid phase: studies of iodine photodissociation and development of new laser techniques

    Energy Technology Data Exchange (ETDEWEB)

    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. (WRF)

  9. Study of the intermediate-energy nucleon-nucleus reactions in terms of the quantum molecular dynamics

    International Nuclear Information System (INIS)

    The double-differential (p,xp') and (p,xn) reaction cross sections of 58Ni and 90Zr 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)

  10. Are classical molecular dynamics calculations accurate for state-to-state transition probabilities in the H + D2 reaction?

    International Nuclear Information System (INIS)

    We present converged quantum dynamics for the H + D2 reaction at a total energy high enough to produce HD in the v' = 3, j' = 7 vibrational-rotational state and for total angular momenta J = 0, 1, and 2. We compare state-to-state partial cross sections for H + D2 (v = 0-2, j = 0, J = 0-2) → HD (v' = 0-2, j') + H and H + D2 (v = 1, j = 6, J = 0-2) → HD (v' = 0-2, j') + H as calculated from classical trajectory calculations with quantized initial conditions, i.e., a quasiclassical trajectory (QCT) simulation, to the results of converged quantum dynamics calculations involving up to 654 coupled channels. Final states in the QCT calculations are assigned by the quadratic smooth sampling (QSS) method. Since the quasiclassical and quantal calculations are carried out with the same potential energy surface, the comparison provides a direct test of the accuracy of the quasiclassical simulations as a function of the initial vibrational-rotational state and the final vibrational-rotational state

  11. Near Fermi Energy reaction dynamics and clustering in alpha-conjugate systems

    Science.gov (United States)

    Cao, Xiguang; Schmidt, Katarzyna; Kim, E.-J.; Hagel, K.; Barbui, M.; Wuenschel, S.; Natowitz, J. B.; Zheng, H.; Blando, N.; Bonasera, A.; Giuliani, G.

    2015-10-01

    Theoretical study predicted that the self-organizing of alpha cluster is favored over deuteron below a critical density with moderate temperature, where the possible Bose-Einstein condensation (BEC) is expected to occur. However the experimental information about the alpha states at low density is scarce. It is natural to pursue experiments with α conjugate beams and advanced detection apparatus to explore the collective dynamics of alpha clustered systems at low density. Systematical experiments were carried out with 40Ca and 28Si beams at 10, 25, 35 MeV/u incident on 28Si, 12C, 40Ca and 180Ta targets, detected with the NIMROD-ISiS 4 Pi detector array. It is found that there is a strong neck-like emission, which consists mainly of alpha-like fragments. The characteristic of the α emission source is explored by shape analysis, multi-particle correlation and quantum fluctuation approaches. How these observables reveal the possible alpha BEC in low density and possible exotic toroidal and linear chain configurations made out of alpha clusters is discussed.

  12. Molecular Dynamics of Reaction-Driven, Diffusiophoretic, Colloid Self-Propulsion

    Science.gov (United States)

    Sharifi-Mood, Nima; Koplik, Joel; Maldarelli, Charles

    2013-11-01

    Chemical-mechanical transduction mechanisms which can actuate the movement of colloids through pathways in liquids are highly sought after as engines to propel miniaturized micro and nanobots. One mechanism involves harnessing van der Waals attractive forces between the colloid and solute molecules. Self propulsion can be achieved by arranging for the solute to react on one face of the colloid, creating an asymmetric distribution which can propel the particle. We use molecular dynamics calculations to elucidate this propulsion for nanocolloids. The calculations assume Lennard-Jones interactions between the colloid (modelled as a rigid cluster of atoms), solvent atoms and solute atoms which react with the colloid atoms on one face of the cluster. The solute reacts when localized within the attractive landscape of the cluster atoms and is converted for simplicity to solvent. Quantitative calculations of the diffusiophoretic velocity demonstrate the interplay of Brownian rotation and diffusiophoretic propulsion, the dependence of the nano-colloid velocity on its radius and an agreement with a continuum model which therefore allows a description of the phenomena for propulsion of objects in size and over trajectories from the nanometer to the micron scale. Levich Instiute, Department of Physics, City College of New York.

  13. Dynamical Dipole mode in the 40,48 Ca +152,144Sm fusion reactions at 11 MeV/nucleon

    Directory of Open Access Journals (Sweden)

    Parascandolo C.

    2016-01-01

    Full Text Available The excitation of the dynamical dipole mode along the fusion path was investigated in the formation of a heavy compound nucleus in the A=190 mass region. To form the compound nucleus, the 40Ca + 152Sm and 48Ca + 144Sm reactions were employed at Elab=11 and 10.1 MeV/nucleon, respectively. Both fusion–evaporation and fission events were studied simultaneously for the first time. Our results for evaporation and fission events (preliminary show that the dynamical dipole mode survives in reactions involving heavier nuclei than those studied previously.

  14. Theoretical study of N (4S, 2D)+CH3 (2A2″) reaction mechanisms revisited: The importance of spin-forbidden and roaming dynamics processes

    Science.gov (United States)

    Chiba, Sachie; Yoshida, Fuka; Takayanagi, Toshiyuki

    2014-03-01

    Extensive electronic structure calculations have been performed to understand the reaction mechanisms of the N(4S, 2D) + CH3 reaction using ab initio multi-configurational methods. We have located a total of seven structures for the minimum on the seam of singlet/triplet potential energy crossing. According to our computational results, we conclude that triplet/singlet spin-forbidden processes are playing an essential role in this reaction in high contrast with previous theoretical studies. In addition, it is likely that singlet HCN + H2 products are formed through so-called ‘roaming' dynamics.

  15. Dynamic infrared imaging of the skin reaction in melanoma patients treated with boron neutron capture therapy

    International Nuclear Information System (INIS)

    As part of the Boron Neutron Capture Therapy (BNCT) project conducted jointly by the Comision Nacional de Energia Atomica and the oncology institute A. Roffo, Argentina, we have recently started a program designed to investigate the ability of dynamic infrared imaging for following-up our cutaneous melanoma patients. BNCT offers a unique opportunity to study the response of the integumentary system to single fractions and high doses of neutrons and heavy ions, providing information that could be potentially important in radiation accidents for people exposed to these kinds of radiation fields. Medical infrared thermography is a non-invasive and functional imaging method, that provides information on the normal and abnormal status and response of the nervous and vascular systems, as well as the local metabolic rate and inflammatory processes that appear as differences in the skin infrared emission. Although it is highly sensitive, it is unspecific, like other conventional imaging techniques. For this reason, infrared thermography must be employed as an adjunct method to other diagnostic procedures and the clinical observation. An infrared camera is employed, with an uncooled ferroelectric focal plane array of 320x240 detector elements, providing a video signal of the infrared emission in the 8-14 μm wavelength band. After patient preparation and acclimation, a basal study of the irradiated region is performed, including high and low dose areas, as well as normal and tumor tissues, and eventually other detectable structures (e.g. scars and veins). Thereafter, a provocation test (a cold stimulus) is applied and the temperature recovery is registered as a function of time. In addition, a 3D computational dosimetry of the irradiated region is performed, which allows a complete representation of the isodose contours mapped onto the 3D reconstruction representing the skin. This reconstruction permits selecting regions of different doses for studying the local response

  16. Simulation study of the losses and influences of geminate and bimolecular recombination on the performances of bulk heterojunction organic solar cells

    Institute of Scientific and Technical Information of China (English)

    朱键卓; 祁令辉; 杜会静; 柴莺春

    2015-01-01

    We use the method of device simulation to study the losses and influences of geminate and bimolecular recombinations on the performances and properties of the bulk heterojunction organic solar cells. We find that a fraction of electrons (holes) in the device are collected by anode (cathode). The direction of the corresponding current is opposite to the direction of photocurrent. And the current density increases with the bias increasing but decreases as bimolecular recombination (BR) or geminate recombination (GR) intensity increases. The maximum power, short circuit current, and fill factor display a stronger dependence on GR than on BR. While the influences of GR and BR on open circuit voltage are about the same. Our studies shed a new light on the loss mechanism and may provide a new way of improving the efficiency of bulk heterojunction organic solar cells.

  17. Characterization of the latent membrane protein 1 signaling complex of Epstein-Barr virus in the membrane of mammalian cells with bimolecular fluorescence complementation

    OpenAIRE

    Everly David N; Emery Amanda; Talaty Pooja

    2011-01-01

    Abstract Background Bimolecular fluorescence complementation (BiFC) is a novel technique to examine protein-protein interaction through the assembly of fluorescent proteins. In the present study, BiFC was used to study the assembly of the Epstein-Barr virus latent membrane protein 1 (LMP1) signaling complex within the membrane of mammalian cells. LMP1 signaling requires oligomerization, localization to lipid rafts, and association of the cytoplasmic domain to adaptor proteins, such as the tum...

  18. Parallel reaction monitoring (PRM) and selected reaction monitoring (SRM) exhibit comparable linearity, dynamic range and precision for targeted quantitative HDL proteomics

    OpenAIRE

    Ronsein, Graziella E.; Pamir, Nathalie; von Haller, Priska D.; Kim, Daniel S.; Oda, Michael N.; Jarvik, Gail P.; Vaisar, Tomas; Heinecke, Jay W.

    2014-01-01

    High-density lipoprotein (HDL), a lipid nanoparticle containing many different low abundance proteins, is an attractive target for clinical proteomics because its compositional heterogeneity is linked to its cardioprotective effects. Selected reaction monitoring (SRM) is currently the method of choice for targeted quantification of proteins in such a complex biological matrix. However, model system studies suggest that parallel reaction monitoring (PRM) is more specific than SRM because many ...

  19. Innovative Bimolecular-Based Advanced Logic Operations: A Prime Discriminator and An Odd Parity Checker.

    Science.gov (United States)

    Zhou, Chunyang; Liu, Dali; Dong, Shaojun

    2016-08-17

    Herein, a novel logic operation of prime discriminator is first performed for the function of identifying the prime numbers from natural numbers less than 10. The prime discriminator logic operation is developed by DNA hybridizations and the conjugation of graphene oxide and single-stranded DNA as a reacting platform. On the basis of the similar reaction principle, an odd parity checker is also developed. The odd parity checker logic operation can identify the even numbers and odd numbers from natural numbers less than 10. Such advanced logic operations with digital recognition ability can provide a new field of vision toward prototypical DNA-based logic operations and promote the development of advanced logic circuits. PMID:27459592

  20. Tight-binding quantum chemical molecular dynamics simulations for the elucidation of chemical reaction dynamics in SiC etching with SF6/O2 plasma.

    Science.gov (United States)

    Ito, Hiroshi; Kuwahara, Takuya; Kawaguchi, Kentaro; Higuchi, Yuji; Ozawa, Nobuki; Kubo, Momoji

    2016-03-01

    We used our etching simulator [H. Ito et al., J. Phys. Chem. C, 2014, 118, 21580-21588] based on tight-binding quantum chemical molecular dynamics (TB-QCMD) to elucidate SiC etching mechanisms. First, the SiC surface is irradiated with SF5 radicals, which are the dominant etchant species in experiments, with the irradiation energy of 300 eV. After SF5 radicals bombard the SiC surface, Si-C bonds dissociate, generating Si-F, C-F, Si-S, and C-S bonds. Then, etching products, such as SiS, CS, SiFx, and CFx (x = 1-4) molecules, are generated and evaporated. In particular, SiFx is the main generated species, and Si atoms are more likely to vaporize than C atoms. The remaining C atoms on SiC generate C-C bonds that may decrease the etching rate. Interestingly, far fewer Si-Si bonds than C-C bonds are generated. We also simulated SiC etching with SF3 radicals. Although the chemical reaction dynamics are similar to etching with SF5 radicals, the etching rate is lower. Next, to clarify the effect of O atom addition on the etching mechanism, we also simulated SiC etching with SF5 and O radicals/atoms. After bombardment with SF5 radicals, Si-C bonds dissociate in a similar way to the etching without O atoms. In addition, O atoms generate many C-O bonds and COy (y = 1-2) molecules, inhibiting the generation of C-C bonds. This indicates that O atom addition improves the removal of C atoms from SiC. However, for a high O concentration, many C-C and Si-Si bonds are generated. When the O atoms dissociate the Si-C bonds and generate dangling bonds, the O atoms terminate only one or two dangling bonds. Moreover, at high O concentrations there are fewer S and F atoms to terminate the dangling bonds than at low O concentration. Therefore, few dangling bonds of dissociated Si and C atoms are terminated, and they form many Si-Si and C-C bonds. Furthermore, we propose that the optimal O concentration is 50-60% because both Si and C atoms generate many etching products producing fewer C

  1. 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.

  2. Origin of the high open circuit voltage in planar heterojunction perovskite solar cells: Role of the reduced bimolecular recombination

    Science.gov (United States)

    Yang, Wenchao; Yao, Yao; Wu, Chang-Qin

    2015-03-01

    The high open circuit voltage is an attractive feature for the currently popular organic-inorganic hybrid perovskite solar cells. In this paper, by employing the macroscopic device model simulation, we investigate its origin for the planar heterojunction perovskite solar cells. Based on the calculated current density-voltage characteristics, it is revealed that compared to the excitonic solar cells, the fast thermal-activated exciton dissociation in the bulk due to the small exciton binding energy may improve the short circuit current and the fill factor, but its beneficial role on the open circuit voltage is marginal. The most significant contribution for the open circuit voltage comes from the reduced bimolecular recombination. In the perovskites, with the recombination prefactor many orders of magnitude smaller than that based on the Langevin's theory, the internal charge density level is significantly enhanced and the density gradient is removed, leading to the high quasi-Fermi level splitting and thus the small open circuit voltage loss. For the nonradiative recombination pathway due to the deep trap states, it may induce significant loss of open circuit voltage as the trap density is high, while for the moderately low density its effect on the open circuit voltage is small and negligible.

  3. 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

    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...... using the hybrid model composed of Michaelis–Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large-scale networks where the exact rate laws are unknown.......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......, 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...

  4. A Combined Experimental and Theoretical Study on the Formation of the 2-Methyl-1-silacycloprop-2-enylidene Molecule via the Crossed Beam Reactions of the Silylidyne Radical (SiH; X(2)Π) with Methylacetylene (CH3CCH; X(1)A1) and D4-Methylacetylene (CD3CCD; X(1)A1).

    Science.gov (United States)

    Yang, Tao; Dangi, Beni B; Kaiser, Ralf I; Bertels, Luke W; Head-Gordon, Martin

    2016-07-14

    The bimolecular gas-phase reactions of the ground-state silylidyne radical (SiH; X(2)Π) with methylacetylene (CH3CCH; X(1)A1) and D4-methylacetylene (CD3CCD; X(1)A1) were explored at collision energies of 30 kJ mol(-1) under single-collision conditions exploiting the crossed molecular beam technique and complemented by electronic structure calculations. These studies reveal that the reactions follow indirect scattering dynamics, have no entrance barriers, and are initiated by the addition of the silylidyne radical to the carbon-carbon triple bond of the methylacetylene molecule either to one carbon atom (C1; [i1]/[i2]) or to both carbon atoms concurrently (C1-C2; [i3]). The collision complexes [i1]/[i2] eventually isomerize via ring-closure to the c-SiC3H5 doublet radical intermediate [i3], which is identified as the decomposing reaction intermediate. The hydrogen atom is emitted almost perpendicularly to the rotational plane of the fragmenting complex resulting in a sideways scattering dynamics with the reaction being overall exoergic by -12 ± 11 kJ mol(-1) (experimental) and -1 ± 3 kJ mol(-1) (computational) to form the cyclic 2-methyl-1-silacycloprop-2-enylidene molecule (c-SiC3H4; p1). In line with computational data, experiments of silylidyne with D4-methylacetylene (CD3CCD; X(1)A1) depict that the hydrogen is emitted solely from the silylidyne moiety but not from methylacetylene. The dynamics are compared to those of the related D1-silylidyne (SiD; X(2)Π)-acetylene (HCCH; X(1)Σg(+)) reaction studied previously in our group, and from there, we discovered that the methyl group acts primarily as a spectator in the title reaction. The formation of 2-methyl-1-silacycloprop-2-enylidene under single-collision conditions via a bimolecular gas-phase reaction augments our knowledge of the hitherto poorly understood silylidyne (SiH; X(2)Π) radical reactions with small hydrocarbon molecules leading to the synthesis of organosilicon molecules in cold molecular

  5. Decay of 202Pb* formed in 48Ca+154Sm reaction using the dynamical cluster-decay model

    International Nuclear Information System (INIS)

    The decay of compound nucleus 202Pb*, formed in entrance channel reaction 48Ca+154Sm at different incident energies, is studied by using the dynamical cluster-decay model (DCM) where all decay products are calculated as emissions of preformed clusters through the interaction barriers. The calculated results show an excellent agreement with experimental data for the fusion-evaporation residue cross-section σER together with the fusion-fission cross-section σFF (taken as a sum of the energetically favored symmetric ACN*/2 ± 20 and near symmetric A=65–75 plus complementary fragments), and the competing, non-compound-nucleus quasi-fission cross-section σQF where the entrance channel is considered not to lose its identity (and hence with preformation factor P0=1). The interesting feature of this study is that the three decay processes (ER, FF and QF) are quite comparable at low energies, ER being the most dominant, whereas at higher energies FF becomes most probable followed by ER and QF. The prediction of two fission windows, the symmetric fission (SF) and the near symmetric fission (nSF) whose contribution is more at lower incident energies, suggests the presence of a fine structure effect in the fusion-fission of 202Pb*. This result is attributed to the shell effects (magic shells) playing effective role in the fragment preformation yields for 48Ca+154Sm reaction at lower excitation energies, giving rise to shoulders, to an otherwise Gaussian FF mass distribution, responsible for the QF process. As a further verification of this result, absence of "shoulders" (hence, the QF component) in the decay of 192Pb* due to 48Ca+144Sm reaction is also shown to be given by the calculations, in agreement with experiments. The only parameter of the model is the neck-length ΔR which shows that the ER occurs first, having the largest values of ΔR, and the FF and QF processes occur almost simultaneously at lower incident energies but the FF takes over QF at higher incident

  6. Theoretical Study on the Reaction Mechanism of F2+2HBr=2HF+Br2

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The gas phase reaction mechanism of F2 + 2HBr = 2HF + Br2 has been investigated by (U)MP2 at 6-311G** level, and a series of four-center and three-center transition states have been obtained. The reaction mechanism was achieved by comparing the activation energy of seven reaction paths, i.e. the dissociation energy of F2 is less than the activation energy of the bimolecular elementary reaction F2 + HBr → HF + BrF. Thus it is theoretically proved that the title reaction occurs more easily inthe free radical reaction with three medium steps.

  7. The smallest chemical reaction system with bistability

    Directory of Open Access Journals (Sweden)

    Wilhelm Thomas

    2009-09-01

    Full Text Available Abstract Background Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity. Results Biological systems are based upon elementary mono- and bimolecular chemical reactions. In order to definitely clarify all necessary conditions for bistability we here present the corresponding minimal system. According to our definition, it contains the minimal number of (i reactants, (ii reactions, and (iii terms in the corresponding ordinary differential equations (decreasing importance from i-iii. The minimal bistable system contains two reactants and four irreversible reactions (three bimolecular, one monomolecular. We discuss the roles of the reactions with respect to the necessary conditions for bistability: two reactions comprise the positive feedback loop, a third reaction filters out small stimuli thus enabling a stable 'off' state, and the fourth reaction prevents explosions. We argue that prevention of explosion is a third general necessary condition for bistability, which is so far lacking discussion in the literature. Moreover, in addition to proving that in two-component systems three steady states are necessary for bistability (five for tristability, etc., we also present a simple general method to design such systems: one just needs one production and three different degradation mechanisms (one production, five degradations for tristability, etc.. This helps modelling multistable systems and it is important for corresponding synthetic biology projects. Conclusion The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with

  8. Mass asymmetry dependence of fusion time-scales in 11B+237Np and 12C, 16O, 19F+232Th reactions in a dynamical trajectory model

    International Nuclear Information System (INIS)

    Dynamical trajectory calculations were carried out for the reactions of 11B+237Np and 12C, 16O and 19F+232Th, having mass asymmetries on either side of the Businaro-Gallone critical mass asymmetry αBG, in order to examine the mass asymmetry dependence of fusion reactions in these systems. The compound nucleus formation times were calculated as a function of the partial wave of the reaction for all the systems. This study brings out that for systems with αBG, the formation times are significantly larger than for α>αBG, which is caused by the dynamical effects involved in the large scale shape changes taking place in the fusion process as well as due to the interplay between the thermal and the collective motion during the collision process. The calculated time scales are comparable to the experimental values derived from the pre-fission neutron multiplicity measurements. (author). 16 refs., 4 figs., 1 tab

  9. Ring-Polymer Molecular Dynamics for the Prediction of Low-Temperature Rates: An Investigation of the C((1)D) + H2 Reaction.

    Science.gov (United States)

    Hickson, Kevin M; Loison, Jean-Christophe; Guo, Hua; Suleimanov, Yury V

    2015-11-01

    Quantum mechanical calculations are important tools for predicting the rates of elementary reactions, particularly for those involving hydrogen and at low temperatures where quantum effects become increasingly important. These approaches are computationally expensive, however, particularly when applied to complex polyatomic systems or processes characterized by deep potential wells. While several approximate techniques exist, many of these have issues with reliability. The ring-polymer molecular dynamics method was recently proposed as an accurate and efficient alternative. Here, we test this technique at low temperatures (300-50 K) by analyzing the behavior of the barrierless C((1)D) + H2 reaction over the two lowest singlet potential energy surfaces. To validate the theory, rate coefficients were measured using a supersonic flow reactor down to 50 K. The experimental and theoretical rates are in excellent agreement, supporting the future application of this method for determining the kinetics and dynamics of a wide range of low-temperature reactions. PMID:26538033

  10. Dynamics of the reaction H2+(He,H)HeH+. Endoergic channels with H2+ in γ=0,1 vibrational states: beam experiment and trajectory calculations

    International Nuclear Information System (INIS)

    A vibrationally selected beam of H2+ was used to investigate experimentally the reaction dynamics of the lowest two (endoergic) channels of the process H2+(γ=0,1)+He=HeH++H at the relative collision energy 3.58 eV, and to provide data for comparison with quasi-classical trajectory calculations. The process proceeds via a direct mechanism. In comparison with the reaction dynamics observed for the non-selected beam, where various vibrationally excited reactant ions participated, the results show - in a good agreement between theory and experiment - a prominent decrease of the forward 'stripping' scattering, and apparently an increased peak value of the recoil translational energy. This is consistent with the simple idea that small impact-parameter collisions leading to large-angle scattering are required to achieve an effective translational energy transfer necessary to overcome the reaction barrier. (Auth.)

  11. Probing the dynamics of polyatomic multichannel elementary reactions by crossed molecular beam experiments with soft electron-ionization mass spectrometric detection.

    Science.gov (United States)

    Casavecchia, Piergiorgio; Leonori, Francesca; Balucani, Nadia; Petrucci, Raffaele; Capozza, Giovanni; Segoloni, Enrico

    2009-01-01

    In this Perspective we highlight developments in the field of chemical reaction dynamics. Focus is on the advances recently made in the investigation of the dynamics of elementary multichannel radical-molecule and radical-radical reactions, as they have become possible using an improved crossed molecular beam scattering apparatus with universal electron-ionization mass spectrometric detection and time-of-flight analysis. These improvements consist in the implementation of (a) soft ionization detection by tunable low-energy electrons which has permitted us to reduce interfering signals originating from dissociative ionization processes, usually representing a major complication, (b) different beam crossing-angle set-ups which have permitted us to extend the range of collision energies over which a reaction can be studied, from very low (a few kJ mol(-1), as of interest in astrochemistry or planetary atmospheric chemistry) to quite high energies (several tens of kJ mol(-1), as of interest in high temperature combustion systems), and (c) continuous supersonic sources for producing a wide variety of atomic and molecular radical reactant beams. Exploiting these new features it has become possible to tackle the dynamics of a variety of polyatomic multichannel reactions, such as those occurring in many environments ranging from combustion and plasmas to terrestrial/planetary atmospheres and interstellar clouds. By measuring product angular and velocity distributions, after having suppressed or mitigated, when needed, the problem of dissociative ionization of interfering species (reactants, products, background gases) by soft ionization detection, essentially all primary reaction products can be identified, the dynamics of each reaction channel characterized, and the branching ratios determined as a function of collision energy. In general this information, besides being of fundamental relevance, is required for a predictive description of the chemistry of these

  12. Full-dimensional quantum dynamics study of the H2 + C2H → H + C2H2 reaction on an ab initio potential energy surface.

    Science.gov (United States)

    Chen, Liuyang; Shao, Kejie; Chen, Jun; Yang, Minghui; Zhang, Dong H

    2016-05-21

    This work performs a time-dependent wavepacket study of the H2 + C2H → H + C2H2 reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H2 + C2H↔H + C2H2, H + C2H2 → HCCH2, and HCCH2 radial isomerization reaction regions. The reaction dynamics of H2 + C2H → H + C2H2 are investigated using full-dimensional quantum dynamics method. The initial-state selected reaction probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H2 vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C2H slightly inhibits the reaction. The excitations of two stretching modes of C2H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values. PMID:27208951

  13. Establishing mass spectrum of $S=-1$ hyperon resonances via a dynamical coupled-channels analysis of $K^-p$ reactions

    CERN Document Server

    Kamano, Hiroyuki

    2016-01-01

    We report our recent effort for the extraction of resonance parameters (complex pole mass and residues etc.) associated with Lambda* and Sigma* hyperons. This was accomplished via a comprehensive partial-wave analysis of the data for K^- p --> barK N, pi Sigma, pi Lambda, eta Lambda, K Xi reactions from the thresholds up to W=2.1 GeV within a dynamical coupled-channels approach. The results suggest a possible existence of new narrow J^P=3/2^+ \\Lambda resonance with pole mass 1671^{+2}_{-8} -i(5^{+11}_{-2}) MeV, located close to the eta Lambda threshold. This resonance is found to be responsible for reproducing the data for K^-p --> eta Lambda differential cross sections near the threshold, and thus the data seem favor its existence. The extracted poles for J^P=1/2^- Lambda resonances below the barK N threshold, including Lambda(1405), are also presented.

  14. Decay studies of 59Cu* formed in the 35Cl + 24Mg reaction using the dynamical cluster-decay model

    Science.gov (United States)

    Karthikraj, C.; Balasubramaniam, M.

    2013-02-01

    The reformulated dynamical cluster-decay model (DCM) is applied to study the decay of odd-A and non-α structured 59Cu* formed in the 35Cl+24Mg reaction at Elab=275 MeV. Here, the temperature (T)-dependent binding energies due to Krappe are used. The roles of Wigner and pairing energies in the fragmentation potential are explicitly shown in this work. For the temperature T=4.1898 MeV corresponding to Elab=275 MeV, the contribution of pairing vanishes and the resulting structure of the fragmentation potential due to Wigner term is shown. In addition to this, we have studied the role of factor α appearing in the inertia part of the equation of motion dictating the mass-transfer process. It is shown that this factor has significant effect in the structure of preformation probability values and hence in turn we see significant changes in the cross sections. We compare the cross sections of the measured charge distributions of the fission fragments for two limiting values of the parameter α with the experimental data. In order to fit the total cross-section values, a linear relation is obtained between the free parameter of the model ▵R and the factor α appearing in the hydrodynamical mass.

  15. Microscopic study of the $^{132,124}$Sn+$^{96}$Zr reactions: dynamic excitation energy, energy-dependent heavy-ion potential, and capture cross section

    CERN Document Server

    Oberacker, V E; Maruhn, J A; Reinhard, P -G

    2010-01-01

    We study reactions between neutron-rich $^{132}$Sn nucleus and $^{96}$Zr within a dynamic microscopic theory at energies in the vicinity of the ion-ion potential barrier peak, and we compare the properties to those of the stable system $^{124}$Sn+$^{96}$Zr. The calculations are carried out on a three-dimensional lattice using the density-constrained Time-Dependent Hartree-Fock method. In particular, we calculate the dynamic excitation energy $E^*(t)$ and the quadrupole moment of the dinuclear system, $Q_{20}(t)$, during the initial stages of the heavy-ion collision. Capture cross sections for the two reactions are analyzed in terms of dynamic effects and a comparison with recently measured data is given.

  16. 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)

    Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D2→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++D2→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

  17. 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. PMID:27307079

  18. Chemical dynamics simulations of the monohydrated OH−(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

    International Nuclear Information System (INIS)

    Direct dynamics simulations, with B97-1/ECP/d theory, were performed to study the role of microsolvation for the OH−(H2O) + CH3I reaction. The SN2 reaction dominates at all reactant collision energies, but at higher collision energies proton transfer to form CH2I−, and to a lesser extent CH2I− (H2O), becomes important. The SN2 reaction occurs by direct rebound and stripping mechanisms, and 28 different indirect atomistic mechanisms, with the latter dominating. Important components of the indirect mechanisms are the roundabout and formation of SN2 and proton transfer pre-reaction complexes and intermediates, including [CH3--I--OH]−. In contrast, for the unsolvated OH− + CH3I SN2 reaction, there are only seven indirect atomistic mechanisms and the direct mechanisms dominate. Overall, the simulation results for the OH−(H2O) + CH3I SN2 reaction are in good agreement with experiment with respect to reaction rate constant, product branching ratio, etc. Differences between simulation and experiment are present for the SN2 velocity scattering angle at high collision energies and the proton transfer probability at low collision energies. Equilibrium solvation by the H2O molecule is unimportant. The SN2 reaction is dominated by events in which H2O leaves the reactive system as CH3OH is formed or before CH3OH formation. Formation of solvated products is unimportant and participation of the (H2O)CH3OH---I− post-reaction complex for the SN2 reaction is negligible

  19. 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

  20. Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

    CERN Document Server

    Del Razo, Mauricio J; Qian, Hong; Lin, Guang

    2014-01-01

    The currently existing theory of fluorescence correlation spectroscopy(FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems here are no closed solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Our results show that current linear FCS theory could be adequate ...

  1. Neutral products from cation-molecule reactions in the gas phase

    International Nuclear Information System (INIS)

    The use of neutral product analysis for examining ionic reaction pathways from electron impact is described. This approach merges techniques of mass spectrometry with those of radiation chemistry. Comparisons are made between experimental results and predictions based on density-of-states arguments using RRKM microscopic rate coefficients. The importance of examining isomer distributions is stressed with special attention given to the question of the mechanism of bimolecular proton transfer in the gas phase. (author)

  2. Oscillatory reaction cross sections caused by normal mode sampling in quasiclassical trajectory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Nagy, Tibor; Vikár, Anna; Lendvay, György, E-mail: lendvay.gyorgy@ttk.mta.hu [Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2., H-1117 Budapest (Hungary)

    2016-01-07

    The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH{sub 4} + H → CH{sub 3} + H{sub 2} and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling.

  3. Oscillatory reaction cross sections caused by normal mode sampling in quasiclassical trajectory calculations.

    Science.gov (United States)

    Nagy, Tibor; Vikár, Anna; Lendvay, György

    2016-01-01

    The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH4 + H → CH3 + H2 and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C-H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C-H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling. PMID:26747798

  4. Oscillatory reaction cross sections caused by normal mode sampling in quasiclassical trajectory calculations

    International Nuclear Information System (INIS)

    The quasiclassical trajectory (QCT) method is an efficient and important tool for studying the dynamics of bimolecular reactions. In this method, the motion of the atoms is simulated classically, and the only quantum effect considered is that the initial vibrational states of reactant molecules are semiclassically quantized. A sensible expectation is that the initial ensemble of classical molecular states generated this way should be stationary, similarly to the quantum state it is supposed to represent. The most widely used method for sampling the vibrational phase space of polyatomic molecules is based on the normal mode approximation. In the present work, it is demonstrated that normal mode sampling provides a nonstationary ensemble even for a simple molecule like methane, because real potential energy surfaces are anharmonic in the reactant domain. The consequences were investigated for reaction CH4 + H → CH3 + H2 and its various isotopologs and were found to be dramatic. Reaction probabilities and cross sections obtained from QCT calculations oscillate periodically as a function of the initial distance of the colliding partners and the excitation functions are erratic. The reason is that in the nonstationary ensemble of initial states, the mean bond length of the breaking C–H bond oscillates in time with the frequency of the symmetric stretch mode. We propose a simple method, one-period averaging, in which reactivity parameters are calculated by averaging over an entire period of the mean C–H bond length oscillation, which removes the observed artifacts and provides the physically most reasonable reaction probabilities and cross sections when the initial conditions for QCT calculations are generated by normal mode sampling

  5. Dinámica de reacciones unimoleculares en fase gas: Desviaciones del comportamiento estadístico Dynamics of unimolecular reactions in gas phase: deviations from statistical behavior

    Directory of Open Access Journals (Sweden)

    Emilio Martínez-Núñez

    2002-07-01

    Full Text Available The present review summarizes the most relevant results of our research group obtained recently in the field of unimolecular reaction dynamics. The following processes are specifically analyzed: the isomerization, dissociation and elimination in methyl nitrite, the fragmentation reactions of the mercaptomethyl cation, the C-CO dissociation in the acetyl and propionyl radicals, and the decomposition of vinyl fluoride. In all the cases, only state- or energy-selected systems are considered. Special emphasis is paid to the possibility of systems exhibiting non-statistical behavior.

  6. Lipid-assisted protein transport: A diffusion-reaction model supported by kinetic experiments and molecular dynamics simulations

    Science.gov (United States)

    La Rosa, Carmelo; Scalisi, Silvia; Lolicato, Fabio; Pannuzzo, Martina; Raudino, Antonio

    2016-05-01

    The protein transport inside a cell is a complex phenomenon that goes through several difficult steps. The facilitated transport requires sophisticated machineries involving protein assemblies. In this work, we developed a diffusion-reaction model to simulate co-transport kinetics of proteins and lipids. We assume the following: (a) there is always a small lipid concentration of order of the Critical Micellar Concentration (CMC) in equilibrium with the membrane; (b) the binding of lipids to proteins modulates the hydrophobicity of the complexes and, therefore, their ability to interact and merge with the bilayer; and (c) some lipids leave the bilayer to replenish those bound to proteins. The model leads to a pair of integral equations for the time-evolution of the adsorbed proteins in the lipid bilayer. Relationships between transport kinetics, CMC, and lipid-protein binding constants were found. Under particular conditions, a perturbation analysis suggests the onset of kinks in the protein adsorption kinetics. To validate our model, we performed leakage measurements of vesicles composed by either high or low CMC lipids interacting with Islet Amyloid PolyPeptide (IAPP) and Aβ (1-40) used as sample proteins. Since the lipid-protein complex stoichiometry is not easily accessible, molecular dynamics simulations were performed using monomeric IAPP interacting with an increasing number of phospholipids. Main results are the following: (a) 1:1 lipid-protein complexes generally show a faster insertion rate proportional to the complex hydrophobicity and inversely related to lipid CMC; (b) on increasing the number of bound lipids, the protein insertion rate decreases; and (c) at slow lipids desorption rate, the lipid-assisted proteins transport might exhibit a discontinuous behavior and does non-linearly depend on protein concentration.

  7. 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.

  8. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

    Science.gov (United States)

    Johnson, Margaret E.; Hummer, Gerhard

    2014-07-01

    We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions.

  9. Microscopic study of the $^{132,124}$Sn+$^{96}$Zr reactions: dynamic excitation energy, energy-dependent heavy-ion potential, and capture cross section

    OpenAIRE

    Oberacker, V. E.; Umar, A. S.; Maruhn, J. A.; Reinhard, P.-G.

    2010-01-01

    We study reactions between neutron-rich $^{132}$Sn nucleus and $^{96}$Zr within a dynamic microscopic theory at energies in the vicinity of the ion-ion potential barrier peak, and we compare the properties to those of the stable system $^{124}$Sn+$^{96}$Zr. The calculations are carried out on a three-dimensional lattice using the density-constrained Time-Dependent Hartree-Fock method. In particular, we calculate the dynamic excitation energy $E^*(t)$ and the quadrupole moment of the dinuclear...

  10. A Time-Dependent Quantum Dynamics Study of the H2 + CH3 yields H + CH4 Reaction

    Science.gov (United States)

    Wang, Dunyou; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We present a time-dependent wave-packet propagation calculation for the H2 + CH3 yields H + CH4 reaction in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probability for different initial rotational-vibrational states are presented in this study. The cumulative reaction probability (CRP) is obtained by summing over initial-state-selected reaction probability. The energy-shift approximation to account for the contribution of degrees of freedom missing in the 6D calculation is employed to obtain an approximate full-dimensional CRP. Thermal rate constant is compared with different experiment results.

  11. Efficient Bimolecular Mechanism of Photochemical Hydrogen Production Using Halogenated Boron-Dipyrromethene (Bodipy) Dyes and a Bis(dimethylglyoxime) Cobalt(III) Complex.

    Science.gov (United States)

    Sabatini, Randy P; Lindley, Brian; McCormick, Theresa M; Lazarides, Theodore; Brennessel, William W; McCamant, David W; Eisenberg, Richard

    2016-01-28

    A series of Boron-dipyrromethene (Bodipy) dyes were used as photosensitizers for photochemical hydrogen production in conjunction with [Co(III)(dmgH)2pyCl] (where dmgH = dimethylglyoximate, py = pyridine) as the catalyst and triethanolamine (TEOA) as the sacrificial electron donor. The Bodipy dyes are fully characterized by electrochemistry, X-ray crystallography, quantum chemistry calculations, femtosecond transient absorption, and time-resolved fluorescence, as well as in long-term hydrogen production assays. Consistent with other recent reports, only systems containing halogenated chromophores were active for hydrogen production, as the long-lived triplet state is necessary for efficient bimolecular electron transfer. Here, it is shown that the photostability of the system improves with Bodipy dyes containing a mesityl group versus a phenyl group, which is attributed to increased electron donating character of the mesityl substituent. Unlike previous reports, the optimal ratio of chromophore to catalyst is established and shown to be 20:1, at which point this bimolecular dye/catalyst system performs 3-4 times better than similar chemically linked systems. We also show that the hydrogen production drops dramatically with excess catalyst concentration. The maximum turnover number of ∼ 700 (with respect to chromophore) is obtained under the following conditions: 1.0 × 10(-4) M [Co(dmgH)2pyCl], 5.0 × 10(-6) M Bodipy dye with iodine and mesityl substituents, 1:1 v:v (10% aqueous TEOA):MeCN (adjusted to pH 7), and irradiation by light with λ > 410 nm for 30 h. This system, containing discrete chromophore and catalyst, is more active than similar linked Bodipy-Co(dmg)2 dyads recently published, which, in conjunction with our other measurements, suggests that the nominal dyads actually function bimolecularly. PMID:26730460

  12. Dynamical phase transition in the two-point functions of the autonomous one-dimensional single-species reaction-diffusion systems

    OpenAIRE

    Aghamohammadi, Amir; Khorrami, Mohammad

    2003-01-01

    The evolution of the two-point functions of autonomous one-dimensional single-species reaction-diffusion systems with nearest-neighbor interaction and translationally-invariant initial conditions is investigated. It is shown that the dynamical phase structure of such systems consists of five phases. As an example, a one-parameter family is introduced which can be in each of these phases.

  13. Using high resolution and dynamic reaction cell for the improvement of the sensitivity of direct silicon determination in uranium materials by inductively coupled plasma mass spectrometry

    OpenAIRE

    Golik, V. M.; Kuz'mina, N. V.; Saprygin, A. V.; Trepachev, S. A.

    2013-01-01

    The paper describes solving the problem of direct silicon determination at low levels in uranium materials, caused by the spectral interferences of polyatomic ions and the high value of blank levels, using inductively coupled plasma mass spectrometry (ICP MS). To overcome the interference problem, two primary techniques have been applied: double focusing high-resolution ICP MS and dynamic reaction cell (DRC) filled with highly reactive ammonia gas. All measurements were performed at high reso...

  14. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    CERN Document Server

    Zobač, Vladmír; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2014-01-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code Fireball, suitable for the computational study of these problems. Our methodology enables simulating photo-induced reaction mechanisms over hundreds of trajectories; therefore, large statistically significant ensembles can be calculated to accurately represent a reaction profile. As an example of the application of this approach, we report results on the [2+2] cycloaddition of ethylene with maleic anhydride and on the [2+2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  15. Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cells

    Directory of Open Access Journals (Sweden)

    Kuang Lin-Yun

    2008-10-01

    Full Text Available Abstract Background The investigation of protein-protein interactions is important for characterizing protein function. Bimolecular fluorescence complementation (BiFC has recently gained interest as a relatively easy and inexpensive method to visualize protein-protein interactions in living cells. BiFC uses "split YFP" tags on proteins to detect interactions: If the tagged proteins interact, they may bring the two split fluorophore components together such that they can fold and reconstitute fluorescence. The sites of interaction can be monitored using epifluorescence or confocal microscopy. However, "conventional" BiFC can investigate interactions only between two proteins at a time. There are instances when one may wish to offer a particular "bait" protein to several "prey" proteins simultaneously. Preferential interaction of the bait protein with one of the prey proteins, or different sites of interaction between the bait protein and multiple prey proteins, may thus be observed. Results We have constructed a series of gene expression vectors, based upon the pSAT series of vectors, to facilitate the practice of multi-color BiFC. The bait protein is tagged with the C-terminal portion of CFP (cCFP, and prey proteins are tagged with the N-terminal portions of either Venus (nVenus or Cerulean (nCerulean. Interaction of cCFP-tagged proteins with nVenus-tagged proteins generates yellow fluorescence, whereas interaction of cCFP-tagged proteins with nCerulean-tagged proteins generates blue fluorescence. Additional expression of mCherry indicates transfected cells and sub-cellular structures. Using this system, we have determined in both tobacco BY-2 protoplasts and in onion epidermal cells that Agrobacterium VirE2 protein interacts with the Arabidopsis nuclear transport adapter protein importin α-1 in the cytoplasm, whereas interaction of VirE2 with a different importin α isoform, importin α-4, occurs predominantly in the nucleus. Conclusion Multi

  16. Spatially Organized Enzymes Drive Cofactor-Coupled Cascade Reactions.

    Science.gov (United States)

    Ngo, Tien Anh; Nakata, Eiji; Saimura, Masayuki; Morii, Takashi

    2016-03-01

    We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes. PMID:26881296

  17. Time-dependent quantum dynamics study for reaction of D+CH4→CH3+HD

    Institute of Scientific and Technical Information of China (English)

    Liu Xin-Guo; Zhang Qing-Gang; Zhang Yi-Ci; Wang Ming-Liang; John Zhang Zeng-Hui

    2004-01-01

    The semirigid vibrating rotor target (SVRT) model has been applied to the study of the reaction of D+CH4 →CH3+HD using a time-dependent wave packet method. The energy dependence of the calculated reaction probability shows oscillatory structures similar to those observed in the abstraction reaction of H+H2, H+CH4 etc. We have also studied the influence of rotational and vibrational excitation of the reacting molecule (CH4) on reaction probability.The excitation of the H-CH3 stretching vibration gives significant enhancement of reaction probability, which rises significantly with the enhancement of rotational quantum number j. Finally, we have compared the cross section and the rate constant of the D+CH4 system with that of the H+CH4 system.

  18. Rate constants for chemical reactions in high-temperature nonequilibrium air

    Science.gov (United States)

    Jaffe, R. L.

    1986-01-01

    In the nonequilibrium atmospheric chemistry regime that will be encountered by the proposed Aeroassisted Orbital Transfer Vehicle in the upper atmosphere, where air density is too low for thermal and chemical equilibrium to be maintained, the detailed high temperature air chemistry plays a critical role in defining radiative and convective heating loads. Although vibrational and electronic temperatures remain low (less than 15,000 K), rotational and translational temperatures may reach 50,000 K. Attention is presently given to the effects of multiple temperatures on the magnitudes of various chemical reaction rate constants, for the cases of both bimolecular exchange reactions and collisional excitation and dissociation reactions.

  19. Testing the Palma-Clary Reduced Dimensionality Model Using Classical Mechanics on the CH4 + H → CH3 + H2 Reaction.

    Science.gov (United States)

    Vikár, Anna; Nagy, Tibor; Lendvay, György

    2016-07-14

    Application of exact quantum scattering methods in theoretical reaction dynamics of bimolecular reactions is limited by the complexity of the equations of nuclear motion to be solved. Simplification is often achieved by reducing the number of degrees of freedom to be explicitly handled by freezing the less important spectator modes. The reaction cross sections obtained in reduced-dimensionality (RD) quantum scattering methods can be used in the calculation of rate coefficients, but their physical meaning is limited. The accurate test of the performance of a reduced-dimensionality method would be a comparison of the RD cross sections with those obtained in accurate full-dimensional (FD) calculations, which is not feasible because of the lack of complete full-dimensional results. However, classical mechanics allows one to perform reaction dynamics calculations using both the RD and the FD model. In this paper, an RD versus FD comparison is made for the 8-dimensional Palma-Clary model on the example of four isotopologs of the CH4 + H → CH3 + H2 reaction, which has 12 internal dimensions. In the Palma-Clary model, the only restriction is that the methyl group is confined to maintain C3v symmetry. Both RD and FD opacity and excitation functions as well as differential cross sections were calculated using the quasiclassical trajectory method. The initial reactant separation has been handled according to our one-period averaging method [ Nagy et al. J. Chem. Phys. 2016, 144, 014104 ]. The RD and FD excitation functions were found to be close to each other for some isotopologs, but in general, the RD reactivity parameters are lower than the FD reactivity parameters beyond statistical error, and for one of the isotopologs, the deviation is significant. This indicates that the goodness of RD cross sections cannot be taken for granted. PMID:26918703

  20. Reaction dynamics during pulsed light activation of ATX-S10 Na(II)-sensitized cell cultures: analysis based on fluorescence-oxygen diagram

    Science.gov (United States)

    Kawauchi, Satoko; Sato, Shunichi; Morimoto, Yuji; Kikuchi, Makoto

    2005-04-01

    To elucidate the mechanism of photosensitization with pulsed light excitation, we previously introduced fluorescence-oxygen diagram that shows the correlation between photochemical oxygen consumption and photobleaching during a treatment (Kawauchi et al., Photochem. Photobiol., 80, 216-223, 2004). In pulsed photodynamic treatment of A549 cells with ATX-S10"Na(II), the diagrams for treatments at relatively high repetition rates of 10 and 30 Hz showed the complex behaviors of photochemical reaction; photobleaching initially occurred with oxygen consumption but it was switched to oxygen-independent photobleaching, which was followed by a secondary oxygen-consuming regime. In this study, fluorescence microscopy revealed that for treatments at 10 and 30 Hz, subcellular fluorescence distribution of ATX-S10×Na(II) changed drastically from the high-intensity spotty patterns showing lysosomal accumulation to the diffusive patterns within the cytosol during certain ranges of total light dose. These ranges were found to coincide with those in which oxygen-independent reaction appeared. These findings suggest that the sensitizer started to be redistributed from lysosomes to the cytosol during the oxygen-independent reaction regime. On the other hand, at 5 Hz, such reaction switching was not clearly seen during whole irradiation period in the diagram; this was consistent with the observation that sensitizer redistribution efficiently occurred even in the early phase of irradiation. The appearance of oxygen-independent reaction at the higher repetition rates may be caused by high local concentration of the sensitizer and the resultant low concentration of oxygen in the reaction sites due to the shorter pulse-to-pulse time intervals. In pulsed photodynamic treatment, pulse frequency is an important parameter that affects the intracellular kinetics of the sensitizer and hence the photochemical reaction dynamics.