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Sample records for bimolecular reaction dynamics

  1. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

    KAUST Repository

    Lipková, Jana

    2011-01-01

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

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

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

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

  3. 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

  4. Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

    Energy Technology Data Exchange (ETDEWEB)

    Bradforth, S.E.

    1992-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Blank, David Andrew [Univ. of California, Berkeley, CA (United States)

    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.

  6. 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.

  7. On the possibility of negative activation energies in bimolecular reactions

    Science.gov (United States)

    Jaffe, R. L.

    1978-01-01

    The temperature dependence of the rate constants for model reacting systems was studied to understand some recent experimental measurements which imply the existence of negative activation energies. A collision theory model and classical trajectory calculations are used to demonstrate that the reaction probability can vary inversely with collision energy for bimolecular reactions occurring on attractive potential energy surfaces. However, this is not a sufficient condition to ensure that the rate constant has a negative temperature dependence. On the basis of these calculations, it seems unlikely that a true bimolecular reaction between neutral molecules will have a negative activation energy.

  8. Universal model for exoergic bimolecular reactions and inelastic processes

    CERN Document Server

    Gao, Bo

    2010-01-01

    From a rigorous multichannel quantum-defect formulation of bimolecular processes, we derive a fully quantal and analytic model for the total rate of exoergic bimolecular reactions and/or inelastic processes that is applicable over a wide range of temperatures including the ultracold regime. The theory establishes a connection between the ultracold chemistry and the regular chemistry by showing that the same theory that gives the quantum threshold behavior agrees with the classical Gorin model at higher temperatures. In between, it predicts that the rates for identical bosonic molecules and distinguishable molecules would first decrease with temperature outside of the Wigner threshold region, before rising after a minimum is reached.

  9. Perspective: Vibrational-induced steric effects in bimolecular reactions

    Science.gov (United States)

    Liu, Kopin

    2015-02-01

    The concept of preferred collision geometry in a bimolecular reaction is at the heart of reaction dynamics. Exemplified by a series of crossed molecular beam studies on the reactions of a C-H stretch-excited CHD3(v1 = 1) with F, Cl, and O(3P) atoms, two types of steric control of chemical reactivity will be highlighted. A passive control is governed in a reaction with strong anisotropic entry valley that can significantly steer the incoming trajectories. This disorientation effect is illustrated by the F and O(3P) + CHD3(v1 = 1) reactions. In the former case, the long-range anisotropic interaction acts like an optical "negative" lens by deflecting the trajectories away from the favored transition-state geometry, and thus inhibiting the bond rupture of the stretch-excited CHD3. On the contrary, the interaction between O(3P) and CHD3(v1 = 1) behaves as a "positive" lens by funneling the large impact-parameter collisions into the cone of acceptance, and thereby enhances the reactivity. As for reactions with relatively weak anisotropic interactions in the entry valley, an active control can be performed by exploiting the polarization property of the infrared excitation laser to polarize the reactants in space, as demonstrated in the reaction of Cl with a pre-aligned CHD3(v1 = 1) reactant. A simpler case, the end-on versus side-on collisions, will be elucidated for demonstrating a means to disentangle the impact-parameter averaging. A few general remarks about some closely related issues, such as mode-, bond-selectivity, and Polanyi's rules, are made.

  10. 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.

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

    Science.gov (United States)

    Ghaderi, Nima

    2016-03-28

    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.

  12. 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.

  13. Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.

    Science.gov (United States)

    Zhou, G; Somasundaram, T; Blanc, E; Parthasarathy, G; Ellington, W R; Chapman, M S

    1998-07-21

    Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar gamma-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions, their role appears to be secondary to substrate alignment in this bimolecular reaction.

  14. Bimolecular reactions of activated species: An analysis of problematic HC(O)C(O) chemistry

    Science.gov (United States)

    Shannon, Robin J.; Robertson, Struan H.; Blitz, Mark A.; Seakins, Paul W.

    2016-09-01

    Experimental studies have demonstrated the importance of non-thermal bimolecular association chemistry. Recently a fully reversible method for incorporating any number of such non-thermal reactions into a single master equation has been developed (Green and Robertson, 2014) [10]. Using this methodology experimental results for the system: (1) (CHO)2 + OH → HC(O)C(O) + H2O, (2) HC(O)C(O) → HCO + CO, (3) HC(O)C(O) + O2 → OH + CO + CO2, are modeled, reproducing the temperature and pressure dependence of the OH yield. An issue remains as to how to model energy partition into HC(O)C(O).

  15. Force-activated reactivity switch in a bimolecular chemical reaction at the single molecule level

    Science.gov (United States)

    Szoszkiewicz, Robert; Garcia-Manyes, Sergi; Liang, Jian; Kuo, Tzu-Ling; Fernandez, Julio M.

    2010-03-01

    Mechanical force can deform the reacting molecules along a well-defined direction of the reaction coordinate. However, the effect of mechanical force on the free-energy surface that governs a chemical reaction is still largely unknown. The combination of protein engineering with single-molecule AFM force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by some reducing agents in a bimolecular substitution reaction (so-called SN2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity ``switch'' at 500 pN, after which the accelerating effect of force on the rate of an SN2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in SN2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule. References: Sergi Garcia-Manyes, Jian Liang, Robert Szoszkiewicz, Tzu-Ling Kuo and Julio M. Fernandez, Nature Chemistry, 1, 236-242, 2009.

  16. Benchmark Study on the Smallest Bimolecular Nucleophilic Substitution Reaction: H−+CH4 →CH4+H−

    Directory of Open Access Journals (Sweden)

    Marcel Swart

    2013-07-01

    Full Text Available We report here a benchmark study on the bimolecular nucleophilic substitution (SN2 reaction between hydride and methane, for which we have obtained reference energies at the coupled cluster toward full configuration-interaction limit (CC-cf/CBS. Several wavefunction (HF, MP2, coupled cluster and density functional methods are compared for their reliability regarding these reference data.

  17. 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.

  18. 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

  19. Experimental evidence of the relevance of orientational correlations in photoinduced bimolecular reactions in solution.

    Science.gov (United States)

    Angulo, Gonzalo; Cuetos, Alejandro; Rosspeintner, Arnulf; Vauthey, Eric

    2013-09-12

    A major problem in the extraction of the reaction probability in bimolecular processes is the disentanglement from the influence of molecular diffusion. One of the strategies to overcome it makes use of reactive solvents in which the reactants do not need to diffuse to encounter each other. However, most of our quantitative understanding of chemical reactions in solution between free partners is based on the assumption that they can be approximated by spheres because rotation averages their mutual orientations. This condition may not be fulfilled when the reaction takes place on time scales faster than that of molecular reorientation. In this work, the fluorescence quenching of two very similar polyaromatic hydrocarbons with different electric dipole moments is measured. The concentration of a liquid electron-donating quencher is varied from very dilute solutions to pure quencher solutions. In both cases, the thermodynamics of the reactions are very similar and, according to the Marcus expression, the kinetics are expected to proceed at similar rates. However, one of them is 10 times faster in the pure quencher solution. This difference starts at relatively low quencher concentrations. An explanation based on the fluorophore-solvent dipole-dipole interaction and the consequent orientational solvent structure is provided. The orientational correlation between fluorophore and quencher is calculated by means of computer simulations. Important differences depending on the fluorophore dipole moment are found. The kinetics can be explained quantitatively with a reaction-diffusion model that incorporates the effects of the presence of the dipole moment and the rotational diffusion, only in the highest quencher concentration case, but not in dilute solutions, most likely due to fundamental limitations of the kinetic theory.

  20. Gas phase studies of the Pesci decarboxylation reaction: synthesis, structure, and unimolecular and bimolecular reactivity of organometallic ions.

    Science.gov (United States)

    O'Hair, Richard A J; Rijs, Nicole J

    2015-02-17

    promoting the formation of the organometallic ion. Where isomeric organometallic ions are generated and normal MS approaches cannot distinguish them, we describe approaches to elucidate the decarboxylation mechanism via determination of their structure. These "unmasked" organometallic ions, [RM(L)n](x), can also be structurally interrogated spectroscopically or via CID. We have thus compared the gas-phase structures and decomposition of several highly reactive and synthetically important organometallic ions for the first time. Perhaps the most significant aspect of this work is the study of bimolecular reactions, which provides experimental information on mechanistically obscure bond-formation and cross-coupling steps and the intrinsic reactivity of ions. We have sought to understand transformations of substrates including acid-base and hydrolysis reactions, along with reactions resulting in C-C bond formation. Our studies also allow a direct comparison of the performance of different metal catalysts in the individual elementary steps associated with protodecarboxylation and decarboxylative alkylation cycles. Electronic structure (DFT and ab initio) and dynamics (RRKM) calculations provide further mechanistic insights into these reactions. The broad implications of this research are that new reactions can be discovered and that the performance of metal catalysts can be evaluated in terms of each of their elementary steps. This has been particularly useful for the study of metal-mediated decarboxylation reactions.

  1. Rotational effects in complex-forming bimolecular substitution reactions: A quantum-mechanical approach

    Science.gov (United States)

    Hennig, Carsten; Schmatz, Stefan

    2009-12-01

    The quantum dynamics of the complex-forming SN2 reaction Cl-+CH3Br→ClCH3+Br- is studied with emphasis on rotational effects. The pseudotriatomic system Cl-Me-Br is treated with a corresponding three-dimensional (3D) potential energy surface as a function of the two scattering coordinates and the enclosed angle where the geometry of the methyl group Me is optimized at each point. The 3D space is divided into three different parts, the interaction region, an intermediate region, and the asymptotic region. In line with simple classical-mechanical arguments and previous classical trajectory calculations, initial rotational motion of CH3Br seemingly decreases the reaction probability. However, the dynamical inclusion of the rotational degree of freedom and the presence of the many rovibrational product states overall lead to a large increase in reactivity compared to our previous collinear study on this reaction. If the reactant is rotationally excited, the higher vibrational product states are depleted in favor of lower-lying levels. Starting the reaction with rotationless reactants may end up in significant rotational excitation in the product molecules (translation-to-rotation energy transfer). On the other hand, initial rotational energy in rotationally highly excited reactants is to a large amount converted into translational and vibrational energy. The average amount of rotational energy in the products shows a twofold vibrational excitation-independent saturation (i.e., memorylessness), with respect to both initial rotational excitation and translational energy. Since only about one-half of all reactant states end in rotationless products, the reaction probability should be increased by a factor of 2; the actually larger reactivity points to other dynamical effects that play an important role in the reaction.

  2. LET dependence of the response of EBT2 films in proton dosimetry modeled as a bimolecular chemical reaction

    Science.gov (United States)

    Perles, L. A.; Mirkovic, D.; Anand, A.; Titt, U.; Mohan, R.

    2013-12-01

    The dose response for films exposed to clinical x-ray beams is not linear and a calibration curve based on absorbed dose can be used to account for this effect. However for proton dosimetry the dose response of films exhibits an additional dependence because of the variation of the linear energy transfer (LET) as the protons penetrate matter. In the present study, we hypothesized that the dose response for EBT2 films can be mathematically described as a bimolecular chemical reaction. Furthermore, we have shown that the LET effect can be incorporated in the dose-response curve. A set of EBT2 films was exposed to pristine 161.6 MeV proton beams. The films were exposed to doses ranging from 0.93 to 14.82 Gy at a depth of 2 cm in water. The procedure was repeated with one film exposed to a lower energy beam (85.6 MeV). We also computed the LET and dose to water in the sensitive layer of the films with a validated Monte Carlo system, taking into account the film construction (polyester, adhesive and sensitive layers). The bimolecular model was able to accurately fit the experimental data with a correlation factor of 0.9998, and the LET correction factor was determined and incorporated into the dose-response function. We also concluded that the film orientation is important when determining the LET correction factor because of the asymmetric construction of the film.

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

    Science.gov (United States)

    Doktorov, Alexander B

    2015-08-21

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

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

    KAUST Repository

    Alsam, Amani Abdu

    2016-09-21

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

  5. The mechanism of the NHC catalyzed aza-Morita-Baylis-Hillman reaction: insights into a new substrate-catalyzed bimolecular pathway.

    Science.gov (United States)

    Verma, Pritha; Verma, Pragya; Sunoj, Raghavan B

    2014-04-14

    The first mechanistic study on the NHC-catalyzed aza-MBH reaction between cyclopentenone and N-mesylbenzaldimine using density functional theory reveals that a bimolecular mechanism, involving two molecules of benzaldimine in the proton transfer, is energetically more preferred over the conventional direct proton transfer.

  6. Charge-carrier relaxation dynamics in highly ordered poly( p -phenylene vinylene): Effects of carrier bimolecular recombination and trapping

    Science.gov (United States)

    Soci, Cesare; Moses, Daniel; Xu, Qing-Hua; Heeger, Alan J.

    2005-12-01

    We have studied the charge-carrier relaxation dynamics in highly ordered poly( p -phenylene vinylene) over a broad time range using fast (t>100ps) transient photoconductivity measurements. The carrier density was also monitored (t>100fs) by means of photoinduced absorption probed at the infrared active vibrational modes. We find that promptly upon charge-carrier photogeneration, the initial polaron dynamics is governed by bimolecular recombination, while later in the subnanosecond time regime carrier trapping gives rise to an exponential decay of the photocurrent. The more sensitive transient photocurrent measurements indicate that in the low excitation regime, when the density of photocarriers is comparable to that of the trapping states (˜1016cm-3) , carrier hopping between traps along with transport via extended states determines the carrier relaxation, a mechanism that is manifested by a long-lived photocurrent “tail.” This photocurrent tail is reduced by lowering the temperature and/or by increasing the excitation density. Based on these data, we develop a comprehensive kinetic model that takes into account the bipolar charge transport, the free-carrier bimolecular recombination, the carrier trapping, and the carrier recombination involving free and trapped carriers.

  7. 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.

  8. Mode-Specific SN2 Reaction Dynamics.

    Science.gov (United States)

    Wang, Yan; Song, Hongwei; Szabó, István; Czakó, Gábor; Guo, Hua; Yang, Minghui

    2016-09-01

    Despite its importance in chemistry, the microscopic dynamics of bimolecular nucleophilic substitution (SN2) reactions is still not completely elucidated. In this publication, the dynamics of a prototypical SN2 reaction (F(-) + CH3Cl → CH3F + Cl(-)) is investigated using a high-dimensional quantum mechanical model on an accurate potential energy surface (PES) and further analyzed by quasi-classical trajectories on the same PES. While the indirect mechanism dominates at low collision energies, the direct mechanism makes a significant contribution. The reactivity is found to depend on the specific reactant vibrational mode excitation. The mode specificity, which is more prevalent in the direct reaction, is rationalized by a transition-state-based model.

  9. Pseudo-bimolecular [2+2] cycloaddition studied by time-resolved photoelectron spectroscopy

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Y; Boguslavskiy, Andrey E; Schalk, Oliver

    2011-01-01

    The first study of pseudo-bimolecular cycloaddition reaction dynamics in the gas phase is presented. We used femtosecond time-resolved photoelectron spectroscopy (TRPES) to study the [2+2] photocycloaddition in the model system pseudo-gem-divinyl[2.2]paracyclophane. From X-ray crystal diffraction...

  10. Studies on the Mechanism for the Bimolecular Metathesis Reaction CH3+HCl(←→)CH4+Cl

    Institute of Scientific and Technical Information of China (English)

    ZHOU,Zheng-Yu (周正宇); ZHOU,Zheng-Yu; CHEN,Guang(陈光); CHEN,Guang; ZHOU,Xin-Ming(周欣明); ZHOU,Xin-Ming; FU,Hui(傅惠); FU,Hui

    2001-01-01

    The geometry optimization of the transition state, the precursor complex and the successor complex was performed at the 6-311G* basis set level. From the analysis of the vibrational frequency of the precursor complex, transition state, successor complex and the isolated state, the reaction mechanism was derived which was complicated with the boni-rupture electron transfer theory. The atom H in molecule HCl attacks the atom C, forming a transition state via the precursor complex and the electron-transfer happens in precursor complex.Ami the active energy, electronic coupling matrix element,the reorganization energy, and the reaction rate are obtained.

  11. Theoretical Analysis on the Kinetic Isotope Effects of Bimolecular Nucleophilic Substitution (SN2 Reactions and Their Temperature Dependence

    Directory of Open Access Journals (Sweden)

    Wan-Chen Tsai

    2013-04-01

    Full Text Available Factors affecting the kinetic isotope effects (KIEs of the gas-phase SN2 reactions and their temperature dependence have been analyzed using the ion-molecule collision theory and the transition state theory (TST. The quantum-mechanical tunneling effects were also considered using the canonical variational theory with small curvature tunneling (CVT/SCT. We have benchmarked a few ab initio and density functional theory (DFT methods for their performance in predicting the deuterium KIEs against eleven experimental values. The results showed that the MP2/aug-cc-pVDZ method gave the most accurate prediction overall. The slight inverse deuterium KIEs usually observed for the gas-phase SN2 reactions at room temperature were due to the balance of the normal rotational contribution and the significant inverse vibrational contribution. Since the vibrational contribution is a sensitive function of temperature while the rotation contribution is temperature independent, the KIEs are thus also temperature dependent. For SN2 reactions with appreciable barrier heights, the tunneling effects were predicted to contribute significantly both to the rate constants and to the carbon-13, and carbon-14 KIEs, which suggested important carbon atom tunneling at and below room temperature.

  12. New methods for quantum mechanical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, W.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States)

    1996-12-01

    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 (L{sup 2}) 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{sup -} can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC{sup -} geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H{sub 3}O{sup -} system, providing information about the potential energy surface for the OH + H{sub 2} 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.

  13. High temperature shock tube and theoretical studies on the thermal decomposition of dimethyl carbonate and its bimolecular reactions with H and D-atoms.

    Science.gov (United States)

    Peukert, S L; Sivaramakrishnan, R; Michael, J V

    2013-05-09

    for reactions B and C are in good agreement with the experimental rate constants. The theoretical rate constants for these bimolecular processes can be represented by modified Arrhenius expressions over the T-range 500-2000 K as, kB(T) = 1.45 × 10(-19)T(2.827) exp(-3398 K/T) cm(3) molecule(-1) s(-1) and kC(T) = 2.94 × 10(-19)T(2.729) exp(-3215 K/T) cm(3) molecule(-1) s(-1).

  14. Bimolecular recombination in organic photovoltaics.

    Science.gov (United States)

    Lakhwani, Girish; Rao, Akshay; Friend, Richard H

    2014-01-01

    The recombination of electrons and holes is a major loss mechanism in photovoltaic devices that controls their performance. We review scientific literature on bimolecular recombination (BR) in bulk heterojunction organic photovoltaic devices to bring forward existing ideas on the origin and nature of BR and highlight both experimental and theoretical work done to quantify its extent. For these systems, Langevin theory fails to explain BR, and recombination dynamics turns out to be dependent on mobility, temperature, electric field, charge carrier concentration, and trapped charges. Relationships among the photocurrent, open-circuit voltage, fill factor, and morphology are discussed. Finally, we highlight the recent emergence of a molecular-level picture of recombination, taking into account the spin and delocalization of charges. Together with the macroscopic picture of recombination, these new insights allow for a comprehensive understanding of BR and provide design principles for future materials and devices.

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

    Science.gov (United States)

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

    2013-11-21

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

  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

    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.)

  19. Kinematically complete chemical reaction dynamics

    Science.gov (United States)

    Trippel, S.; Stei, M.; Otto, R.; Hlavenka, P.; Mikosch, J.; Eichhorn, C.; Lourderaj, U.; Zhang, J. X.; Hase, W. L.; Weidemüller, M.; Wester, R.

    2009-11-01

    Kinematically complete studies of molecular reactions offer an unprecedented level of insight into the dynamics and the different mechanisms by which chemical reactions occur. We have developed a scheme to study ion-molecule reactions by velocity map imaging at very low collision energies. Results for the elementary nucleophilic substitution (SN2) reaction Cl- + CH3I → ClCH3 + I- are presented and compared to high-level direct dynamics trajectory calculations. Furthermore, an improved design of the crossed-beam imaging spectrometer with full three-dimensional measurement capabilities is discussed and characterization measurements using photoionization of NH3 and photodissociation of CH3I are presented.

  20. State-to-state dynamics of elementary chemical reactions using Rydberg H-atom translational spectroscopy

    Science.gov (United States)

    Yang, Xueming

    In this review, a few examples of state-to-state dynamics studies of both unimolecular and bimolecular reactions using the H-atom Rydberg tagging TOF technique were presented. From the H2O photodissociation at 157 nm, a direction dissociation example is provided, while photodissociation of H2O at 121.6 has provided an excellent dynamical case of complicated, yet direct dissociation process through conical intersections. The studies of the O(1D) + H2 → OH + H reaction has also been reviewed here. A prototype example of state-to-state dynamics of pure insertion chemical reaction is provided. Effect of the reagent rotational excitation and the isotope effect on the dynamics of this reaction have also been investigated. The detailed mechanism for abstraction channel in this reaction has also been closely studied. The experimental investigations of the simplest chemical reaction, the H3 system, have also been described here. Through extensive collaborations between theory and experiment, the mechanism for forward scattering product at high collision energies for the H + HD reaction was clarified, which is attributed to a slow down mechanism on the top of a quantized barrier transition state. Oscillations in the product quantum state resolved different cross sections have also been observed in the H + D2 reaction, and were attributed to the interference of adiabatic transition state pathways from detailed theoretical analysis. The results reviewed here clearly show the significant advances we have made in the studies of the state-to-state molecular reaction dynamics.

  1. Rate constants for the thermal decomposition of ethanol and its bimolecular reactions with OH and D: reflected shock tube and theoretical studies.

    Science.gov (United States)

    Sivaramakrishnan, R; Su, M-C; Michael, J V; Klippenstein, S J; Harding, L B; Ruscic, B

    2010-09-09

    The thermal decomposition of ethanol and its reactions with OH and D have been studied with both shock tube experiments and ab initio transition state theory-based master equation calculations. Dissociation rate constants for ethanol have been measured at high T in reflected shock waves using OH optical absorption and high-sensitivity H-atom ARAS detection. The three dissociation processes that are dominant at high T are C2H5OH--> C2H4+H2O (A) -->CH3+CH2OH (B) -->C2H5+OH (C).The rate coefficient for reaction C was measured directly with high sensitivity at 308 nm using a multipass optical White cell. Meanwhile, H-atom ARAS measurements yield the overall rate coefficient and that for the sum of reactions B and C , since H-atoms are instantaneously formed from the decompositions of CH(2)OH and C(2)H(5) into CH(2)O + H and C(2)H(4) + H, respectively. By difference, rate constants for reaction 1 could be obtained. One potential complication is the scavenging of OH by unreacted ethanol in the OH experiments, and therefore, rate constants for OH+C2H5OH-->products (D)were measured using tert-butyl hydroperoxide (tBH) as the thermal source for OH. The present experiments can be represented by the Arrhenius expression k=(2.5+/-0.43) x 10(-11) exp(-911+/-191 K/T) cm3 molecule(-1) s(-1) over the T range 857-1297 K. For completeness, we have also measured the rate coefficient for the reaction of D atoms with ethanol D+C2H5OH-->products (E) whose H analogue is another key reaction in the combustion of ethanol. Over the T range 1054-1359 K, the rate constants from the present experiments can be represented by the Arrhenius expression, k=(3.98+/-0.76) x10(-10) exp(-4494+/-235 K/T) cm3 molecule(-1) s(-1). The high-pressure rate coefficients for reactions B and C were studied with variable reaction coordinate transition state theory employing directly determined CASPT2/cc-pvdz interaction energies. Reactions A , D , and E were studied with conventional transition state theory

  2. Dynamic Reaction Mechanisms of ClO(-) with CH3Cl: Comparison Between Direct Dynamics Trajectory Simulations and Experiment.

    Science.gov (United States)

    Yu, Feng

    2016-03-24

    We have investigated the dynamic reaction mechanisms of *ClO¯ with CH3Cl (the asterisk is utilized to label a different Cl atom). Ab initio molecular dynamics simulations at the MP2/6-31+G(d,p) level of theory have been employed to compute the dynamic trajectories. On the basis of our simulations, the dynamic reaction pathways for the bimolecular nucleophilic substitution (SN2) reaction channel and SN2-induced elimination reaction channel are clearly illustrated. For the SN2 reaction channel, some trajectories directly dissociate to the final products of CH3O*Cl and Cl¯, whereas the others involve the dynamic Cl¯···CH3O*Cl intermediate complex. As to the SN2-induced elimination reaction channel, the trajectories lead to the final products of CH2O, HCl, and *Cl¯ through the dynamic Cl¯···CH3O*Cl intermediate complex. More significantly, the product branching ratios of Cl¯ and *Cl¯ predicted by our simulations are basically consistent with previous experimental results (Villano et al. J. Am. Chem. Soc. 2009, 131, 8227-8233).

  3. Comparison of the Rates of Uni- and Bi-Molecular Diffusion Controlled Reactions on Circular, Filled Aggregate and DLA Fractal Aggregate in Two Dimensions.

    Science.gov (United States)

    1987-05-07

    CLASSIFICATION Of THIS PAGIL(Whan Data Entered) It is found that the reaction rates of OLA agigregates are comnatible with * that of circular aggregates with...NOSC Wayne State University Code 521 Detroit, Michigan 49207 San Diego, California 91232 Or. W.E. Moerner I.B.M. Corporation Almaden Research Center 650

  4. A Simple Method for Calculating Quantum Effects on the Temperature Dependence of Bimolecular Reaction Rates An Application to $CH_{4} + H \\rightarrow CH_{3} + H_{2}$

    CERN Document Server

    Goodson, D Z; Chiang, W T; Valone, S M; Doll, J D; Goodson, David Z.; Roelse, Dustin W.; Chiang, Wan-Ting; Valone, Steven M.

    1997-01-01

    The temperature dependence of the rate of the reaction CH_4+H \\to CH_3+H_2 is studied using classical collision theory with a temperature-dependent effective potential derived from a path integral analysis. Analytical expressions are obtained for the effective potential and for the rate constant. The rate constant expressions use a temperature-dependent activation energy. They give better agreement with the available experimental results than do previous empirical fits. Since all but one of the parameters in the present expressions are obtained from theory, rather than by fitting to experimental reaction rates, the expressions can be expected to be more dependable than purely empirical expressions at temperatures above 2000 K or below 350 K, where experimental results are not available.

  5. Bimolecular reaction of CH{sub 3} + CO in solid p-H{sub 2}: Infrared absorption of acetyl radical (CH{sub 3}CO) and CH{sub 3}-CO complex

    Energy Technology Data Exchange (ETDEWEB)

    Das, Prasanta [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Lee, Yuan-Pern, E-mail: yplee@mail.nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan (China); Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan (China)

    2014-06-28

    complex was observed instead. This rapid quenching poses a limitation in production of free radicals via bimolecular reactions in p-H{sub 2}.

  6. 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…

  7. Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?

    CERN Document Server

    Hele, Timothy J H

    2015-01-01

    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 (TST) 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+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. 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 less accurate than Ring Polymer Molecular Dynamics (RPMD) for symmetric reactions, and in certain asymmetric systems closer to the q...

  8. 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....

  9. 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...

  10. Dynamical Model of Weak Pion Production Reactions

    CERN Document Server

    Sato, T; Lee, T S H

    2003-01-01

    The dynamical model of pion electroproduction has been extended to investigate the weak pion production reactions. The predicted cross sections of neutrino-induced pion production reactions are in good agreement with the existing data. We show that the renormalized(dressed) axial N-$\\Delta$ form factor contains large dynamical pion cloud effects and this renormalization effects are crucial in getting agreement with the data. We conclude that the N-$\\Delta$ transitions predicted by the constituent quark model are consistent with the existing neutrino induced pion production data in the $\\Delta$ region.

  11. 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.

  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. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  14. 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

  15. 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.

  16. 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.

  17. A chirped-pulse Fourier-transform microwave/pulsed uniform flow spectrometer. II. Performance and applications for reaction dynamics.

    Science.gov (United States)

    Abeysekera, Chamara; Zack, Lindsay N; Park, G Barratt; Joalland, Baptiste; Oldham, James M; Prozument, Kirill; Ariyasingha, Nuwandi M; Sims, Ian R; Field, Robert W; Suits, Arthur G

    2014-12-01

    This second paper in a series of two reports on the performance of a new instrument for studying chemical reaction dynamics and kinetics at low temperatures. Our approach employs chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy to probe photolysis and bimolecular reaction products that are thermalized in pulsed uniform flows. Here we detail the development and testing of a new K(a)-band CP-FTMW spectrometer in combination with the pulsed flow system described in Paper I [J. M. Oldham, C. Abeysekera, B. Joalland, L. N. Zack, K. Prozument, I. R. Sims, G. B. Park, R. W. Field, and A. G. Suits, J. Chem. Phys. 141, 154202 (2014)]. This combination delivers broadband spectra with MHz resolution and allows monitoring, on the μs timescale, of the appearance of transient reaction products. Two benchmark reactive systems are used to illustrate and characterize the performance of this new apparatus: the photodissociation of SO2 at 193 nm, for which the vibrational populations of the SO product are monitored, and the reaction between CN and C2H2, for which the HCCCN product is detected in its vibrational ground state. The results show that the combination of these two well-matched techniques, which we refer to as chirped-pulse in uniform flow, also provides insight into the vibrational and rotational relaxation kinetics of the nascent reaction products. Future directions are discussed, with an emphasis on exploring the low temperature chemistry of complex polyatomic systems.

  18. Photochemical Reactions of Cyclohexanone: Mechanisms and Dynamics.

    Science.gov (United States)

    Shemesh, Dorit; Nizkorodov, Sergey A; Gerber, R Benny

    2016-09-15

    Photochemistry of carbonyl compounds is of major importance in atmospheric and organic chemistry. The photochemistry of cyclohexanone is studied here using on-the-fly molecular dynamics simulations on a semiempirical multireference configuration interaction potential-energy surface to predict the distribution of photoproducts and time scales for their formation. Rich photochemistry is predicted to occur on a picosecond time scale following the photoexcitation of cyclohexanone to the first singlet excited state. The main findings include: (1) Reaction channels found experimentally are confirmed by the theoretical simulations, and a new reaction channel is predicted. (2) The majority (87%) of the reactive trajectories start with a ring opening via C-Cα bond cleavage, supporting observations of previous studies. (3) Mechanistic details, time scales, and yields are predicted for all reaction channels. These benchmark results shed light on the photochemistry of isolated carbonyl compounds in the atmosphere and can be extended in the future to photochemistry of more complex atmospherically relevant carbonyl compounds in both gaseous and condensed-phase environments.

  19. Stereoselective bimolecular phenoxyl radical coupling by an auxiliary (dirigent) protein without an active center

    Energy Technology Data Exchange (ETDEWEB)

    Davin, L.B.; Wang, Huai-Bin; Crowell, A.L. [Washington State Univ., Pullman, WA (United States)] [and others

    1997-01-17

    The regio- and stereospecificity of bimolecular phenoxy radical coupling reactions, of especial importance in lignin and lignan biosynthesis, are clearly controlled in some manner in vivo; yet in vitro coupling by oxidases, such as laccases, only produce racemic products. In other words, laccases, peroxidases, and comparable oxidases are unable to control regio- or stereospecificity by themselves and thus some other agent must exist. A 78-kilodalton protein has been isolated that, in the presence of an oxidase or one electron oxidant, effects stereoselective bimolecular phenoxy radical coupling in vitro. Itself lacking a catalytically active (oxidative) center, its mechanism of action is presumed to involve capture of E-coniferyl alcohol-derived free-radical intermediates, with consequent stereoselective coupling to give (+)-pinoresinol. 25 refs., 6 figs., 3 tabs.

  20. Ab initio direct classical trajectory investigation on the SN2 reaction of F- with NH2F: nonstatistical central barrier recrossing dynamics.

    Science.gov (United States)

    Yu, Feng

    2012-02-05

    The bimolecular nucleophilic substitution (S(N)2) reaction of F(a)(-) with NH(2)F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2)F(a) moiety in the dynamic F(b)(-)…H-NH-F(a) complex to the intermolecular modes of the dynamic F(b)(-)…H-NH-F(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N)2 reaction.

  1. Photoinduced Bimolecular Electron Transfer from Cyano Anions in Ionic Liquids.

    Science.gov (United States)

    Wu, Boning; Liang, Min; Maroncelli, Mark; Castner, Edward W

    2015-11-19

    Ionic liquids with electron-donating anions are used to investigate rates and mechanisms of photoinduced bimolecular electron transfer to the photoexcited acceptor 9,10-dicyanoanthracene (9,10-DCNA). The set of five cyano anion ILs studied comprises the 1-ethyl-3-methylimidazolium cation paired with each of these five anions: selenocyanate, thiocyanate, dicyanamide, tricyanomethanide, and tetracyanoborate. Measurements with these anions dilute in acetonitrile and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide show that the selenocyanate and tricyanomethanide anions are strong quenchers of the 9,10-DCNA fluorescence, thiocyanate is a moderately strong quencher, dicyanamide is a weak quencher, and no quenching is observed for tetracyanoborate. Quenching rates are obtained from both time-resolved fluorescence transients and time-integrated spectra. Application of a Smoluchowski diffusion-and-reaction model showed that the complex kinetics observed can be fit using only two adjustable parameters, D and V0, where D is the relative diffusion coefficient between donor and acceptor and V0 is the value of the electronic coupling at donor-acceptor contact.

  2. Quantum state-resolved differential cross sections for complex-forming chemical reactions: Asymmetry is the rule, symmetry the exception

    Energy Technology Data Exchange (ETDEWEB)

    Larrégaray, Pascal, E-mail: pascal.larregaray@u-bordeaux.fr; Bonnet, Laurent, E-mail: laurent.bonnet@u-bordeaux.fr [ISM, UMR 5255, CNRS, F-33400 Talence (France); ISM, UMR 5255, Univ. Bordeaux, F-33400 Talence (France)

    2015-10-14

    We argue that statistical theories are generally unable to accurately predict state-resolved differential cross sections for triatomic bimolecular reactions studied in beam experiments, even in the idealized limit where the dynamics are fully chaotic. The basic reason is that quenching of interferences between partial waves is less efficient than intuitively expected, especially around the poles.

  3. 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.

  4. Stochastic dynamics of complexation reaction in the limit of small numbers.

    Science.gov (United States)

    Ghosh, Kingshuk

    2011-05-21

    We study stochastic dynamics of the non-linear bimolecular reaction A + B↔AB. These reactions are common in several bio-molecular systems such as binding, complexation, protein multimerization to name a few. We use master equation to compute the full distribution of several stochastic equilibrium properties such as number of complexes formed (N(c)), equilibrium constant (K). We provide exact analytical and simpler approximate expression for equilibrium fluctuation quantities to quickly estimate the amount of noise as a function of reactant molecules and rates. We construct the phase diagram for a fluctuational quantity f, defined as the ratio of standard deviation to average (f=√(ΔN(c))(2)/N(c)), as a function of different number of reactant molecules and reaction rates. One of the striking result is, it is possible to have f as high as 45% or higher in significant regions of the phase diagram even when number of reactants involved are around 20-40, typical in biology. Our finding indicates studying averages alone using mass action law needs careful scrutiny. We also outline possible application of our findings in gene expression. Furthermore, we compute average and fluctuation properties of time dependent quantities and derive equations of motion for different moments such as N(c)(t) and N(c)(t)(2). While mean-field mass action law fails to reproduce the exact time dependence, approximate solutions of coupled equations of motions for different moments, capturing fluctuation, is in good agreement with exact results. This may be a way to compute time development of averages and fluctuations in such non-linear systems where mass action law breaks down. Moreover, for this reaction, we outline connection to variational principle of maximum caliber and other more traditional approaches such as chemical Langevin equation. We derive noise statistics for the equivalent Langevin equation and show possible departure from Gaussian white noise. We believe quantitative

  5. 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}.

  6. 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.

  7. Electromagnetic Reactions and Few-Nucleon Dynamics

    CERN Document Server

    Bacca, Sonia

    2013-01-01

    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.

  8. Dynamic CT of tuberculous meningeal reactions

    Energy Technology Data Exchange (ETDEWEB)

    Jinkins, J.R.

    1987-07-01

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

  9. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations

    NARCIS (Netherlands)

    De Jong, Djurre H.; Schafer, Lars V.; De Vries, Alex H.; Marrink, Siewert J.; Berendsen, Herman J. C.; Grubmueller, Helmut

    2011-01-01

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices c

  10. Programming the dynamics of biochemical reaction networks.

    Science.gov (United States)

    Simmel, Friedrich C

    2013-01-22

    The development of complex self-organizing molecular systems for future nanotechnology requires not only robust formation of molecular structures by self-assembly but also precise control over their temporal dynamics. As an exquisite example of such control, in this issue of ACS Nano, Fujii and Rondelez demonstrate a particularly compact realization of a molecular "predator-prey" ecosystem consisting of only three DNA species and three enzymes. The system displays pronounced oscillatory dynamics, in good agreement with the predictions of a simple theoretical model. Moreover, its considerable modularity also allows for ecological studies of competition and cooperation within molecular networks.

  11. 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...

  12. 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.

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

    Science.gov (United States)

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

    2016-09-01

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

  14. Mathematics of small stochastic reaction networks: a boundary layer theory for eigenstate analysis.

    Science.gov (United States)

    Mjolsness, Eric; Prasad, Upendra

    2013-03-14

    We study and analyze the stochastic dynamics of a reversible bimolecular reaction A + B ↔ C called the "trivalent reaction." This reaction is of a fundamental nature and is part of many biochemical reaction networks. The stochastic dynamics is given by the stochastic master equation, which is difficult to solve except when the equilibrium state solution is desired. We present a novel way of finding the eigenstates of this system of difference-differential equations, using perturbation analysis of ordinary differential equations arising from approximation of the difference equations. The time evolution of the state probabilities can then be expressed in terms of the eigenvalues and the eigenvectors.

  15. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  16. Switching Dynamics in Reaction Networks Induced by Molecular Discreteness

    CERN Document Server

    Togashi, Y; Kaneko, Kunihiko; Togashi, Yuichi

    2006-01-01

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

  17. Quantum Dynamics of Radical-Ion-Pair Reactions

    OpenAIRE

    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 r...

  18. Dynamical dipole mode in heavy-ion fusion reactions

    Energy Technology Data Exchange (ETDEWEB)

    Parascandolo, C., E-mail: concetta.parascandolo@na.infn.i [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Pierroutsakou, D. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Martin, B. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Agodi, C.; Alba, R. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Boiano, A. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Coniglione, R. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); De Filippo, E. [INFN - Sezione di Catania, 95123, Catania (Italy); Del Zoppo, A. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Emanuele, U. [INFN, Gruppo Collegato di Messina and Dip. di Fisica, Universita di Messina, Messina (Italy); Farinon, F. [GSI, Planckstrasse 1, D-64291, Darmstadt (Germany); Guglielmetti, A. [Universita degli Studi di Milano and INFN, Sezione di Milano, via Celoria 16, I-20133 Milano (Italy); Inglima, G.; La Commara, M. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Maiolino, C. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy); Mazzocchi, C. [Universita degli Studi di Milano and INFN, Sezione di Milano, via Celoria 16, I-20133 Milano (Italy); Mazzocco, M. [Dip. di Fisica and INFN, Universita di Padova, via F. Marzolo 8, I-35131 Padova (Italy); Romoli, M. [INFN - Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Sandoli, M. [Universita degli Studi di Napoli ' Federico II' and INFN, Sezione di Napoli, via Cintia, I-80126 Napoli (Italy); Santonocito, D. [INFN - LNS, via Santa Sofia 62, I-95125 Catania (Italy)

    2010-03-01

    The dynamical dipole mode, excited in charge asymmetric heavy-ion collisions, was investigated in the mass region of the {sup 192}Pb compound nucleus, formed by using the {sup 40,48}Ca + {sup 152,144}Sm reactions at approx11 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.

  19. 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.

  20. 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.

  1. Reaction Profiles and Molecular Dynamics Simulations of Cyanide Radical Reactions Relevant to Titan's Atmosphere

    Science.gov (United States)

    Trinidad Pérez-Rivera, Danilo; Romani, Paul N.; Lopez-Encarnacion, Juan Manuel

    2016-10-01

    Titan's atmosphere is arguably the atmosphere of greatest interest that we have an abundance of data for from both ground based and spacecraft observations. As we have learned more about Titan's atmospheric composition, the presence of pre-biotic molecules in its atmosphere has generated more and more fascination about the photochemical process and pathways it its atmosphere. Our computational laboratory has been extensively working throughout the past year characterizing nitrile synthesis reactions, making significant progress on the energetics and dynamics of the reactions of .CN with the hydrocarbons acetylene (C2H2), propylene (CH3CCH), and benzene (C6H6), developing a clear picture of the mechanistic aspects through which these three reactions proceed. Specifically, first principles calculations of the reaction profiles and molecular dynamics studies for gas-phase reactions of .CN and C2H2, .CN and CH3CCH, and .CN and C6H6 have been carried out. A very accurate determination of potential energy surfaces of these reactions will allow us to compute the reaction rates which are indispensable for photochemical modeling of Titan's atmosphere.The work at University of Puerto Rico at Cayey was supported by Puerto Rico NASA EPSCoR IDEAS-ER program (2015-2016) and DTPR was sponsored by the Puerto Rico NASA Space Grant Consortium Fellowship. *E-mail: juan.lopez15@upr.edu

  2. 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

  3. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    Science.gov (United States)

    Wu, Emilia L

    2010-12-01

    The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context.

  4. Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damköhler numbers

    Science.gov (United States)

    Bandopadhyay, Aditya; Le Borgne, Tanguy; Méheust, Yves; Dentz, Marco

    2017-02-01

    Mixing fronts, where fluids of different chemical compositions mix with each other, are known to represent hotspots of chemical reaction in hydrological systems. These fronts are typically subjected to velocity gradients, ranging from the pore scale due to no slip boundary conditions at fluid solid interfaces, to the catchment scale due to permeability variations and complex geometry of the Darcy velocity streamlines. A common trait of these processes is that the mixing interface is strained by shear. Depending on the Péclet number Pe , which represents the ratio of the characteristic diffusion time to the characteristic shear time, and the Damköhler 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. So far, this impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either low or high Da. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damköhler numbers, for a bimolecular reaction and an initial interface with separated reactants. Approximate analytical expressions for the global production rate and reactive mixing scale are derived based on a reactive lamella approach that allows for a general coupling between stretching enhanced mixing and chemical reactions. While for Pe stretching effects are decoupled, a scenario which we name "weak stretching", for Pe > Da , we uncover a "strong stretching" scenario where new scaling laws emerge from the interplay between reaction kinetics, diffusion, and stretching. The analytical results are validated against numerical simulations. These findings shed light on the effect of flow heterogeneity on the enhancement of chemical reaction and the creation of spatially localized hotspots of reactivity for a broad range of systems ranging from kinetic limited to mixing limited situations.

  5. 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...

  6. 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.

  7. Quantum dynamics of the abstraction reaction of H with cyclopropane.

    Science.gov (United States)

    Shan, Xiao; Clary, David C

    2014-10-30

    The dynamics of the abstraction reaction of H atoms with the cyclopropane molecule is studied using quantum mechanical scattering theory. The quantum scattering calculations are performed in hyperspherical coordinates with a two-dimensional (2D) potential energy surface. The ab initio energy calculations are carried out with CCSD(T)-F12a/cc-pVTZ-F12 level of theory with the geometry and frequency calculations at the MP2/cc-pVTZ level. The contribution to the potential energy surface from the spectator modes is included as the projected zero-point energy correction to the ab initio energy. The 2D surface is fitted with a 29-parameter double Morse potential. An R-matrix propagation scheme is carried out to solve the close-coupled equations. The adiabatic energy barrier and reaction enthalpy are compared with high level computational calculations as well as experimental data. The calculated reaction rate constants shows very good agreement when compared with the experimental data, especially at lower temperature highlighting the importance of quantum tunnelling. The reaction probabilities are also presented and discussed. The special features of performing quantum dynamics calculation on the chemical reaction of a cyclic molecule are discussed.

  8. Unimolecular reaction dynamics of well characterized ionic reactions. Final report, 1993--1997

    Energy Technology Data Exchange (ETDEWEB)

    Baer, T.

    1997-12-31

    The dissociation dynamics of well characterized and energy selected ions have been investigated by photoelectron photoion coincidence (PEPICO) spectrometry. A number of ions have been found which dissociate in competition with isomerization and which thus lead to multi-component decay rates. The dissociation dynamics on such complex potential energy surfaces are common for many free radical reactions, including some of importance to combustion processes. Individual reaction rates for isomerization and dissociation have been extracted from the data. In addition, all rates have been successfully modeled with the RRKM theory in combination with ab initio molecular orbital calculations. The dissociation dynamics of a dimer ion system has been studied on the UNC PEPICO apparatus as well as at the Chemical Dynamics Beam line of the ALS. This proof of principle experiment shows that it is possible to investigate such systems and to determine the heats of formation of free radicals by this approach. Finally, a dissociation involving a loose transition state with no exit barrier has been successfully modeled with a simplified version of the variational transition state theory (VTST). The aim of all of these studies is to develop protocols for modeling moderately complex unimolecular reactions with simple models.

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Tian, Tianhai

    2013-01-01

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

  12. Effect of Coriolis coupling in chemical reaction dynamics.

    Science.gov (United States)

    Chu, Tian-Shu; Han, Ke-Li

    2008-05-14

    It is essential to evaluate the role of Coriolis coupling effect in molecular reaction dynamics. Here we consider Coriolis coupling effect in quantum reactive scattering calculations in the context of both adiabaticity and nonadiabaticity, with particular emphasis on examining the role of Coriolis coupling effect in reaction dynamics of triatomic molecular systems. We present the results of our own calculations by the time-dependent quantum wave packet approach for H + D2 and F(2P3/2,2P1/2) + H2 as well as for the ion-molecule collisions of He + H2 +, D(-) + H2, H(-) + D2, and D+ + H2, after reviewing in detail other related research efforts on this issue.

  13. 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.

  14. 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.

  15. 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].

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

    Science.gov (United States)

    De Wispelaere, Kristof; Ensing, Bernd; Ghysels, An; Meijer, Evert Jan; Van Speybroeck, Veronique

    2015-06-22

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first-principle molecular dynamics approach enables unprecedented insights into zeolite-catalyzed reactions at the nanometer scale to be obtained.

  17. Geometrical Models of the Phase Space Structures Governing Reaction Dynamics

    CERN Document Server

    Waalkens, Holger

    2009-01-01

    Hamiltonian dynamical systems possessing equilibria of ${saddle} \\times {centre} \\times...\\times {centre}$ stability type display \\emph{reaction-type dynamics} for energies close to the energy of such equilibria; entrance and exit from certain regions of the phase space is only possible via narrow \\emph{bottlenecks} created by the influence of the equilibrium points. In this paper we provide a thorough pedagogical description of the phase space structures that are responsible for controlling transport in these problems. Of central importance is the existence of a \\emph{Normally Hyperbolic Invariant Manifold (NHIM)}, whose \\emph{stable and unstable manifolds} have sufficient dimensionality to act as separatrices, partitioning energy surfaces into regions of qualitatively distinct behavior. This NHIM forms the natural (dynamical) equator of a (spherical) \\emph{dividing surface} which locally divides an energy surface into two components (`reactants' and `products'), one on either side of the bottleneck. This di...

  18. Dynamic biochemical reaction process analysis and pathway modification predictions.

    Science.gov (United States)

    Conejeros, R; Vassiliadis, V S

    2000-05-05

    Recently, the area of model predictive modification of biochemical pathways has received attention with the aim to increase the productivity of microbial systems. In this study, we present a generalization of previous work, where, using a sensitivity study over the fermentation as a dynamic system, the optimal selection of reaction steps for modification (amplification or attenuation) is determined. The influence of metabolites in the activity of enzymes has also been considered (through activation or inhibition). We further introduce a new concept in the dynamic modeling of biochemical reaction systems including a generalized continuous superstructure in which two artificial multiplicative terms are included to account for: (a) enzyme overexpression or underexpression (attenuation or amplification) for the whole enzyme pool; and (b) modification of the apparent order of a kinetic expression with respect to the concentration of a metabolite or any subset of metabolites participating in the pathway. This new formulation allows the prediction of the sensitivity of the pathway performance index (objective function) with respect to the concentration of the enzyme, as well as the interaction of the enzyme with other metabolites. Using this framework, a case study for the production of penicillin V is analyzed, obtaining the most sensitive reaction steps (or bottlenecks) and the most significant regulations of the system, due to the effect of concentration of intracellular metabolites on the activity of each enzyme.

  19. Coriolis-coupled wave packet dynamics of H + HLi reaction.

    Science.gov (United States)

    Padmanaban, R; Mahapatra, S

    2006-05-11

    We investigated the effect of Coriolis coupling (CC) on the initial state-selected dynamics of H+HLi reaction by a time-dependent wave packet (WP) approach. Exact quantum scattering calculations were obtained by a WP propagation method based on the Chebyshev polynomial scheme and ab initio potential energy surface of the reacting system. Partial wave contributions up to the total angular momentum J=30 were found to be necessary for the scattering of HLi in its vibrational and rotational ground state up to a collision energy approximately 0.75 eV. For each J value, the projection quantum number K was varied from 0 to min (J, K(max)), with K(max)=8 until J=20 and K(max)=4 for further higher J values. This is because further higher values of K do not have much effect on the dynamics and also because one wishes to maintain the large computational overhead for each calculation within the affordable limit. The initial state-selected integral reaction cross sections and thermal rate constants were calculated by summing up the contributions from all partial waves. These were compared with our previous results on the title system, obtained within the centrifugal sudden and J-shifting approximations, to demonstrate the impact of CC on the dynamics of this system.

  20. Imaging the dynamics of chlorine atom reactions with alkenes

    Science.gov (United States)

    Estillore, Armando D.; Visger, Laura M.; Suits, Arthur G.

    2010-08-01

    We report a study of chlorine atom reactions with a series of target monounsaturated alkene molecules: 1-pentene, 1-hexene, 2-hexene, and cyclohexene. These reactions were studied using crossed-beam dc slice ion imaging at collision energies of 4 and 7 kcal/mol. Images of the reactively scattered alkenyl radical products were obtained via single photon ionization at 157 nm. The angular distributions at low collision energy are largely isotropic, suggesting the formation of a complex that has a lifetime comparable to or longer than its rotational period, followed by HCl elimination. At high collision energy, the distributions show a sharp forward peak superimposed on the isotropic component accounting for ˜13% of the product flux. The translational energy distributions peak near zero for the backscattered product, in sharp contrast to the results for alkanes. In the forward direction, the translational energy distributions change dramatically with collision energy. At the high collision energy, a sharp forward peak at ˜80% of the collision energy appears, quite reminiscent of results of our recent study of Cl+pentane reactions. The scattering distributions for all target molecules are similar, suggesting similarity of the reaction dynamics among these molecules. Ab initio calculations of the energetics and ionization energies for the various product channels were performed at the CBS-QB3 level to aid in interpreting the results.

  1. Molecular-dynamics study of detonation. II. The reaction mechanism

    Science.gov (United States)

    Rice, Betsy M.; Mattson, William; Grosh, John; Trevino, S. F.

    1996-01-01

    In this work, we investigate mechanisms of chemical reactions that sustain an unsupported detonation. The chemical model of an energetic crystal used in this study consists of heteronuclear diatomic molecules that, at ambient pressure, dissociate endothermically. Subsequent association of the products to form homonuclear diatomic molecules provides the energy release that sustains the detonation. A many-body interaction is used to simulate changes in the electronic bonding as a function of local atomic environment. The consequence of the many-body interaction in this model is that the intramolecular bond is weakened with increasing density. The mechanism of the reaction for this model was extracted by investigating the details of the molecular properties in the reaction zone with two-dimensional molecular dynamics. The mechanism for the initiation of the reaction in this model is pressure-induced atomization. There was no evidence of excitation of vibrational modes to dissociative states. This particular result is directly attributable to the functional form and choice of parameters for this model, but might also have more general applicability.

  2. 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.

  3. 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 ...

  4. 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

  5. Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics

    CERN Document Server

    Franz, Benjamin; Chapman, S Jonathan; Erban, Radek

    2012-01-01

    Two algorithms that combine Brownian dynamics (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 to accurately compute variances using the PBD simulation requires the overlap region. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.

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

    Energy Technology Data Exchange (ETDEWEB)

    Szilner, S; Jelavic-Malenica, D; Mijatovic, T; Soic, N [Ruder Botkovic Institute and University of Zagreb, Zagreb (Croatia); Corradi, L; Fioretto, E; Gadea, A; Mengoni, D; Stefanini, A M; Valiente-Dobon, J J [INFN - Laboratori Nazionali di Legnaro, Legnaro (Italy); Pollarolo, G [INFN and Universita di Torino (Italy); Beghini, S; Farnea, E; Lunardi, S; Montagnoli, G; Scarlassara, F; Ur, C A [INFN and Universita di Padova, Padova (Italy); Courtin, S; Haas, F; Lebhertz, D, E-mail: szilner@irb.hr [IPHC, CNRS/IN2P3 and Universite de Strasbourg, Strasbourg (France)

    2011-02-01

    The revival of transfer reaction studies benefited from the construction of the new generation large solid angle spectrometers based on trajectory reconstruction that reached an unprecedented efficiency and selectivity. The coupling of these spectrometers with large {gamma} arrays allowed the identification of individual excited states, their population pattern and decay modes via particle-{gamma} coincidences. In the present paper aspects of fragment-{gamma} coincidence studies measured with the Prisma-Clara set up in {sup 40}Ca+{sup 96}Zr and {sup 40}Ar+{sup 208}Pb are discussed. In particular, we report about states of particle-phonon character, supporting the idea that the relevant degrees of freedom acting in the reaction dynamics define the final yield distributions.

  7. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

    Science.gov (United States)

    De Jong, Djurre H; Schäfer, Lars V; De Vries, Alex H; Marrink, Siewert J; Berendsen, Herman J C; Grubmüller, Helmut

    2011-07-15

    With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.

  8. Measurements of Dynamical Dipole in isospin asymmetric fusion reactions

    Science.gov (United States)

    Giaz, A.; Corsi, A.; Camera, F.; Bracco, A.; Crespi, F. C. L.; Leoni, S.; Nicolini, R.; Vandone, V.; Benzoni, G.; Blasi, N.; Brambilla, S.; Million, B.; Wieland, O.; Cinausero, M.; Degelier, M.; Gramegna, F.; Kravchuk, V. L.; Marchi, T.; Rizzi, V.; Bardelli, L.; Barlini, S.; Bini, M.; Carboni, S.; Casini, G.; Chiari, M.; Nannini, A.; Pasquali, G.; Piantelli, S.; Poggi, G.; Baiocco, G.; Bruno, M.; D'agostino, M.; Morelli, L.; Vannini, V.; Colonna, M.; Di Toro, M.; Rizzo, C.; Bednarcyk, P.; Ciemala, M.; Kmiecik, M.; Maj, A.; Mazurek, K.; Menczynski, W.; Alba, R.; Maiolino, C.; Santonocito, D.; Montanari, D.; Ordine, A.

    2012-05-01

    In heavy ion nuclear reactions the process leading to complete fusion is expected to produce pre-equilibrium γ-ray emission, if particular conditions are met. Indeed, when there is an N/Z asymmetry between projectile and target, charge equilibration takes place with a collective dipole oscillation, called Dynamical Dipole (DD), associated to a γ-ray emission. The existing experimental data concerning this pre-equilibrium γ-ray emission are still rather scarce and manly concentrated in the A≊132 mass region. The very preliminary results concerning the measurement of the DD γ-ray emission in the fusion reaction 16O (Elab=192 MeV) + 116Sn at 12 MeV/u will be presented and compared with the γ yield measured for the same reaction at 8.1 and 15.6 MeV/u. The present experiment aims at the measurement of the total emission yield of the DD at 12 MeV/u where the predicted theoretical yield does not completely reproduce the experimental data. The experiment has been performed at the INFN Legnaro Laboratories using the GARFIELD-HECTOR array.

  9. Systematic development of reduced reaction mechanisms for dynamic modeling

    Science.gov (United States)

    Frenklach, M.; Kailasanath, K.; Oran, E. S.

    1986-01-01

    A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.

  10. Multiscale simulations of anisotropic particles combining Brownian Dynamics and Green's Function Reaction Dynamics

    CERN Document Server

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

    2016-01-01

    The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic Molecular Dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P.G. Bolhuis and P.R. ten Wolde, J. Chem. Phys. {\\bf 43}, 21: 214102 (2015)]. Here we extend this multiscale BD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm we discuss its performance. The rotational BD-GFRD multiscale method will open up the possibility for large scale simulations of e.g. protein signalling networks.

  11. 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.

  12. 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.

  13. Mechanical reaction-diffusion model for bacterial population dynamics

    CERN Document Server

    Ngamsaad, Waipot

    2015-01-01

    The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.

  14. Ring opening reaction dynamics in the reaction of hydrogen atoms with ethylene oxide

    Science.gov (United States)

    Shin, S. K.; Jarek, R. L.; Böhmer, E.; Wittig, C.

    1994-10-01

    Ethylene oxide, C2H4O, is a three-membered ring with a single oxygen atom bridging the two carbons. Reactions of H and D atoms with ethylene oxide have been studied in the gas phase to provide insight into the dynamics of three-membered ring opening. H atoms were produced by photolyzing HI in the wavelength range 240-266 nm. The channel leading to OH+C2H4 was monitored via laser-induced fluorescence (LIF) of the OH A 2Σ←X 2Π system. The D atom reaction yields OD with no hydrogen scrambling. With an available energy of 23 000 cm-1, the average OH D rotational energy is ˜350 cm-1 for OH(v=0) and OD(v=0) and ˜250 cm-1 for OD(v=1). OH(v=1) was not observed, while the OD(v=1) population was about one-tenth that of OD(v=0). There was no apparent bias in populations between Λ doublets in each of the spin-orbit states for both OH and OD. Doppler broadening of OH(v=0) rotational lines was measured to evaluate the average center-of-mass (c.m.) translational energy, which was found to be ˜2300 cm-1. On average, the ring opening process deposits ˜10% of the available energy into c.m. translation, ˜2% into OH rotation, and ˜88% into ethylene internal energy. Comparison with CH2CH2OH unimolecular dissociation dynamics and theoretical transition state calculations leads to a likely mechanism in which hydrogen abstracts oxygen via sequential C-O bond fission without involving a long-lived CH2CH2OH intermediate.

  15. Reaction of Np atom with H₂O in the gas phase: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-01

    The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.

  16. Chemical kinetics of gas reactions

    CERN Document Server

    Kondrat'Ev, V N

    2013-01-01

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

  17. 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...

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

    Directory of Open Access Journals (Sweden)

    Stephanie eGoldfarb

    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.

  19. 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.

  20. 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…

  1. Detailed Molecular Dynamics of the Photochromic Reaction of Spiropyran: A Semiclassical Dynamics Study

    Directory of Open Access Journals (Sweden)

    Gaohong Zhai

    2014-01-01

    Full Text Available A realistic semiclassical dynamics simulation study is reported for the photoinduced ring-opening reaction of spiropyran. The main simulation results show that one pathway involves hydrogen out-of-plane (HOOP torsion of phenyl ring nearby N atom in 254 fs on the excited state and the isomerization from cis- to trans-SP that is complete in about 10 ps on the ground state after the electron transition πσ*; the other dominate pathway corresponds to the ring-opening reaction of trans-SP to form the most stable merocyanine (MC product. Unlike the previous theoretical finding, one C−C bond cleavage on the real molecule rather than the C−N dissociation of the model one is more probable than the ring-opening reaction after the photoexcitation of SP. The simulation findings provide more important complementarity for interpreting experimental observations, confirming the previously theoretical studies of photochromic ring-opening process and even supplying other possible reaction mechanisms.

  2. 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.

  3. Why the apparent order of bimolecular recombination in blend organic solar cells can be larger than two: A topological consideration

    Science.gov (United States)

    Nenashev, A. V.; Wiemer, M.; Dvurechenskii, A. V.; Gebhard, F.; Koch, M.; Baranovskii, S. D.

    2016-07-01

    The apparent order δ of non-geminate recombination higher than δ = 2 has been evidenced in numerous experiments on organic bulk heterojunction (BHJ) structures intensively studied for photovoltaic applications. This feature is claimed puzzling, since the rate of the bimolecular recombination in organic BHJ systems is proportional to the product of the concentrations of recombining electrons and holes and therefore the reaction order δ = 2 is expected. In organic BHJ structures, electrons and holes are confined to two different material phases: electrons to the acceptor material (usually a fullerene derivative) while holes to the donor phase (usually a polymer). The non-geminate recombination of charge carriers can therefore happen only at the interfaces between the two phases. Considering a simple geometrical model of the BHJ system, we show that the apparent order of recombination can deviate from δ = 2 due solely to the topological structure of the system.

  4. Physical chemistry of reaction dynamics in ionic liquid

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-02

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

  5. Physical Chemistry of Reaction Dynamics in Ionic Liquid

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-02

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

  6. Tethered bimolecular lipid membranes - A novel model membrane platform

    Energy Technology Data Exchange (ETDEWEB)

    Knoll, Wolfgang; Koeper, Ingo; Naumann, Renate; Sinner, Eva-Kathrin [Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz (Germany)

    2008-10-01

    This contribution summarizes some of our efforts in designing, synthesizing, assembling, and characterizing functional tethered bimolecular lipid membranes (tBLMs) as a novel platform for biophysical studies of and with artificial membranes or for sensor development employing, e.g., membrane integral receptor proteins. Chemical coupling schemes based on thiol groups for Au substrates or silanes used in the case of oxide surfaces allow for the covalent and, hence, chemically and mechanically robust attachment of anchor lipids to the solid support, stabilizing the proximal layer of a tethered membrane on the transducer surface. Surface plasmon optics, the quartz crystal microbalance, fluorescence- and IR spectroscopies, and electrochemical techniques are used to characterize the build-up of these complex supramolecular interfacial architectures. We demonstrate, in particular, that bilayers with a specific electrical resistance of better than 10 M{omega} cm{sup 2} can be achieved routinely with this approach. The functionalization of the lipid membranes by the incorporation of peptides is demonstrated for the carrier valinomycin which shows in our tBLMs the expected discrimination by four orders of magnitude between the translocation of K{sup +}- and Na{sup +}-ions across the hydrophobic barrier. For the synthetic channel-forming peptide M2 the high electrical resistance of the bilayer with the correspondingly low background current allows for the recording of even single channel current fluctuations. From the many membrane proteins that we reconstituted so far we describe results obtained with the redox-protein cytochrome c oxidase. Here, we also use a genetically modified mutant with a His-tag at either the C- or the N-terminus for the oriented attachment of the protein via the NTA/Ni{sup 2+} approach. With this strategy, we not only can control the density of the immobilized functional units, we introduce a completely new and alternative concept for the

  7. Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Saria

    Science.gov (United States)

    2009-09-15

    a SN2 -like transition geometry, Figure 3c, the axial O-C-H bond angle is slightly bent more for reaction 4, Figure 3d. The products of reaction 4 are...Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Sarin Patrick F. Conforti and Matthew Braunstein* Spectral...calculations were performed on the reaction systems O(3P) + sarin and O(3P) + dimethyl methylphosphonate (DMMP), a sarin simulant. Transition state

  8. Dual control cell reaction ensemble molecular dynamics: A method for simulations of reactions and adsorption in porous materials

    Science.gov (United States)

    Lísal, Martin; Brennan, John K.; Smith, William R.; Siperstein, Flor R.

    2004-09-01

    We present a simulation tool to study fluid mixtures that are simultaneously chemically reacting and adsorbing in a porous material. The method is a combination of the reaction ensemble Monte Carlo method and the dual control volume grand canonical molecular dynamics technique. The method, termed the dual control cell reaction ensemble molecular dynamics method, allows for the calculation of both equilibrium and nonequilibrium transport properties in porous materials such as diffusion coefficients, permeability, and mass flux. Control cells, which are in direct physical contact with the porous solid, are used to maintain the desired reaction and flow conditions for the system. The simulation setup closely mimics an actual experimental system in which the thermodynamic and flow parameters are precisely controlled. We present an application of the method to the dry reforming of methane reaction within a nanoscale reactor model in the presence of a semipermeable membrane that was modeled as a porous material similar to silicalite. We studied the effects of the membrane structure and porosity on the reaction species permeability by considering three different membrane models. We also studied the effects of an imposed pressure gradient across the membrane on the mass flux of the reaction species. Conversion of syngas (H2/CO) increased significantly in all the nanoscale membrane reactor models considered. A brief discussion of further potential applications is also presented.

  9. 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.

  10. 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...

  11. Bimolecular Recombination Kinetics of an Exciton-Trion Gas

    Science.gov (United States)

    2015-07-01

    The second and third reactions are catalytic agents for the loss of excitons. This implies that the constants R and S will appear only in the exciton...change the electron density. 3 Note that Reaction 3 in Table 2 is catalytic as defined above, because it changes the electron and e−trion...from the PL laser, which is fixed. Table 2 Reactions that change νe Reaction Rate Constant 1. νe + νh → ϕ A 2. νe + τh → Ex P 3

  12. 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.

  13. Kinetics of carbon monoxide binding to phenobarbital-induced cytochrome P-450 from rat liver microsomes: a simple bimolecular process.

    Science.gov (United States)

    Oertle, M; Richter, C; Winterhalter, K H; Di Iorio, E E

    1985-01-01

    The kinetics of carbon monoxide binding to phenobarbital-induced cytochrome P-450 (P-450PB) and to its enzymatically inactive form P-420PB have been investigated by both stopped-flow and flash-photolysis spectrophotometry. When the simultaneous presence of both forms of the enzyme is taken into account, the binding of CO to these two proteins can be described in terms of two bimolecular processes with rate constants of 4.5 X 10(6) M-1.S-1 and 4.7 X 10(5) M-1.S-1 for P-450PB and 1.7 X 10(7) M-1.S-1 and 1.5 X 10(6) M-1.S-1 for P-420PB. From kinetic studies of the binding of CO to P-450PB under different experimental conditions, investigations of the homogeneity of our P-450PB preparations, and comparative kinetic investigations of P-450s from different sources, we conclude that CO binding to reduced P-450PB is a simple bimolecular process and that the observed biphasic traces are due to heterogeneity of the proteins. This conclusion is in contrast with previous reports of complex reaction mechanisms for the binding of CO to P-450PB. Optical spectroscopy studies indicate the existence of an equilibrium between P-450PB and P-420PB, at least for the reduced carbonyl derivatives of the enzymes. The interconversion is strongly influenced by the aggregation state of the protein. Large differences between the CO binding properties of P-450PB and those of P-420PB are found. These are discussed in terms of possible effects of the proximal ligation state of the iron on heme reactivity. PMID:3860832

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...

  15. A fractional model of a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions

    Science.gov (United States)

    Singh, Jagdev; Rashidi, M. M.; Kumar, Devendra; Swroop, Ram

    2016-12-01

    In this paper, we study a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions with time fractional Caputo derivative. The present article involves a more generalized effective approach, proposed for the Brusselator system say q-homotopy analysis transform method (q-HATM), providing the family of series solutions with nonlocal generalized effects. The convergence of the q-HATM series solution is adjusted and controlled by auxiliary parameter ℏ and asymptotic parameter n. The numerical results are demonstrated graphically. The outcomes of the study show that the q-HATM is computationally very effective and accurate to analyze nonlinear fractional differential equations.

  16. Dynamical coupled-channels study of meson production reactions from EBAC@Jlab

    Energy Technology Data Exchange (ETDEWEB)

    Hiroyuki Kamano

    2011-10-01

    We present the current status of a combined and simultaneous analysis of meson production reactions based on a dynamical coupled-channels (DCC) model, which is conducted at Excited Baryon Analysis Center (EBAC) of Jefferson Lab.

  17. 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.

  18. 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)

  19. 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.

  20. Dynamical Dipole mode in heavy-ion fusion reactions in the 192Pb mass region

    Science.gov (United States)

    Parascandolo, C.; Pierroutsakou, D.; Alba, R.; Del Zoppo, A.; Maiolino, C.; Santonocito, D.; Agodi, C.; Baran, V.; Boiano, A.; Colonna, M.; Coniglione, R.; De Filippo, E.; Di Toro, M.; Emanuele, U.; Farinon, F.; Guglielmetti, A.; La Commara, M.; Martin, B.; Mazzocchi, C.; Mazzocco, M.; Rizzo, C.; Romoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Strano, E.; Torresi, D.; Trifiró, A.; Trimarchi, M.

    2015-04-01

    The dynamical dipole mode was investigated in the mass region of the 192Pb compound nucleus, by using the 40Ca + 152Sm and 48Ca + 144Sm reactions 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.

  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...

  2. Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence

    Science.gov (United States)

    Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K. L.; Sum, Tze Chien; Huang, Wei

    2017-01-01

    The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 1015 cm−3, defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence. PMID:28239146

  3. Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence.

    Science.gov (United States)

    Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K L; Sum, Tze Chien; Huang, Wei

    2017-02-27

    The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 10(15) cm(-3), defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence.

  4. Resonances and reactions from mean-field dynamics

    Directory of Open Access Journals (Sweden)

    Stevenson P. D.

    2016-01-01

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

  5. Reaction dynamics of initial O2 sticking on Pd(100).

    Science.gov (United States)

    den Dunnen, Angela; Wiegman, Sandra; Jacobse, Leon; Juurlink, Ludo B F

    2015-06-07

    We have determined the initial sticking probability of O2 on Pd(100) using the King and Wells method for various kinetic energies, surface temperatures, and incident angles. The data suggest two different mechanisms to sticking and dissociation. Dissociation proceeds mostly through a direct process with indirect dissociation contributing only at low kinetic energies. We suggest a dynamical precursor state to account for the indirect dissociation channel, while steering causes the high absolute reactivity. A comparison of our results to those previously obtained for Pd(111) and Pd(110) highlights how similar results for different surfaces are interpreted to suggest widely varying dynamics.

  6. Reaction dynamics of initial O2 sticking on Pd(100)

    Science.gov (United States)

    den Dunnen, Angela; Wiegman, Sandra; Jacobse, Leon; Juurlink, Ludo B. F.

    2015-06-01

    We have determined the initial sticking probability of O2 on Pd(100) using the King and Wells method for various kinetic energies, surface temperatures, and incident angles. The data suggest two different mechanisms to sticking and dissociation. Dissociation proceeds mostly through a direct process with indirect dissociation contributing only at low kinetic energies. We suggest a dynamical precursor state to account for the indirect dissociation channel, while steering causes the high absolute reactivity. A comparison of our results to those previously obtained for Pd(111) and Pd(110) highlights how similar results for different surfaces are interpreted to suggest widely varying dynamics.

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  8. The dynamics of reaction of Cl atoms with tetramethylsilane.

    Science.gov (United States)

    Retail, Bertrand; Rose, Rebecca A; Pearce, Julie K; Greaves, Stuart J; Orr-Ewing, Andrew J

    2008-03-28

    Rotational state distributions and state-selected CM-frame angular distributions were measured for HCl (v' = 0, j') products from the reaction of Cl-atoms with tetramethylsilane (TMS) under single collision conditions at a collision energy, E(coll), of 8.2 +/- 2.0 kcal mol(-1). The internal excitation of these products was very low with only 2% of the total energy available partitioned into HCl rotation. A transition state with a quasi-linear C-H-Cl moiety structure was computed and used to explain this finding. A backward peaking differential cross section was also reported together with a product translational energy (T') distribution with a maximum at T' approximately E(coll). This scattering behaviour is accounted for by reactions proceeding through a tight transition state on a highly skewed potential energy surface, which favours collisions at low impact parameters with a strong kinematic constraint on the internal excitation of the products. The large Arrhenius pre-exponential factor previously reported for this reaction is reconciled with the tight differential scattering observed in our study by considering the large size of the TMS molecule.

  9. 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.

  10. Real-time electron dynamics simulation of two-electron transfer reactions induced by nuclear motion

    Science.gov (United States)

    Suzuki, Yasumitsu; Yamashita, Koichi

    2012-04-01

    Real-time electron dynamics of two-electron transfer reactions induced by nuclear motion is calculated by three methods: the numerically exact propagation method, the time-dependent Hartree (TDH) method and the Ehrenfest method. We find that, as long as the nuclei move as localized wave packets, the TDH and Ehrenfest methods can reproduce the exact electron dynamics of a simple charge transfer reaction model containing two electrons qualitatively well, even when nonadiabatic transitions between adiabatic states occur. In particular, both methods can reproduce the cases where a complete two-electron transfer reaction occurs and those where it does not occur.

  11. Nonstatistical dynamics on potentials exhibiting reaction path bifurcations and valley-ridge inflection points

    CERN Document Server

    Collins, Peter; Ezra, Gregory S; Wiggins, Stephen

    2013-01-01

    We study reaction dynamics on a model potential energy surface exhibiting post-transition state bifurcation in the vicinity of a valley ridge inflection point. We compute fractional yields of products reached after the VRI region is traversed, both with and without dissipation. It is found that apparently minor variations in the potential lead to significant changes in the reaction dynamics. Moreover, when dissipative effects are incorporated, the product ratio depends in a complicated and highly non-monotonic fashion on the dissipation parameter. Dynamics in the vicinity of the VRI point itself play essentially no role in determining the product ratio, except in the highly dissipative regime.

  12. 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.

  13. Quantum Dynamics Study on D+OD+ Reaction: Competition between Exchange and Abstraction Channels

    Institute of Scientific and Technical Information of China (English)

    Wen-wu Xu; Pei-yu Zhang; Guo-zhong He

    2013-01-01

    Quantum dynamics for the D+OD+ reaction at the collision energy range of 0.0-1.0 eV was studied on an accurate ab initio potential energy surface.Both of the endothermic abstraction (D+OD+-O++D2) and thermoneutral exchange (D+OD+-D+OD+) channels were investigated from the same set of time-dependent quantum wave packets method under centrifugal sudden approximation.The reaction probability dependence with collision energy,the integral cross sections,and the thermal rate constant of the both channels are calculated.It is found that there is a convex structure in the reaction path of the exchange reaction.The calculated time evolution of the wave packet distribution at J=0 clearly indicates that the convex structure significantly influences the dynamics of the exchange and abstraction channels of title reaction.

  14. Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions

    Science.gov (United States)

    2008-06-26

    CH3Br, Ar + H2O are given below. 3.1 Cl− + CH3Br Reaction A global RS-HDMR input/output map for the SN2 reaction Cl− +CH3Br→ ClCH3 +Br − (9) 3 was...2257-2266. [16] Wang H. B., Hase W. L. (1996). Reaction path Hamiltonian analysis of the dynamics for Cl− + CH3Br→ ClCH3 + Br − SN2 nucleophilic... reaction Cl − + CH3Br → ClCH3 + Br −, J. Chem. Phys., 111(24), 10887- 10894. [18] Sun, L., Hase, W. L., Song, K. (2001). Trajectory studies of SN2

  15. Thermodynamic Study of Hydrolysis Reactions in Aqueous Solution from Ab Initio Potential and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    S. Tolosa

    2013-01-01

    Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.

  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. Chiral dynamics in the gamma p --> p pi0 reaction

    CERN Document Server

    Blin, A N Hiller; Vacas, M J Vicente

    2014-01-01

    We investigate the neutral pion photoproduction on the proton near threshold in covariant chiral perturbation theory with the explicit inclusion of Delta degrees of freedom. This channel is specially sensitive to chiral dynamics and the advent of very precise data from the Mainz microtron has shown the limits of the convergence of the chiral series for both the heavy baryon and the covariant approaches. We show that the inclusion of the Delta resonance substantially improves the convergence leading to a good agreement with data for a wider range of energies.

  18. 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.

  19. Platelet reactions to modified surfaces under dynamic conditions.

    Science.gov (United States)

    Rhodes, N P; Shortland, A P; Rattray, A; Williams, D F

    1998-12-01

    The influence of surfaces on the reactions of platelets in whole blood under laminar flow was investigated in a cone and plate viscometer. Citrated whole blood was exposed to steel, PMMA and PMMA modified with PEO at low (500 s(-1)) and high (4000 s(-1)) wall shear rates at room temperature for a period of 100 s. Treated blood samples were fixed with paraformaldehyde, stained with a monoclonal antibody for CD41 (platelet GPIIb/IIIa) conjugated with phycoerythrin and analyzed by flow cytometry. The reactions of platelets (microparticle generation and formation of platelet-platelet, platelet-red blood cell and red blood cell-microparticle aggregates) to these environments were quantified. Additionally, the size of platelet-platelet aggregates was assessed. The percentage platelet aggregation and numbers of microparticles generated were independent of surface type at any shear rate. The composition of the aggregates formed was influenced by the surface: at low and high shear rates PMMA caused the generation of platelet-platelet aggregates of the greatest size. The numbers of red blood cell-platelet and red blood cell-microparticle aggregates also varied depending on the surface. Fewer red blood cell-platelet aggregates were formed at higher shear rates, whereas the reverse was true for red blood cell-microparticle aggregates. It is concluded that these variations may help to explain the differential effects of surfaces to the induction of distant thrombotic events: microparticles may be protected from loss from the blood stream by their association with red blood cells at high shear rates.

  20. Comparative assessment of continuum-scale models of bimolecular reactive transport in porous media under pre-asymptotic conditions

    Science.gov (United States)

    Porta, G. M.; Ceriotti, G.; Thovert, J.-F.

    2016-02-01

    We compare the ability of various continuum-scale models to reproduce the key features of a transport setting associated with a bimolecular reaction taking place in the fluid phase and numerically simulated at the pore-scale level in a disordered porous medium. We start by considering a continuum-scale formulation which results from formal upscaling of this reactive transport process by means of volume averaging. The resulting (upscaled) continuum-scale system of equations includes nonlocal integro-differential terms and the effective parameters embedded in the model are quantified directly through computed pore-scale fluid velocity and pore space geometry attributes. The results obtained through this predictive model formulation are then compared against those provided by available effective continuum models which require calibration through parameter estimation. Our analysis considers two models recently proposed in the literature which are designed to embed incomplete mixing arising from the presence of fast reactions under advection-dominated transport conditions. We show that best estimates of the parameters of these two models heavily depend on the type of data employed for model calibration. Our upscaled nonlocal formulation enables us to reproduce most of the critical features observed through pore-scale simulation without any model calibration. As such, our results clearly show that embedding into a continuum-scale model the information content associated with pore-scale geometrical features and fluid velocity yields improved interpretation of typically available continuum-scale transport observations.

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

    Science.gov (United States)

    Xu, Zheng; Yasuda, Keiji; Liu, Xiao-Jun

    2015-10-01

    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. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404245, 11204129, and 11211140039).

  3. ThermoData engine (TDE): software implementation of the dynamic data evaluation concept. 4. Chemical reactions.

    Science.gov (United States)

    Diky, Vladimir; Chirico, Robert D; Kazakov, Andrei F; Muzny, Chris D; Frenkel, Michael

    2009-12-01

    ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. This paper describes the first application of this concept to the evaluation of thermodynamic properties for chemical reactions. Reaction properties evaluated are the enthalpies, entropies, Gibbs energies, and thermodynamic equilibrium constants. Details of key considerations in the critical evaluation of enthalpies of formation and of standard entropies for organic compounds are discussed in relation to their application in the calculation of reaction properties. Extensions to the class structure of the program are described that allow close linkage between the derived reaction properties and the underlying pure-component properties. Derivation of pure-component enthalpies of formation and of standard entropies through the use of directly measured reaction properties (enthalpies of reaction and equilibrium constants) is described. Directions for future enhancements are outlined.

  4. 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.

  5. Dynamic/Thermochemical Balance Drives Unusual Alkyl/F Exchange Reactions in Siloxides and Analogs.

    Science.gov (United States)

    Correra, Thiago C; Fernandes, André S; Riveros, José M

    2016-03-17

    A recent report has shown that siloxides can undergo an unusual Me/F exchange reaction promoted by NF3 in the gas phase ( Angew. Chem. Int. Ed. 2012, 51, 8632-8635). A more extensive study of this kind of exchange has been carried out using mass spectrometry techniques (FT-ICR), DFT calculations, natural bond orbital (NBO) analysis, and Born-Oppenheimer molecular dynamics simulations (BOMD), using NF3, SO2F2, and CF4 as fluorine donors and evaluating the effect of replacing the Si center by Ge and C. This comprehensive approach shows that NF3 is crucial for the exchange reaction, as SO2F2 forms SO3F(-) via a pentacoordinated channel whereas no reaction is observed for CF4. The uniqueness of NF3 is caused by favorable thermochemical consideration and by dynamic effects that preclude the formation of the ubiquitous Si-F pentacoordinated species. Me3GeO(-) was shown to be as reactive as siloxides toward NF3, whereas C analogs showed no reactions under our experimental conditions. The exchange reaction was also shown to take place for triethylsiloxides. These exchange reactions are examples of reaction systems that avoid the lower energy pathway and are driven by dynamic effects that cannot be explained by the potential energy surface.

  6. 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.

  7. Analysis of dynamic foot pressure distribution and ground reaction forces

    Science.gov (United States)

    Ong, F. R.; Wong, T. S.

    2005-04-01

    The purpose of this study was to assess the relationship between forces derived from in-shoe pressure distribution and GRFs during normal gait. The relationship served to demonstrate the accuracy and reliability of the in-shoe pressure sensor. The in-shoe pressure distribution from Tekscan F-Scan system outputs vertical forces and Centre of Force (COF), while the Kistler force plate gives ground reaction forces (GRFs) in terms of Fz, Fx and Fy, as well as vertical torque, Tz. The two systems were synchronized for pressure and GRFs measurements. Data was collected from four volunteers through three trials for both left and right foot under barefoot condition with the in-shoe sensor. The forces derived from pressure distribution correlated well with the vertical GRFs, and the correlation coefficient (r2) was in the range of 0.93 to 0.99. This is a result of extended calibration, which improves pressure measurement to give better accuracy and reliability. The COF from in-shoe sensor generally matched well with the force plate COP. As for the maximum vertical torque at the forefoot during toe-off, there was no relationship with the pressure distribution. However, the maximum torque was shown to give an indication of the rotational angle of the foot.

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

    Science.gov (United States)

    Yang, Xueming; Zhang, Dong H

    2008-08-01

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

  9. 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.

  10. Dynamic input to determine hip joint moments, power and work on the prosthetic limb of transfemoral amputees: ground reaction vs knee reaction

    OpenAIRE

    FROSSARD, Laurent; Cheze, Laurence; Dumas, Raphaël

    2011-01-01

    Background: Calculation of lower limb kinetics is limited by floor-mounted force-plates. Objectives: Comparison of hip joint moments, power and mechanical work on the prosthetic limb of a transfemoral amputee calculated by inverse dynamics using either the ground reactions (force-plates) or knee reactions (transducer). Study design: Comparative analysis. Methods: Kinematics, ground reaction and knee reaction data were collected using a motion analysis system, two forceplates, and a multi-axia...

  11. 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.

  12. Reaction dynamics of small molecules at metal surfaces

    CERN Document Server

    Samson, P A

    1999-01-01

    directed angular distributions suggest the influence of a trapping mechanism, recombining molecules scattering through a molecularly adsorbed state, with a transition state of large d sub N sub N responsible for the product vibrational excitation. Although N sub 2 dissociation on Fe(100) forms a simple overlayer structure, on Fe(110), molecular chemisorption does not occur at or above room temperature and the sticking is extremely small (approx 10 sup - sup 6 to 10 sup - sup 7). Activated nitrogen bombardment can be used to prepare a 'surface nitride' with a structure related to the geometry of bulk Fe sub 4 N. Scanning tunnelling microscopy yields atomic scale features that cannot be explained by simple overlayers. It is proposed that the uppermost iron layer reconstructs to generate quasi-octahedral sites between the top two layers, with sub-surface nitrogen in these sites forming a model for the 'surface nitride' structure. The dissociation-desorption dynamics of D sub 2 upon the Sn/Pt(111) surface alloy a...

  13. A review of dynamical resonances in A  +  BC chemical reactions

    Science.gov (United States)

    Ren, Zefeng; Sun, Zhigang; Zhang, Donghui; Yang, Xueming

    2017-02-01

    The concept of the transition state has played an important role in the field of chemical kinetics and reaction dynamics. Reactive resonances in the transition-state region can dramatically enhance the reaction probability; thus investigation of the reactive resonances has attracted great attention from chemical physicists for many decades. In this review, we mainly focus on the recent progress made in probing the elusive resonance phenomenon in the simple A  +  BC reaction and understanding its nature, especially in the benchmark F/Cl  +  H2 and their isotopic variants. The signatures of reactive resonances in the integral cross section, differential cross section (DCS), forward- and backward-scattered DCS, and anion photodetachment spectroscopy are comprehensively presented in individual prototype reactions. The dynamical origins of reactive resonances are also discussed in this review, based on information on the wave function in the transition-state region obtained by time-dependent quantum wave-packet calculations.

  14. 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...

  15. 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.

  16. [Age-related dynamics of the motion reaction in school children].

    Science.gov (United States)

    Makarenko, M V; Petrenko, Iu O; Baĭda, O H; Men'shykh, O E

    2009-01-01

    We studied functional state of the central nervous system of boys and girls aged from 7 to 17 years old. Peculiarities of age-dependent dynamics of functional level of the central nervous system, stability of the reactions, levels of functional possibilities were described. The age-dependent periods of strengthening and weakening of correlation between the indexes of motive reaction and the criteria of the functional state of central nervous system were determined.

  17. 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.

  18. Nanosecond pump and probe observation of bimolecular exciton effects in rubrene single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Ward, Kebra A.; Richman, Brittany R.; Biaggio, Ivan [Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015 (United States)

    2015-06-01

    Transient grating pump and probe experiments are used to investigate excitonic processes on the nanosecond time scale in rubrene single crystals. We find that bimolecular interactions cause a photoinduced excited state density on the order of 0.5 × 10{sup 20 }cm{sup −3}—corresponding to an average distance of ∼3 nm between individual states—to decrease by a factor of 2 after 2 ns, following a typical power-law decay. We assign the observed power-law decays to high-density interactions between excited states. Because of the high efficiency singlet exciton fission observed in rubrene, these bimolecular interactions are likely those between triplet excitons or between coherent quantum superpositions of a singlet and a pair of triplet-excitons.

  19. Biofunctional hybrid materials: bimolecular organosilane monolayers on FeCr alloys

    Science.gov (United States)

    Vuori, Leena; Leppiniemi, Jenni; Hannula, Markku; Lahtonen, Kimmo; Hirsimäki, Mika; Nõmmiste, Ergo; Costelle, Leila; Hytönen, Vesa P.; Valden, Mika

    2014-10-01

    Hybrid organic-inorganic interfaces are the key to functionalization of stainless steel (SS). We present a solution-based deposition method for fabricating uniform bimolecular organosilane monolayers on SS and show that their properties and functionalities can be further developed through site-specific biotinylation. We correlate molecular properties of the interface with its reactivity via surface sensitive synchrotron radiation mediated high-resolution photoelectron spectroscopy (HR-PES) and chemical derivatization (CD), and we demonstrate specific bonding of streptavidin proteins to the hybrid interface. The method facilitates efficient growth of uniform bimolecular organosilane monolayers on SS under ambient conditions without the need to prime the SS surface with vacuum-deposited inorganic buffer layers. The obtained insights into molecular bonding, orientation, and behaviour of surface-confined organofunctional silanes on SS enable a new generic approach to functionalization of SS surfaces with versatile nanomolecular organosilane layers.

  20. Influence of the leaving group on the dynamics of a gas-phase SN2 reaction

    Science.gov (United States)

    Stei, Martin; Carrascosa, Eduardo; Kainz, Martin A.; Kelkar, Aditya H.; Meyer, Jennifer; Szabó, István; Czakó, Gábor; Wester, Roland

    2016-02-01

    In addition to the nucleophile and solvent, the leaving group has a significant influence on SN2 nucleophilic substitution reactions. Its role is frequently discussed with respect to reactivity, but its influence on the reaction dynamics remains unclear. Here, we uncover the influence of the leaving group on the gas-phase dynamics of SN2 reactions in a combined approach of crossed-beam imaging and dynamics simulations. We have studied the reaction F- + CH3Cl and compared it to F- + CH3I. For the two leaving groups, Cl and I, we find very similar structures and energetics, but the dynamics show qualitatively different features. Simple scaling of the leaving group mass does not explain these differences. Instead, the relevant impact parameters for the reaction mechanisms are found to be crucial and the differences are attributed to the relative orientation of the approaching reactants. This effect occurs on short timescales and may also prevail in solution-phase conditions.

  1. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency.

    Science.gov (United States)

    Peters, Baron; Bolhuis, Peter G; Mullen, Ryan G; Shea, Joan-Emma

    2013-02-01

    We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.

  2. Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.

    Science.gov (United States)

    Matsuura, Tomoaki; Tanimura, Naoki; Hosoda, Kazufumi; Yomo, Tetsuya; Shimizu, Yoshihiro

    2017-02-21

    To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.

  3. Vectorially oriented monolayers of the cytochrome c/cytochrome oxidase bimolecular complex.

    OpenAIRE

    Edwards, A M; Blasie, J. K.; Bean, J. C.

    1998-01-01

    Vectorially oriented monolayers of yeast cytochrome c and its bimolecular complex with bovine heart cytochrome c oxidase have been formed by self-assembly from solution. Both quartz and Ge/Si multilayer substrates were chemical vapor deposited with an amine-terminated alkylsiloxane monolayer that was then reacted with a hetero-bifunctional cross-linking reagent, and the resulting maleimide endgroup surface then provided for covalent interactions with the naturally occurring single surface cys...

  4. Bimolecular crystals with an intercalated structure improve poly(p-phenylenevinylene)-based organic photovoltaic cells.

    Science.gov (United States)

    Lim, Kyung-Geun; Park, Jun-Mo; Mangold, Hannah; Laquai, Frédéric; Choi, Tae-Lim; Lee, Tae-Woo

    2015-01-01

    The exciton dissociation, recombination, and charge transport of bulk heterojunction organic photovoltaic cells (OPVs) is influenced strongly by the nanomorphology of the blend, such as the grain size and the molecular packing. Although it is well known that polymers based on amorphous poly(p-phenylenevinylene) (PPV) have a fundamental limit to their efficiency because of low carrier mobility, which leads to increased recombination and unbalanced charge extraction, herein, we demonstrate that the issue can be overcome by forming bimolecular crystals of an amorphous PPV-based polymer:phenyl-C61 -butyric acid methyl ester (PCBM) intercalated structure. We used amorphous poly(2,5-dioctyloxy-p-phenylene vinylene-alt-2',5'-thienylene vinylene) (PPVTV), which has a simple chemical structure. A reasonably high power conversion efficiency (∼3.5 %) was obtained, although the material has an intrinsically amorphous structure and a relatively large band gap (2.0 eV). We demonstrate a correlation between a well-ordered bimolecular crystal of PPVTV:PCBM and an improved hole mobility of a PPVTV:PCBM film compared to a pristine PPVTV film by using 2 D grazing incidence XRD and space-charge-limited current measurements. Furthermore, we show that the bimolecular crystal structure in high-performance OPVs is related to an optimum molecular packing, which is influenced by the PPVTV:PCBM blending ratio, side-chain length, and molecular weight of the PPVTV polymer. Improved charge transport in PPVTV:PCBM bimolecular crystals leads to a fast sweep out of charges and thus suppression of nongeminate recombination under the operating conditions.

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

    KAUST Repository

    Alsulami, Qana A.

    2016-11-30

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

  6. Dynamical theory of primary processes of charge separation in the photosynthetic reaction center.

    Science.gov (United States)

    Lakhno, Victor D

    2005-05-01

    A dynamical theory has been developed for primary separation of charges in the course of photosynthesis. The theory deals with both hopping and superexchange transfer mechanisms. Dynamics of electron transfer from dimeric bacteriochlorophyll to quinone has been calculated. The results obtained agree with experimental data and provide a unified explanation of both the hierarchy of the transfer time in the photosynthetic reaction center and the phenomenon of coherent oscillations accompanying the transfer process.

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

    OpenAIRE

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

    2015-01-01

    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 a...

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

    Science.gov (United States)

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

    2015-01-01

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

  9. Influence of Marangoni flows on the dynamics of isothermal A + B → C reaction fronts

    Science.gov (United States)

    Tiani, R.; Rongy, L.

    2016-09-01

    The nonlinear dynamics of A + B → C fronts is analyzed both numerically and theoretically in the presence of Marangoni flows, i.e., convective motions driven by surface tension gradients. We consider horizontal aqueous solutions where the three species A, B, and C can affect the surface tension of the solution, thereby driving Marangoni flows. The resulting dynamics is studied by numerically integrating the incompressible Navier-Stokes equations coupled to reaction-diffusion-convection (RDC) equations for the three chemical species. We show that the dynamics of the front cannot be predicted solely on the basis of the one-dimensional reaction-diffusion profiles as is the case for buoyancy-driven convection around such fronts. We relate this observation to the structure of Marangoni flows which lead to more complex and exotic dynamics. We find in particular the surprising possibility of a reversal of the front propagation direction in time for some sets of Marangoni numbers, quantifying the influence of each chemical species concentration on the solution surface tension. We explain this reversal analytically and propose a new classification of the convective effects on A + B → C reaction fronts as a function of the Marangoni numbers. The influence of the layer thickness on the RDC dynamics is also presented. Those results emphasize the importance of flow symmetry properties when studying convective front dynamics in a given geometry.

  10. Dynamics of Pickering Emulsions in the Presence of an Interfacial Reaction: A Simulation Study.

    Science.gov (United States)

    Zhao, Shuangliang; Zhan, Bicai; Hu, Yaofeng; Fan, Zhaoyu; Pera-Titus, Marc; Liu, Honglai

    2016-12-13

    Pickering emulsions combining surface-active and catalytic properties offer a promising platform for conducting interfacial reactions between immiscible reagents. Despite the significant progress in the design of Pickering interfacial catalysts for a broad panel of reactions, the dynamics of Pickering emulsions under reaction conditions is still poorly understood. Herein, using benzene hydroxylation with aqueous H2O2 as a model system, we explored the dynamics of benzene/water Pickering emulsions during reaction by dissipative particle dynamics. Our study points out that the surface wettability of the silica nanoparticles is affected to a higher extent by the degree of polymer grafting rather than an increase of the chain length of hydrophobic polymer moieties. A remarkable decline of the oil-in-water (O/W) interfacial tension was observed when increasing the yield of the reaction product (phenol), affecting the emulsion stability. However, phenol did not alter to an important extent the distribution of immiscible reagents around the nanoparticles sitting at the benzene/water interface. A synergistic effect between phenol and silica nanoparticles on the O/W interfacial tension of the biphasic system could be ascertained.

  11. Experimental and numerical investigation of coupled microvibration dynamics for satellite reaction wheels

    Science.gov (United States)

    Addari, D.; Aglietti, G. S.; Remedia, M.

    2017-01-01

    Microvibrations of a satellite reaction wheel assembly are commonly analysed in either hard-mounted or coupled boundary conditions, though coupled wheel-to-structure disturbance models are more representative of the real environment in which the wheel operates. This article investigates the coupled microvibration dynamics of a cantilever configured reaction wheel assembly mounted on either a stiff or flexible platform. Here a method is presented to cope with modern project necessities: (i) need of a model which gives accurate estimates covering a wide frequency range; (ii) reduce the personnel and time costs derived from the test campaign, (iii) reduce the computational effort without affecting the quality of the results. The method involves measurements of the disturbances induced by the reaction wheel assembly in a hard-mounted configuration and of the frequency and speed dependent dynamic mass of the reaction wheel. In addition, it corrects the approximation due to missing speed dependent dynamic mass in conventional reaction wheel assembly microvibration analysis. The former was evaluated experimentally using a previously designed and validated platform. The latter, on the other hand, was estimated analytically using a finite element model of the wheel assembly. Finally, the validation of the coupled wheel-structure disturbance model is presented, giving indication of the level of accuracy that can be achieved with this type of analyses.

  12. Brownian dynamics simulations of an idealized chemical reaction network under spatial confinement and crowding conditions

    CERN Document Server

    Bellesia, Giovanni

    2015-01-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of inert crowders has a non-nontrivial effect on the dynamics of the network and, consequently, that effective modeling efforts aiming at a general understanding of the behavior of biochemical networks in vivo should be stochastic in nature and based on an explicit representation of both spatial confinement and macromolecular crowding.

  13. 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.

  14. Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

    Science.gov (United States)

    Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R

    2013-08-29

    We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.

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

    Science.gov (United States)

    Chen, Li; Ueta, Hirokazu; Bisson, Régis; Beck, Rainer D

    2013-05-01

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

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Molini P.

    2011-10-01

    Full Text Available The existence of the dynamical dipole mode in the 192Pb composite system was investigated through the study of its prompt γ decay employing the 40Ca + 152Sm and 48Ca + 144Sm reactions at Elab =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 γ radiation could be of interest for the synthesis of super-heavy elements through ”hot” fusion reactions. Furthermore, by using radioactive beams and the prompt γ radiation as a probe we could get information on the symmetry energy at sub-saturation densities.

  18. 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.

  19. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

    Science.gov (United States)

    Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

    2015-11-12

    High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

  20. Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.

    Science.gov (United States)

    Yang, Huan; Hankel, M; Varandas, Antonio; Han, Keli

    2010-09-01

    Nonadiabatic quantum dynamics calculations on the two coupled potential energy surfaces (PESs) (1(2)A' and 2(2)A') and also adiabatic quantum calculations on the lowest adiabatic PES are reported for the title reaction. Reaction probabilities for total angular momenta, J, varying from 0 to 160, are calculated to obtain the integral cross section (ICS) for collision energies ranging from 0.05 to 1.0 eV. Calculations using both the close coupling and the Centrifugal Sudden (CS) approximation are carried out to evaluate the role of Coriolis coupling effects for this reaction. The results of the nonadiabatic calculations show that the nonadiabatic effects in the title reaction for the initial state of NH (v = 0, j = 0) could be neglected, at least in the collision energy range considered in this study.

  1. 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 (ℓ(eq)) in the steady state suggests a power-law dependence on the reaction rate ε:ℓ(eq)∼ε(-θ) with θ≃1.0.

  2. Energetics and Dynamics of the Reactions of O(3P) with Dimethyl Methylphosphonate and Sarin

    Science.gov (United States)

    Conforti, Patrick F.; Braunstein, Matthew; Dodd, James A.

    2009-10-01

    Electronic structure and molecular dynamics calculations were performed on the reaction systems O(3P) + sarin and O(3P) + dimethyl methylphosphonate (DMMP), a sarin simulant. Transition state geometries, energies, and heats of reaction for the major reaction pathways were determined at several levels of theory, including AM1, B3LYP/6-311+G(d,p), and CBS-QB3. The major reaction pathways for both systems are similar and include H-atom abstraction, H-atom elimination, and methyl elimination, in rough order from low to high energy. The H-atom abstraction channels have fairly low barriers (˜10 kcal mol-1) and are close to thermoneutral, while the other channels have relatively high energy barriers (>40 kcal mol-1) and a wide range of reaction enthalpies. We have also found a two-step pathway leading to methyl elimination through O-atom attack on the phosphorus atom for DMMP and sarin. For sarin, the two-step methyl elimination pathway is significantly lower in energy than the single-step pathway. We also present results of O(3P) + sarin and O(3P) + DMMP reaction cross sections over a broad range of collision energies (2-10 km s-1 collision velocities) obtained using the direct dynamics method with an AM1 semiempirical potential. These excitation functions are intended as an approximate guide to future hyperthermal measurements, which to our knowledge have not yet examined either of these systems. The reaction barriers, reaction enthalpies, transition state structures, and excitation functions are generally similar for DMMP and sarin, with some moderate differences for methyl elimination energetics, which indicates DMMP will likely be a good substitute for sarin in many O(3P) chemical investigations.

  3. Unified equation for access to rate constants of first-order reactions in dynamic and on-column reaction chromatography.

    Science.gov (United States)

    Trapp, O

    2006-01-01

    A unified equation to evaluate elution profiles of reversible as well as irreversible (pseudo-) first-order reactions in dynamic chromatography and on-column reaction chromatography has been derived. Rate constants k1 and k(-1) and Gibbs activation energies are directly obtained from the chromatographic parameters (retention times tR(A) and tR(B) of the interconverting or reacting species A and B, the peak widths at half-height wA and wB, and the relative plateau height h(p)), the initial amounts A0 and B0 of the reacting species, and the equilibrium constant K(A/B). The calculation of rate constants requires only a few iterative steps without the need of performing a computationally extensive simulation of elution profiles. The unified equation was validated by comparison with a data set of 125,000 simulated elution profiles to confirm the quality of this equation by statistical means and to predict the minimal experimental requirements. Surprisingly, the recovery rate from a defined data set is on average 35% higher using the unified equation compared to the evaluation by iterative computer simulation.

  4. Reaction mechanisms of aqueous monoethanolamine with carbon dioxide: a combined quantum chemical and molecular dynamics study.

    Science.gov (United States)

    Hwang, Gyeong S; Stowe, Haley M; Paek, Eunsu; Manogaran, Dhivya

    2015-01-14

    Aqueous monoethanolamine (MEA) has been extensively studied as a solvent for CO2 capture, yet the underlying reaction mechanisms are still not fully understood. Combined ab initio and classical molecular dynamics simulations were performed to revisit and identify key elementary reactions and intermediates in 25-30 wt% aqueous MEA with CO2, by explicitly taking into account the structural and dynamic effects. Using static quantum chemical calculations, we also analyzed in more detail the fundamental interactions involved in the MEA-CO2 reaction. We find that both the CO2 capture by MEA and solvent regeneration follow a zwitterion-mediated two-step mechanism; from the zwitterionic intermediate, the relative probability between deprotonation (carbamate formation) and CO2 removal (MEA regeneration) tends to be determined largely by the interaction between the zwitterion and neighboring H2O molecules. In addition, our calculations clearly demonstrate that proton transfer in the MEA-CO2-H2O solution primarily occurs through H-bonded water bridges, and thus the availability and arrangement of H2O molecules also directly impacts the protonation and/or deprotonation of MEA and its derivatives. This improved understanding should contribute to developing more comprehensive kinetic models for use in modeling and optimizing the CO2 capture process. Moreover, this work highlights the importance of a detailed atomic-level description of the solution structure and dynamics in order to better understand molecular mechanisms underlying the reaction of CO2 with aqueous amines.

  5. Analysis of dynamical process with mass distribution of fission fragmentin heavy ion reactions

    Directory of Open Access Journals (Sweden)

    Aritomo Y.

    2010-03-01

    Full Text Available We analyzed experimental data obtained for the mass distribution of fission fragments in the reactions 36S+238U and 30Si+238U at several incident energies, which were performed by the JAEA group. Using the dynamical model with the Langevin equation, we precisely investigate the incident energy dependence of the mass distribution of fission fragments. We also consider the fine structures in the mass distribution of fission fragments caused by the nuclear structure at a low incident energy. It is explained why the mass distribution of fission fragments has different features in the two reactions. The fusion cross sections are also estimated.

  6. 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.

  7. 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.

  8. The complex-forming dynamics of Ne + NeH(D)+ (v = 0, 1; j = 0) reactions

    Science.gov (United States)

    Li, Wenliang

    2017-01-01

    The quasi-classical trajectory method has been employed to investigate the dynamics of the title reactions based on an accurate potential energy surface. The agreement between the QCT and quantum wave packet results is good for the integral cross sections and the reaction probabilities. The influences of the collision energy on the average lifetime of the complex-forming are also predicted. The polarization dependent differential cross sections of the title reactions are also calculated to uncover the reaction mechanism. The calculated results indicated that the collision energies play an important role in the complex-forming dynamics of the title reactions.

  9. Interdependence of conformational and chemical reaction dynamics during ion assembly in polar solvents.

    Science.gov (United States)

    Ji, Minbiao; Hartsock, Robert W; Sun, Zheng; Gaffney, Kelly J

    2011-10-01

    We have utilized time-resolved vibrational spectroscopy to study the interdependence of the conformational and chemical reaction dynamics of ion assembly in solution. We investigated the chemical interconversion dynamics of the LiNCS ion pair and the (LiNCS)(2) ion-pair dimer, as well as the spectral diffusion dynamics of these ionic assemblies. For the strongly coordinating Lewis base solvents benzonitrile, dimethyl carbonate, and ethyl acetate, we observe Li(+) coordination by both solvent molecules and NCS(-) anions, while the weak Lewis base solvent nitromethane shows no evidence for solvent coordination of Li(+) ions. The strong interaction between the ion-pair dimer structure and the Lewis base solvents leads to ion-pair dimer solvation dynamics that proceed more slowly than the ion-pair dimer dissociation. We have attributed the slow spectral diffusion dynamics to electrostatic reorganization of the solvent molecules coordinated to the Li(+) cations present in the ion-pair dimer structure and concluded that the dissociation of ion-pair dimers depends more critically on longer length scale electrostatic reorganization. This unusual inversion of the conformational and chemical reaction rates does not occur for ion-pair dimer dissociation in nitromethane or for ion pair association in any of the solvents.

  10. Theoretical Study of Electron Transfer in Bimolecular System of NH3 and H2O

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Mulliken, NPA, MK and CHelpG population analyses have been accomplished at the level of MP2/6-31G(d,p) for the title system. The variations of four kinds of charges on NH3 with intermolecular distance infer that electron transfers from NH3 to H2O. MK and CHelpG population analyses indicate more electron transfer than Mulliken and NPA ones. The atomic charges resulted from MK and CHelpG schemes infer that electron transfers from N in NH3 to H in H2O, which confirms that this bimolecular complex possesses linear structure as H3N…HOH.

  11. Equilibrium properties of the reaction H2 ⇌ 2H by classical molecular dynamics simulations.

    Science.gov (United States)

    Skorpa, Ragnhild; Simon, Jean-Marc; Bedeaux, Dick; Kjelstrup, Signe

    2014-01-21

    We have developed a classical molecular dynamics model for the hydrogen dissociation reaction, containing two- and three-particle potentials derived by Kohen, Tully and Stillinger. Two fluid densities were investigated for a wide range of temperatures, and 11 fluid densities were considered for one temperature. We report the temperature range where the degree of reaction is significant, and also where a stable molecule dominates the population in the energy landscape. The three-particle potential, which is essential for the reaction model and seldom studied, together with the two-particle interaction lead to a large effective excluded volume diameter of the molecules in the molecular fluid. The three-particle interaction was also found to give a large positive contribution to the pressure of the reacting mixture at high density and/or low temperatures. From knowledge of the dissociation constant of the reaction and the fluid pressure, we estimated the standard enthalpy of the dissociation reaction to be 430 kJ mol(-1) (ρ = 0.0695 g cm(-3)) and 380 kJ mol(-1) (ρ = 0.0191 g cm(-3)). These values are in good agreement with the experimental vaule of 436 kJ mol(-1) under ambient pressure. The model is consistent with a Lennard-Jones model of the molecular fluid, and may facilitate studies of the impact of chemical reactions on transport systems.

  12. 17O+58Ni scattering and reaction dynamics around the Coulomb barrier

    Science.gov (United States)

    Strano, E.; Torresi, D.; Mazzocco, M.; Keeley, N.; Boiano, A.; Boiano, C.; Di Meo, P.; Guglielmetti, A.; La Commara, M.; Molini, P.; Manea, C.; Parascandolo, C.; Pierroutsakou, D.; Signorini, C.; Soramel, F.; Filipescu, D.; Gheorghe, A.; Glodariu, T.; Grebosz, J.; Jeong, S.; Kim, Y. H.; Lay, J. A.; Miyatake, H.; Nicoletto, M.; Pakou, A.; Rusek, K.; Sgouros, O.; Soukeras, V.; Stroe, L.; Toniolo, N.; Vitturi, A.; Watanabe, Y.; Zerva, K.

    2016-08-01

    This work aims at investigating the projectile binding energy influence on the reaction dynamics, introducing new results and new data analysis methods in order to overcome some typically encountered problems, such as the identification of reaction products differing by few mass units and the discrimination of direct reaction processes. The 17O+58Ni collision was studied at five near-barrier energies employing a compact experimental setup consisting of four double-sided silicon strip detectors (DSSSDs). Different reaction processes, namely the elastic and inelastic scattering and the 1 n stripping, were discriminated by means of a detailed analysis of the experimental energy spectra based on Monte Carlo simulations. The elastic scattering angular distributions were investigated within the framework of the optical model using Woods-Saxon and double-folding potentials. The total reaction cross sections were extracted and the reduced cross sections compared with those obtained for 17F (Sp=0.600 MeV), the mirror nucleus of 17O (Sn=4.143 MeV), and for the tightly bound 16O projectile. The 17O+58Ni total reaction cross sections were larger than those for 16O on the same target at the lowest energies studied, becoming identical, within errors, as the incident energy increased above the Coulomb barrier. This behavior was related to a strong contribution from the 1 n -stripping channel at the lowest energies.

  13. 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.

  14. Acute effects of static and dynamic stretching on balance, agility, reaction time and movement time.

    Science.gov (United States)

    Chatzopoulos, Dimitris; Galazoulas, Christos; Patikas, Dimitrios; Kotzamanidis, Christos

    2014-05-01

    The purpose of this study was to compare the acute effects of three different stretching protocols on balance, agility, reaction time and movement time of the upper limbs. Participants were thirty one female high school athletes (age = 17.3 ± 0.5 yr.). All participants performed one of the following protocols on different days: (a) 3 min jogging followed by 7 min static stretching (SS), (b) 3 min jogging followed by 7 min dynamic stretching (DS), and (c) 3 min jogging followed by 7 min of rest (NS). After the protocols participants performed the following tests: dynamic balance, 505 agility test, reaction time (time between a sound stimulus and release of a button) and movement time (movement of the upper extremity over a 0.5 m distance). The order of stretching protocols and performance tests were counterbalanced to avoid carryover effects. Repeated measures analysis of variance revealed significant main effects for all variables except reaction time. The DS protocol compared to SS performed significantly better in balance, agility and movement time. Additionally, the DS protocol compared to NS performed significantly better in agility. According to the results of the study, a DS protocol is more appropriate than SS for activities that require balance, rapid change of running direction (agility) and movement time of the upper extremities. Key pointsStatic stretching has a negative effect on balance and agility performance compared to dynamic stretching.There was no effect of the stretching protocols on reaction time.Dynamic stretching was more effective than static stretching for increasing movement time of the upper extremities.

  15. Structural and dynamical control of the reaction rate in protein electron transfer

    Science.gov (United States)

    Balabin, Ilya A.

    Electron transfer (ET) reactions in proteins are key steps in many vital bioenergetic processes, and the reaction rate is known to be highly sensitive to the protein structure in some cases. For most bioenergetic reactions, as described by the Fermi Golden rule, the rate is proportional to a product of the average square of the effective electronic donor to acceptor coupling and a Franck-Condon factor, which accounts for the nuclear control of the energy gap. The nuclear factor is reasonably well described in Marcus theory and its modifications, and this work is focused on the mechanisms that control the effective coupling. About ten years ago, the Pathways model described for the first time how protein environment may control the effective coupling. In this work, a novel theoretical approach is developed to explore the mechanisms of structural and dynamical control beyond the qualitative level of the Pathways model. In Chapter 1, the assumptions of the Pathways model, its limitations and effects of the structure and the electronic Hamiltonian are investigated for model chain-like bridges using the Dyson's equations. In Chapter II, the framework to explore the sensitivity of the effective coupling to quality of the electronic Hamiltonian, the interference among the dominant pathways and the bridge dynamics is presented. This analysis employs the Green's function technique and includes combined molecular dynamics and electronic structure calculations. Finally, in Chapter III, this framework is tested on the bacterial photosynthetic reaction center, and the mechanisms of the structural and dynamical control for different ET steps are discussed.

  16. Dynamics of small autocatalytic reaction network; 2, replication, mutation and catalysis

    CERN Document Server

    Stadler, P F; Först, C J; Schuster, P; Stadler, Peter F; Schnabl, Wolfgang; Forst, Christian V; Schuster, Peter; Biotechnology, Molecuar

    1994-01-01

    Mutation is introduced into autocatalytic reaction networks. Examples of low dimensional dynamical systems --- n = 2, 3 and 4 --- are discussed and complete qualitative analysis is presented. Error thresholds known from simple replication-mutation kinetics with frequency independent replication rates occur here as well. Instead of cooperative transitions or higher order phase transistions the thresholds appear here as supercritical or subcritical bifurcations being analogous to first order phase transitions.

  17. Oxygenation mechanism of ions in dynamic reaction cell ICP-MS.

    Science.gov (United States)

    Narukawa, Tomohiro; Chiba, Koichi

    2013-01-01

    A dynamic reaction cell (DRC) is one of the most effective tools for eliminating spectral interferences caused by polyatomic molecules in inductively coupled plasma mass spectrometry (ICP-MS). Oxygen gas (O2), by producing oxygenated ions, is very effective in reducing some specific spectral interferences. In this study, the oxygenation of elemental ions (M(+)) in the DRC was investigated experimentally, and a new explanation for oxygenation based on the enthalpy changes in the oxygenating reactions is proposed. The enthalpy changes of each M(+) were calculated and the possibility of each reaction occurring was evaluated. The calculations were in good agreement with experimental observations. Theoretical and experimental results supported the hypothesis that the enthalpy changes (ΔH) of M(+)+ O2 → MO(+) + O and M(+) + O → MO(+) and the thermodynamic stability of M(+)-O are key factors controlling oxygenation of M(+) in the DRC.

  18. 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.

  19. Chemical Reaction Rate Coefficients from Ring Polymer Molecular Dynamics: Theory and Practical Applications.

    Science.gov (United States)

    Suleimanov, Yury V; Aoiz, F Javier; Guo, Hua

    2016-11-03

    This Feature Article presents an overview of the current status of ring polymer molecular dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical applications to prototypical chemical reactions in the gas phase, which demonstrate how accurate and reliable RPMD is for calculating thermal chemical reaction rate coefficients 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 rate coefficients. We also hope it will motivate further applications of RPMD to various chemical reactions.

  20. ARTICLE Crossed Beams Study on the Dynamics of F Atom Reaction with 1,2-Butadiene

    Science.gov (United States)

    Xiao, Chong-fa; Shen, Guan-lin; Wang, Xiu-yan; Yang, Xue-ming

    2010-12-01

    We have investigated the dynamics of the F+C4H6 reaction using the universal crossed molecular beam method. The C4H5F+H reaction channel was observed in this experiment. Angular resolved time-of-flight spectra have been measured for the C4H5F product. Product angular distributions as well as kinetic energy distributions were determined for this product channel. Experimental results show that the C4H5F product is largely backward scattered with considerable forward scattering signal, relative to the F atom beam direction. This suggests that the reaction channel mainly proceeds via a long-lived complex formation mechanism, with possible contribution from a direct SN2 type mechanism.

  1. 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.

  2. Reaction dynamics and statistical theory for the growth of hydrogen bonding clusters

    Institute of Scientific and Technical Information of China (English)

    WANG; Haijun; BA; Xinwu(巴信武); ZHAO; Min(赵敏)

    2002-01-01

    The similarities between the formation of hydrogen bonds and polycondensation reactions are stated from the statistical viewpoint, and then taking the hydrogen bonding system of AaDd type as an example, the growing process of hydrogen bonding clusters is investigated in terms of the theory of reaction dynamics and statistical theory for polymeric reactions. The two methods lead to the same conclusions, stating that the statistical theory for polymerization is applicable to the hydrogen bonding systems. Based on this consideration, the explicit relationship between the conversions of proton-donors and proton-acceptors and the Gibbs free energy of the system under study is given. Furthermore, the sol-gel phase transition is predicted to take place in some hydrogen bonding systems, and the corresponding generalized scaling laws describing this kind of phase transition are obtained.

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

    Science.gov (United States)

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

    2014-10-14

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

  4. Dynamics of gecko locomotion: a force-measuring array to measure 3D reaction forces.

    Science.gov (United States)

    Dai, Zhendong; Wang, Zhouyi; Ji, Aihong

    2011-03-01

    Measuring the interaction between each foot of an animal and the substrate is one of the most effective ways to understand the dynamics of legged locomotion. Here, a new facility - the force-measuring array (FMA) - was developed and applied to measure 3D reaction forces of geckos on different slope surfaces. The FMA consists of 16 3D sensors with resolution to the mN level. At the same time the locomotion behaviour of geckos freely moving on the FMA was recorded by high speed camera. The reaction forces acting on the gecko's individual feet measured by the FMA and correlated with locomotion behaviour provided enough information to reveal the mechanical and dynamic secrets of gecko locomotion. Moreover, dynamic forces were also measured by a force platform and correlated with locomotion behaviour. The difference between the forces measured by the two methods is discussed. From the results we conclude that FMA is the best way to obtain true reaction forces acting on the gecko's individual feet.

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

    Science.gov (United States)

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

    2011-12-01

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

  6. 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.

  7. 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 ...

  8. Quantum Theory of Fast Chemical Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Light, John C

    2007-07-30

    The aims of the research under this grant were to develop a theoretical understanding and predictive abiility for a variety of processes occurring in the gas phase. These included bimolecular chemical exchange reactions, photodissociation, predissociation resonances, unimolecular reactions and recombination reactions. In general we assumed a knowledge, from quantum chemistry, of the interactions of the atoms and molecular fragments involved. Our focus was primarily on the accurate (quantum) dynamics of small molecular systems. This has been important for many reactions related to combustion and atmospheric chemistry involving light atom transfer reactions and, for example, resonances in dissociation and recombination reactions. The rates of such reactions, as functions of temperature, internal states, and radiation (light), are fundamental for generating models of overall combustion processes. A number of new approaches to these problems were developed inclluding the use of discrete variable representations (DVR's) for evaluating rate constants with the flux-flux correlation approach, finite range approaches to exact quantum scattering calculations, energy selected basis representations, transition state wave packet approaches and improved semiclassical approaches. These (and others) were applied to a number of reactive systems and molecular systems of interest including (many years ago) the isotopic H + H2 exchange reactions, the H2 + OH (and H + H2O) systems, Ozone resonances, van der Waals molecule reactions, etc. A total of 7 graduate students, and 5 post-doctoral Research Associates were supported, at least in part, under this grant and seven papers were published with a total of 10 external collaborators. The majority of the 36 publications under this grant were supported entirely by DOE.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-09

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

  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. 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.

  12. A ring polymer molecular dynamics study of the Cl + O3 reaction.

    Science.gov (United States)

    de Tudela, R Pérez; Suleimanov, Y V; Menéndez, M; Castillo, J F; Aoiz, F J

    2014-02-21

    We have performed ring polymer molecular dynamics (RPMD) calculations on the Cl + O3 → ClO + O2 reaction at temperatures ranging from 200 K to 400 K, and compared the results with previous theoretical studies and also with the available experimental data. This reaction presents a couple of features which makes it a particularly interesting and challenging case to be studied using RPMD. First, classically, this is essentially a barrierless reaction, with a saddle point located below the reactants. However, the free energy profiles along the reaction coordinate display small barriers due to the fact that the decrease in enthalpy from reactants to the TS is somewhat compensated by a decrease in entropy. To our knowledge this is the first time such a process is studied using this technique. Second, the transition state is located early in the reactant valley, therefore the inclusion of the recrossing correction in the RPMD calculations is crucial to determine rate coefficients. Regarding quantum effects, our calculations show that RPMD results are within the error bars of the purely classical ones. This implies that tunnelling is negligible in this reaction at the temperatures studied, not surprisingly for a system including oxygen and chlorine atoms, and that the zero point energies of reactants, transition state and products are practically the same. Finally, the rate coefficients presented in this work are in a fairly good agreement with the recommended experimental values, somewhat better than those obtained using other approaches.

  13. Motif analysis for small-number effects in chemical reaction dynamics.

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-07

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  14. Dynamic path bifurcation in the Beckmann reaction: support from kinetic analyses.

    Science.gov (United States)

    Yamamoto, Yutaro; Hasegawa, Hiroto; Yamataka, Hiroshi

    2011-06-03

    The reactions of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles when the migrating groups have reasonable stability as cations. The reactions of oxime sulfonates of 1-substituted-phenyl-2-propanone derivatives (7-X) and related substrates (8-X, 9a-X) in aqueous CH(3)CN gave both rearrangement products (amides) and fragmentation products (alcohols), the ratio of which depends on the system; the reactions of 7-X gave amides predominantly, whereas 9a-X yielded alcohols as the major product. The logk-logk plots between the systems gave excellent linear correlations with slopes of near unity. The results support the occurrence of path bifurcation after the rate-determining TS of the Beckmann rearrangement/fragmentation reaction, which has previously been proposed on the basis of molecular dynamics simulations. It was concluded that path-bifurcation phenomenon could be more common than thought and that a reactivity-selectivity argument based on the traditional TS theory may not always be applicable even to a well-known textbook organic reaction.

  15. Motif analysis for small-number effects in chemical reaction dynamics

    Science.gov (United States)

    Saito, Nen; Sughiyama, Yuki; Kaneko, Kunihiko

    2016-09-01

    The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic changes in chemical-reaction dynamics and statistics compared to those observed under a macroscopic system (i.e., with a large number of molecules). In order to understand how salient changes emerge from fluctuations in molecular number, we here quantitatively define small-number effect by focusing on a "mesoscopic" level, in which the concentration distribution is distinguishable both from micro- and macroscopic ones and propose a criterion for determining whether or not such an effect can emerge in a given chemical reaction network. Using the proposed criterion, we systematically derive a list of motifs of chemical reaction networks that can show small-number effects, which includes motifs showing emergence of the power law and the bimodal distribution observable in a mesoscopic regime with respect to molecule number. The list of motifs provided herein is helpful in the search for candidates of biochemical reactions with a small-number effect for possible biological functions, as well as for designing a reaction system whose behavior can change drastically depending on molecule number, rather than concentration.

  16. 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.

  17. Reaction dynamics. Extremely short-lived reaction resonances in Cl + HD (v = 1) → DCl + H due to chemical bond softening.

    Science.gov (United States)

    Yang, Tiangang; Chen, Jun; Huang, Long; Wang, Tao; Xiao, Chunlei; Sun, Zhigang; Dai, Dongxu; Yang, Xueming; Zhang, Dong H

    2015-01-02

    The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed-molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v' = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v' = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.

  18. Controlled state-to-state atom-exchange reaction in an ultracold atom-dimer mixture

    CERN Document Server

    Rui, Jun; Liu, Lan; Zhang, De-Chao; Liu, Ya-Xiong; Nan, Jue; Zhao, Bo; Pan, Jian-Wei

    2016-01-01

    Ultracold molecules offer remarkable opportunities to study chemical reactions at nearly zero temperature. Although significant progresses have been achieved in exploring ultracold bimolecular reactions, the investigations are usually limited to measurements of the overall loss rates of the reactants. Detection of the reaction products will shed new light on understanding the reaction mechanism and provide a unique opportunity to study the state-to-state reaction dynamics. Here we report on the direct observation of an exoergic atom-exchange reaction in an ultracold atom-dimer mixture. Both the atom and molecule products are observed and the quantum states are characterized. By changing the magnetic field, the reaction can be switched on or off, and the reaction rate can be controlled. The reaction is efficient and we have measured a state-to-state reaction rate of up to $1.1(3)\\times10^{-9}$cm$^{3}/$s from the time evolution of the reactants and products. Our work represents the realization of a controlled q...

  19. Acute Effects of Static and Dynamic Stretching on Balance, Agility, Reaction Time and Movement Time

    Directory of Open Access Journals (Sweden)

    Dimitris Chatzopoulos

    2014-06-01

    Full Text Available The purpose of this study was to compare the acute effects of three different stretching protocols on balance, agility, reaction time and movement time of the upper limbs. Participants were thirty one female high school athletes (age = 17.3 ± 0.5 yr.. All participants performed one of the following protocols on different days: (a 3 min jogging followed by 7 min static stretching (SS, (b 3 min jogging followed by 7 min dynamic stretching (DS, and (c 3 min jogging followed by 7 min of rest (NS. After the protocols participants performed the following tests: dynamic balance, 505 agility test, reaction time (time between a sound stimulus and release of a button and movement time (movement of the upper extremity over a 0.5 m distance. The order of stretching protocols and performance tests were counterbalanced to avoid carryover effects. Repeated measures analysis of variance revealed significant main effects for all variables except reaction time. The DS protocol compared to SS performed significantly better in balance, agility and movement time. Additionally, the DS protocol compared to NS performed significantly better in agility. According to the results of the study, a DS protocol is more appropriate than SS for activities that require balance, rapid change of running direction (agility and movement time of the upper extremities.

  20. Excitation of the dynamical dipole in the charge asymmetric reaction {sup 16}O + {sup 116}Sn

    Energy Technology Data Exchange (ETDEWEB)

    Corsi, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Wieland, O. [INFN Sezione di Milano, Milano (Italy); Kravchuk, V.L. [Laboratori Nazionali INFN di Legnaro, Legnaro (Italy); Bracco, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Camera, F. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy)], E-mail: franco.camera@mi.infn.it; Benzoni, G.; Blasi, N.; Brambilla, S. [INFN Sezione di Milano, Milano (Italy); Crespi, F.C.L.; Giussani, A.; Leoni, S. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Million, B. [INFN Sezione di Milano, Milano (Italy); Montanari, D.; Moroni, A. [Dipartimento di Fisica, Universita di Milano, Milano (Italy); INFN Sezione di Milano, Milano (Italy); Gramegna, F.; Lanchais, A.; Mastinu, P. [Laboratori Nazionali INFN di Legnaro, Legnaro (Italy); Brekiesz, M.; Kmiecik, M.; Maj, A. [Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, Krakow (Poland)] (and others)

    2009-08-24

    The {gamma}-ray emission from the dynamical dipole formed in heavy-ion collisions during the process leading to fusion was measured for the N/Z asymmetric reaction {sup 16}O + {sup 116}Sn at beam energies of 8.1 and 15.6 MeV/nucleon. High-energy {gamma}-rays and charged particles were measured in coincidence with the heavy recoiling residual nuclei. The data are compared with those from the N/Z symmetric reaction {sup 64}Ni + {sup 68}Zn at bombarding energies of 4.7 and 7.8 MeV/nucleon, leading to the same CN with the same excitation energies as calculated from kinematics. The measured yield of the high-energy {gamma}-rays from the {sup 16}O-induced reaction is found to exceed that of the thermalized CN and the excess yield increases with bombarding energy. The data are in rather good agreement with the predictions for the dynamical dipole emission based on the Boltzmann-Nordheim-Vlasov model. In addition, a comparison with existing data in the same mass region is performed to extract information on the dipole moment dependence.

  1. Excitation of the dynamical dipole in the charge asymmetric reaction 16O + 116Sn

    Science.gov (United States)

    Corsi, A.; Wieland, O.; Kravchuk, V. L.; Bracco, A.; Camera, F.; Benzoni, G.; Blasi, N.; Brambilla, S.; Crespi, F. C. L.; Giussani, A.; Leoni, S.; Million, B.; Montanari, D.; Moroni, A.; Gramegna, F.; Lanchais, A.; Mastinu, P.; Brekiesz, M.; Kmiecik, M.; Maj, A.; Bruno, M.; D'Agostino, M.; Geraci, E.; Vannini, G.; Barlini, S.; Casini, G.; Chiari, M.; Nannini, A.; Ordine, A.; Di Toro, M.; Rizzo, C.; Colonna, M.; Baran, V.

    2009-08-01

    The γ-ray emission from the dynamical dipole formed in heavy-ion collisions during the process leading to fusion was measured for the N/Z asymmetric reaction 16O + 116Sn at beam energies of 8.1 and 15.6 MeV/nucleon. High-energy γ-rays and charged particles were measured in coincidence with the heavy recoiling residual nuclei. The data are compared with those from the N/Z symmetric reaction 64Ni + 68Zn at bombarding energies of 4.7 and 7.8 MeV/nucleon, leading to the same CN with the same excitation energies as calculated from kinematics. The measured yield of the high-energy γ-rays from the 16O-induced reaction is found to exceed that of the thermalized CN and the excess yield increases with bombarding energy. The data are in rather good agreement with the predictions for the dynamical dipole emission based on the Boltzmann-Nordheim-Vlasov model. In addition, a comparison with existing data in the same mass region is performed to extract information on the dipole moment dependence.

  2. Complex integrated method of dynamic meditation with Buddhists’ breathing in case of neurotic reactions

    Directory of Open Access Journals (Sweden)

    Omelyanenko V.I.

    2014-02-01

    Full Text Available Purpose: to elaborate complex integrated method of psychological influence upon sport dancers in time of training on base of Buddhists’ meditation “conscious breathing” for neurotic reactions elimination, professional skill improvement and psycho emotional stability advance. Material : twenty dancers at the age of 40-50 with neurotic reactions participated in the research. At the first stage of the research all the subjects’ ability to focus attention at breathing during sports dancing performance was examined. At the second stage training in method of dynamic meditation applied for martial arts of the experimental group of 10 subjects was conducted. Both individual and group training sessions were held. At the third stage the experimental group joined dynamic meditation and breathing at dance performance. At the fourth stage the experimental group’s results were compared with the control group’s results. Results : at the first stage of the research all the subjects noted difficulties in focusing attention on Buddhists’ nasal breathing and dance technique come-down. 3-5 sessions of training in method of dynamic meditation were necessary for the subjects of the experimental group at the second stage of the research. At the third stage of the research all the subjects of the experimental group could control their nasal breathing at dance performance without dance technique come-down. At the fourth stage the comparative evaluation of the results of the experimental and control groups revealed that it was necessary 3-7 sport dance practice sessions for elimination of the neurotic reactions. No such effect was observed in the control group. Conclusions : The results of the research prove that Buddhists’ meditation “conscious breathing” may be joined with dynamic meditation successfully. It’s impossible to focus attention continuously on breathing at time of sport dance performance. The elaborated technique of the integration of

  3. Comparative dynamics of the two channels of the reaction of D + MuH.

    Science.gov (United States)

    Aoiz, F J; Aldegunde, J; Herrero, V J; Sáez-Rábanos, V

    2014-06-07

    The dynamics of the asymmetric D + MuH (Mu = Muonium) reaction leading to Mu exchange, DMu + H, and H abstraction, DH + Mu, channels has been investigated using time-independent quantum mechanical (QM) calculations. Reaction probabilities, cross sections, cumulative reaction probabilities, and rate coefficients were determined for the two exit channels of the reaction. Quasiclassical trajectory (QCT) calculations were also performed in order to check the reliability of the method for this reaction and to discern the genuine quantum effects. Overall, the Mu exchange channel exhibits more structured reaction probabilities and cross sections with much larger rate coefficients than the H abstraction counterpart. Over the 100-1000 K temperature interval considered in this study, the QM rate coefficients for the Mu exchange vary between ≈5 × 10(-15) and 2 × 10(-11) cm(3) s(-1) and those for the generation of DH + Mu between 2 × 10(-18) and 3.5 × 10(-12) cm(3) s(-1). In common with the rest of the isotopologues of the H + H2 system, the height of the respective barriers in the collinear (symmetric stretch) vibrationally adiabatic potential energy curves matches the classical total energy threshold very accurately. Indeed, the lower and narrower vibrationally adiabatic collinear barrier as compared with that for the DH + Mu formation determines the preponderance of the DMu + H channel. Comparison of QM and QCT results and their analysis show that tunneling accounts for the reactivity at energies below the height of these barriers and that its effect on the rate coefficients becomes appreciable below 300 K. As expected, with growing temperature the contribution of tunneling to the global reactivity decreases markedly, but the rate coefficients are still much higher for the Mu exchange channel due to the effect of MuH rotational excitation that boosts the formation of DMu while diminishing the H abstraction channel that leads to DH formation. The analysis of the

  4. Comparative Static and Dynamic Study of a Prototype SN2 Reaction.

    Science.gov (United States)

    Joubert, Laurent; Pavone, Michele; Barone, Vincenzo; Adamo, Carlo

    2006-09-01

    Ab initio molecular-dynamic simulations, using density functional theory (DFT) and the recent atom-centered density-matrix propagation method (ADMP), were used to study the bond formation process in a prototypical SN2 reaction, namely the Walden inversion. Using the real space partition schemes of both electronic density and electron localization function gradient fields, we analyzed different quantum chemical topology (QCT) properties along the ADMP trajectory. In particular, atomic charges derived from the Bader's atoms-in-molecules (AIM) theory were used to analyze intra- and intermolecular charge transfers between atoms, while the electronic population of the forming bonding basin obtained from the electron localization function (ELF) gradient field was employed to describe the bond formation process. These results were compared to the corresponding QCT properties issuing from a static approach based on the intrinsic reaction path (IRP). Although similar features are found for both static and dynamic approaches, the dynamic QCT analysis provides some explanation of the differences observed during the formation of the ion-molecule complex. In particular, it suggests a stronger electron exchange leading to an effective maximization of both covalent and noncovalent interactions.

  5. 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.

  6. 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.

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

    Science.gov (United States)

    Wales, D. J.

    2015-04-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-31

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-30

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

  10. Ultrafast chemical reactions in shocked nitromethane probed with dynamic ellipsometry and transient absorption spectroscopy.

    Science.gov (United States)

    Brown, Kathryn E; McGrane, Shawn D; Bolme, Cynthia A; Moore, David S

    2014-04-10

    Initiation of the shock driven chemical reactions and detonation of nitromethane (NM) can be sensitized by the addition of a weak base; however, the chemical mechanism by which sensitization occurs remains unclear. We investigated the shock driven chemical reaction in NM and in NM sensitized with diethylenetriamine (DETA), using a sustained 300 ps shock driven by a chirped Ti:sapphire laser. We measured the solutions' visible transient absorption spectra and measured interface particle and shock velocities of the nitromethane solutions using ultrafast dynamic ellipsometry. We found there to be a volume-increasing reaction that takes place around interface particle velocity up = 2.4 km/s and up = 2.2 km/s for neat NM and NM with 5% DETA, respectively. The rate at which transient absorption increases is similar in all mixtures, but with decreasing induction times for solutions with increasing DETA concentrations. This result supports the hypothesis that the chemical reaction mechanisms for shocked NM and NM with DETA are the same. Data from shocked NM are compared to literature experimental and theoretical data.

  11. 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.

  12. Total Reaction Cross Section in an Isospin-Dependent Quantum Molecular Dynamics Model

    Institute of Scientific and Technical Information of China (English)

    魏义彬; 蔡翔舟; 沈文庆; 马余刚; 张虎勇; 钟晨; 郭威; 陈金根; 马国亮; 王鲲

    2003-01-01

    The isospin-dependent quantum molecular dynamics (IDQMD) model is used to study the total reaction cross section σR. The energy-dependent Pauli volumes of neutrons and protons have been discussed and introduced into the IDQMD calculation to replace the widely used energy-independent Pauli volumes. The modified IDQMD calculation can reproduce the experimental cr R well for both stable and exotic nuclei induced reactions. Comparisons of the calculated σn induced by 11Li with different initial density distributions have been performed. It is shown that the calculation by using the experimentally deduced density distribution with a long tail can fit the experimental excitation function better than that by using the Skyrme-Hartree-Fock calculated density without long tails. It is also found that σR at high energy is sensitive to the long tail of density distribution.

  13. Water O-H bond activation by gas-phase plutonium atoms: reaction mechanisms and ab initio molecular dynamics study.

    Science.gov (United States)

    Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan

    2014-10-06

    A thorough description of the reaction mechanisms, taking into account different possible spin states, offers insights into the gas-phase reaction of plutonium atoms with water. Two possible reactions (isomerization and dehydrogenation) are presented. These reactions are found to be exothermic, with the best thermochemical conditions observed for the dehydrogenation reaction at around 23.5 kcal mol(-1). The nature of the chemical-bonding evolution along the reaction pathways are investigated by employing various methods including electron localization function, atoms in molecules, and Mayer bond order. Total, partial, and overlap population density of state diagrams and analyses are also presented. Reaction rates at elevated temperatures (T=298-2 000 K) are calculated by using variational transition-state theory with one-dimensional tunneling effects. In dynamics simulations, only the dehydrogenation reaction is observed, and found to be in good agreement with experimental values.

  14. 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.

  15. 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

  16. Ultrafast ring-closing reaction dynamics of a photochromic furan-based difurylethene

    Science.gov (United States)

    Khodko, A.; Khomenko, V.; Shynkarenko, Y.; Mamuta, O.; Kapitanchuk, O.; Sysoiev, D.; Kachalova, N.; Huhn, T.; Snegir, S.

    2017-02-01

    The ultrafast photoinduced ring-closing dynamics of a furan-based difurylethene (YnPhT) has been investigated by femtosecond transient absorption spectroscopy. We performed time-dependent density functional theory (TD-DFT) calculations to explain the experimental results in detail. The sub-picosecond time scale of the ring-closing reaction is comparable with thiophene-based analogues, but oxygen atoms at the photochromic core can avoid adverse interaction between switches and metal contacts in further applications. This observation proves that furan-based diarylethenes are potential optoelectronic elements with an ultrafast optical response.

  17. 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.

  18. 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...... induced AR. A detailed description of the dynamics of sperm viability and acrosomal status of boar sperm following in vitro induction of the AR has to our knowledge not previously been conducted. In the present study, a triple color flow cytometric detection technique was used, which gave simultaneous...... 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...

  19. 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.

  20. Dynamic reaction coordinate in thermally fluctuating environment in the framework of the multidimensional generalized Langevin equations.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2010-12-21

    A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in a multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Müller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account thermally fluctuating environments, memory effect, and nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment.

  1. Langevin Equations for Reaction-Diffusion Processes

    Science.gov (United States)

    Benitez, Federico; Duclut, Charlie; Chaté, Hugues; Delamotte, Bertrand; Dornic, Ivan; Muñoz, Miguel A.

    2016-09-01

    For reaction-diffusion processes with at most bimolecular reactants, we derive well-behaved, numerically tractable, exact Langevin equations that govern a stochastic variable related to the response field in field theory. Using duality relations, we show how the particle number and other quantities of interest can be computed. Our work clarifies long-standing conceptual issues encountered in field-theoretical approaches and paves the way for systematic numerical and theoretical analyses of reaction-diffusion problems.

  2. Coupled effects of dehydration reaction, dilatant strengthening and shear heating on dynamic fault slip

    Science.gov (United States)

    Yamashita, T.

    2012-12-01

    It is believed that dynamic fault slip is affected by thermal pressurization. However, dilatant strengthening and dehydration reaction may significantly affect the degree of thermal pressurization. In addition, it is not clear how such effects influence the fault slip as a whole. We theoretically study how dilatant strengthening, frictional heating and dehydration reaction are coupled and how they affect dynamic slip assuming a fault in a thermoporoelastic medium saturated with fluid. After mathematical analysis is carried out for 1D model, the behavior of 2D fault model is studied numerically. The porosity is assumed to increase with increasing fault slip following Suzuki and Yamashita (2008). Our mathematical formulation of dehydration reaction is based on Brantut et al.(2010); the dehydration reaction is assumed to be endothermic. In addition, starting from the temperature Ts, all the frictional energy is assumed to be absorbed by the dehydration reaction rather than converted into heat. Although Brantut et al.(2010) assumed a constant slip velocity, we consider the temporal evolution of slip assuming the Coulomb law of friction on the fault. We first make the analysis assuming adiabatic and undrained conditions for the 1D model. We find that three nondimensional parameters Su, P0 and G0 determine the system behavior if the initial temperature T0 and dehydration starting temperature Ts are given, where Su (>0) is a parameter proportional to the pore creation rate, P0 (>0) is the initial nondimensional frictional stress and G0 (>0) is a parameter proportional to the mass fraction of fluid released per unit of total rock mass divided by the energy change per unit volume of the slip zone. The nondimensional frictional stress P is defined by the Coulomb frictional stress divided by the initial shear stress, which suggests the relation 0Ts, where Te is the temperature. We find for Te>Ts that the evolution of P is described by the equation dP/dT=(1-P)(Su-G0*P), where

  3. 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.

  4. Body-Fitted Detonation Shock Dynamics and the Pseudo-Reaction-Zone Energy Release Model

    Science.gov (United States)

    Meyer, Chad; Quirk, James; Short, Mark; Chqiuete, Carlos

    2016-11-01

    Programmed-burn methods are a class of models used to propagate a detonation wave, without the high resolution cost associated with a direct numerical simulation. They separate the detonation evolution calculation into two components: timing and energy release. The timing component is usually calculated with a Detonation Shock Dynamics model, a surface evolution representation that relates the normal velocity of the surface (Dn) to its local curvature. The energy release component must appropriately capture the degree of energy change associated with chemical reaction while simultaneously remaining synchronized with the timing component. The Pseudo-Reaction-Zone (PRZ) model is a reactive burn like energy release model, converting reactants into products, but with a conversion rate that is a function of the DSD surface Dn field. As such, it requires the DSD calculation produce smooth Dn fields, a challenge in complex geometries. We describe a new body-fitted approach to the Detonation Shock Dynamics calculation which produces the required smooth Dn fields, and a method for calibrating the PRZ model such that the rate of energy release remains as synced as possible with the timing component. We show results for slab, rate-stick and arc geometries.

  5. 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.

  6. Analytic Solution of the Three-Variable Dynamical Equations of Oscillation Phenomena in B-Z Reaction

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The dynamical behaviour of the inorganic bromate oscillator catalyzed by manganese ions in the B-Z reaction is discussed, a three-variable nonlinear dynamical equations of the oscillation phenomena have been obtained, and an analytic solution and numerical results of the equations are given.

  7. Reaction dynamics of Cl + butanol isomers by crossed-beam sliced ion imaging.

    Science.gov (United States)

    Estillore, Armando D; Visger-Kiefer, Laura M; Suits, Arthur G

    2012-01-01

    Butanol is now prominent among the prototype renewable biofuels. We have studied oxidation of a variety of butanol isomers under single collision conditions using chlorine atom as the oxidizing agent to gain detailed insight into the energetics and dynamics of these reactions. The interaction of chlorine atom radicals with butanol isomers: n-butanol, iso-butanol, sec-butanol, and tert-butanol have been studied by crossed-beam dc slice ion imaging techniques. The hydroxybutyl radicals generated from the H-abstraction processes were probed by single photon ionization using an F2 excimer laser. After background subtraction and density-to-flux correction of the raw images, translational energy distribution and product angular distributions were generated. At low collision energy, the hydroxyalkyl products are backscattered with respect to the alcohol beam and the scattering shifts to the forward direction as the collision energy is increased. The translational energy distributions are reminiscent to that of Cl + pentane reactions we studied earlier, i.e. a sharp forward peak -80% of the collision energy appears at the high collision energy. Isomer-specific details of the reactions will be discussed.

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

    Directory of Open Access Journals (Sweden)

    Kansuporn eSriyudthsak

    2016-05-01

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

  9. Towards a nonequilibrium Green's function description of nuclear reactions: one-dimensional mean-field dynamics

    CERN Document Server

    Rios, Arnau; Buchler, Mark; Danielewicz, Pawel

    2010-01-01

    Nonequilibrium Green's function methods allow for an intrinsically consistent description of the evolution of quantal many-body body systems, with inclusion of different types of correlations. In this paper, we focus on the practical developments needed to build a Green's function methodology for nuclear reactions. We start out by considering symmetric collisions of slabs in one dimension within the mean-field approximation. We concentrate on two issues of importance for actual reaction simulations. First, the preparation of the initial state within the same methodology as for the reaction dynamics is demonstrated by an adiabatic switching on of the mean-field interaction, which leads to the mean-field ground state. Second, the importance of the Green's function matrix-elements far away from the spatial diagonal is analyzed by a suitable suppression process that does not significantly affect the evolution of the elements close to the diagonal. The relative lack of importance of the far-away elements is tied t...

  10. 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.

  11. Site and bond-specific dynamics of reactions at the gas-liquid interface.

    Science.gov (United States)

    Tesa-Serrate, Maria A; King, Kerry L; Paterson, Grant; Costen, Matthew L; McKendrick, Kenneth G

    2014-01-01

    The dynamics of the interfacial reactions of O((3)P) with the hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene) have been studied experimentally. Laser-induced fluorescence (LIF) was used to detect the nascent gas-phase OH products. The O((3)P) atoms are acutely sensitive to the chemical differences of the squalane and squalene surfaces. The larger exothermicity of abstraction from allylic C-H sites in squalene is reflected in markedly hotter OH rotational and vibrational distributions. There is a more modest increase in translational energy release. A larger fraction of the available energy is deposited in the liquid for squalene than for squalane, consistent with a more extensive geometry change on formation of the allylic radical co-product. Although the dominant reaction mechanism is direct, impulsive scattering, there is some evidence for OH being accommodated at both liquid surfaces, resulting in thermalised translation and rotational distributions. Despite the H-abstraction reaction being strongly favoured energetically for squalene, the yield of OH is substantially lower than for squalane. This is very likely due to competitive addition of O((3)P) to the unsaturated sites in squalene, implying that double bonds are extensively exposed at the liquid surface.

  12. Dynamics of interfacial reactions between O(3 P) atoms and long-chain liquid hydrocarbons

    Science.gov (United States)

    Allan, Mhairi; Bagot, Paul A. J.; Köhler, Sven P. K.; Reed, Stewart K.; Westacott, Robin E.; Costen, Matthew L.; McKendrick, Kenneth G.

    2007-09-01

    Recent progress that has been made towards understanding the dynamics of collisions at the gas-liquid interface is summarized briefly. We describe in this context a promising new approach to the experimental study of gas-liquid interfacial reactions that we have introduced. This is based on laser-photolytic production of reactive gas-phase atoms above the liquid surface and laser-spectroscopic probing of the resulting nascent products. This technique is illustrated for reaction of O(3P) atoms at the surface of the long-chain liquid hydrocarbon squalane (2,6,10,15,19,23-hexamethyltetracosane). Laser-induced fluorescence detection of the nascent OH has revealed mechanistically diagnostic correlations between its internal and translational energy distributions. Vibrationally excited OH molecules are able to escape the surface. At least two contributions to the product rotational distributions are identified, confirming and extending previous hypotheses of the participation of both direct and trapping-desorption mechanisms. We speculate briefly on future experimental and theoretical developments that might be necessary to address the many currently unanswered mechanistic questions for this, and other, classes of gas-liquid interfacial reaction.

  13. Dynamic Monte Carlo simulation of the NO+H reaction on Pt(100): TPR spectra

    Science.gov (United States)

    Álvarez-Falcón, L.; Alas, S. J.; Vicente, L.

    2011-11-01

    The catalytic reduction of nitric oxide by hydrogen over a Pt surface is studied using a dynamic Monte Carlo (MC) method on a square lattice under low pressure conditions. Using a Langmuir-Hinshelwood reaction mechanism, a simplified model with only four adsorbed species (NO, H, O, and N) is constructed. The effect on the NO dissociation rate, the limiting step in the whole reaction, is inhibited by co-adsorbed NO and H 2 molecules and is enhanced both by the presence of empty sites and adsorbed N atoms at nearest neighbors. In these simulations, several experimental parameter values are included, such as: adsorption, desorption and diffusion of the reactants. The phenomenon is studied while varying the temperature over the 300-550 K range. The model reproduces well-observed TPD and TPR experimental results. For the whole NO+H 2 reaction, the phenomena of “surface explosion” is observed and can be explained as the result of the abrupt production of N 2 due to both the autocatalytic NO decomposition favored by the presence of vacant sites and the development of inhomogeneous fluctuations. MA simulations also allow a visualization of the spatial development of the surface explosion as heating proceeds.

  14. Chemical reaction dynamics of PeCB and TCDD decomposition: A tight-binding quantum chemical molecular dynamics study with first-principles parameterization

    Science.gov (United States)

    Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1999-11-01

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

  16. 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.

  17. 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

  18. STUDY OF THE REACTION DYNAMICS OF Li + HF, HCl BY THE CROSSED MOLECULAR BEAMS METHOD

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Christopher H.; Casavecchia, Piergiorgio; Tiedemann, Peter W.; Valentini, James J.; Lee, Yuan T.

    1980-05-01

    }) are evaluated by integrating the product distributions in the c.m. frame and using small angle nonreactive scattering of Li as an absolute calibrant. Values of {sigma}{sub R} are: for LiF formation {sigma}{sub R} ~ 0.8 {Angstrom}{sup 2} and 0.94 {Angstrom}{sup 2} at E{sub c} = 3 and 8.7 kcal/mole, while for LiCl formation {sigma}{sub R} = 27 {Angstrom}{sup 2} and 42 {Angstrom}{sup 2} at E{sub c} = 2.9 and 9.2 kcal/mole, with estimated absolute and relative uncertainties of a factor of 2, and 30%, respectively. Average opacities for reaction have been estimated from the reaction cross sections and the extent of rotational excitation of products to be about 0.1 for reaction (I) and 1 for reaction (II), for L values allowed to react. These results are discussed in some detail with regard to the kinematic constraints, reaction dynamics and potential energy surfaces for these two reactions, and related experimental and theoretical work are noted. In addition, angular distributions of nonreactive scattering of Li off HF and HCl are measured at 4 different E{sub c} each. Rainbow structure is observed at low E{sub c} and the angular distributions are fit by a spherically symmetric piecewise analytic potential. The resulting values of the potential's well depth ({epsilon}) and minimum position (r{sub m} ) are: for Li + HF {epsilon} = 0.46 kcal/mole and r{sub m} = 4.34 {Angstrom} and for Li + HCl {epsilon} = 0.32 kcal/mole and r{sub m} = 4.7 {Angstrom}. These results differ significantly from some earlier estimates based on the measurements of integral scattering cross sections.

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

    Directory of Open Access Journals (Sweden)

    A. A. Vereikin

    2014-01-01

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

  20. Analysis of the complexation reaction between Ag+ and ethylene

    NARCIS (Netherlands)

    Nymeijer, Kitty; Visser, Tymen; Brilman, Wim; Wessling, Matthias

    2004-01-01

    In the present work the reversible, bimolecular (1,1) reaction between ethylene and Ag+ in concentrated AgNO3(aq) solutions is analyzed. Due to interactions between the positively charged Ag+ ions and the negatively charged NO3- ions, the silver nitrate is not completely dissociated and the actual f

  1. Target Turing patterns and growth dynamics in the chlorine dioxide-iodine-malonic acid reaction.

    Science.gov (United States)

    Preska Steinberg, Asher; Epstein, Irving R; Dolnik, Milos

    2014-04-03

    We study the growth dynamics of Turing patterns in the chlorine dioxide-iodine-malonic acid reaction-diffusion system in response to perturbations with visible light. We describe several mechanisms by which Turing patterns reappear after they are suppressed by illumination with a disc-shaped geometry. We observe that under specific conditions the patterns reorganize from a random configuration of spots and stripes to a set of ordered, concentric rings, which we refer to as target Turing patterns. These patterns closely resemble the unit cells of the Turing hexagonal superlattices known as black eye patterns. However, these target Turing patterns are not part of a larger superlattice structure, and they usually have a larger number of concentric rings. Numerical simulations support the experimental findings.

  2. Dynamic Deuterium Enrichment in Cometary Water via Eley–Rideal Reactions

    Science.gov (United States)

    Yao, Yunxi; Giapis, Konstantinos P.

    2017-01-01

    The deuterium-to-hydrogen ratio (D/H) in water found in the coma of Jupiter family comet (JFC) 67P/Churyumov–Gerasimenko was reported to be (5.3 ± 0.7) × 10‑4, the highest among comets and three times the value for other JFCs with an ocean-like ratio. This discrepancy suggests the diverse origins of JFCs and clouds the issue of the origin of Earth’s oceanic water. Here we demonstrate that Eley–Rideal reactions between accelerated water ions and deuterated cometary surface analogs can lead to instantaneous deuterium enrichment in water scattered from the surface. The reaction proceeds with H2O+ abstracting adsorbed D atoms, forming an excited H2DO* state, which dissociates subsequently to produce energetic HDO. Hydronium ions are also produced readily by the abstraction of H atoms, consistent with H3O+ detection and abundance in various comets. Experiments with water isotopologs and kinematic analysis on deuterated platinum surfaces confirmed the dynamic abstraction mechanism. The instantaneous fractionation process is independent of the surface temperature and may operate on the surface of cometary nuclei or dust grains, composed of deuterium-rich silicates and carbonaceous chondrites. The requisite energetic water ions have been detected in the coma of 67P in two populations. This dynamic fractionation process may temporarily increase the water D/H ratio, especially as the comet gets closer to the Sun. The magnitude of the effect depends on the water ion energy-flux and the deuterium content of the exposed cometary surfaces.

  3. Dynamical coupled-channels study of pi N --> pi pi N reactions

    CERN Document Server

    Kamano, H; Lee, T -S H; Matsuyama, A; Sato, T

    2008-01-01

    As a step toward performing a complete coupled-channels analysis of the world data of pi N, gamma^* N --> pi N, eta N, pi pi N reactions, the pi N --> pi pi N reactions are investigated starting with the dynamical coupled-channels model developed in Phys. Rev. C76, 065201 (2007). The channels included are pi N, eta N, and pi pi N which has pi Delta, rho N, and sigma N resonant components. The non-resonant amplitudes are generated from solving a set of coupled-channels equations with the meson-baryon potentials defined by effective Lagrangians. The resonant amplitudes are generated from 16 bare excited nucleon (N^*) states which are dressed by the non-resonant interactions as constrained by the unitarity condition. The available total cross section data of pi^+ p --> pi^+ pi^+ n, pi^+ pi^0p and pi^- p --> pi^+ pi^- n, pi^- pi^0 n, pi^0 pi^0 n can be reproduced to a very large extent both in magnitudes and energy-dependence. Possible improvements of the model are investigated, in particular on the role of the n...

  4. 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.

  5. 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.

  6. Analysis of dynamical behavior of reactions associated with 118,120,122Xe* isotopes

    Science.gov (United States)

    Grover, Neha; Sharma, Ishita; Kaur, Gurvinder; Sharma, Manoj K.

    2017-03-01

    In reference to recent experiment, the dynamical aspects of reactions forming even mass isotopes of 118,120,122Xe* nuclei are examined using the collective clusterization approach and the ℓ-summed Wong model. The role of excitation energy (or temperature), deformations, orientations and angular momentum etc. has been investigated for the 28Si + 90,92,94Zr reactions. In order to account for the role of deformations, the evaporation residue (ER) cross sections of 122Xe* nucleus have been studied in reference to the available experimental data by using spherical as well as deformed fragmentation approach. We have used optimum and compact orientations respectively for β2 alone and for β4 included, which inturn provide nice agreement with the available experimental cross-sections. Also, the effect of isospin (N/Z ratio) of decay fragments has been explored in view of the fragmentation analysis and preformation probability of 118,120,122Xe* nuclei. Additionally, the role of projectile nucleus is also explored by studying the fragmentation path of 118Xe* nucleus in comparison to 123Ba* system. Further, the ER cross-sections have been predicted for various even mass isotopes of 116,118,120,124Xe. In addition to this, to explore the fusion characteristics of 28Si + 90,92,94Zr reactions, the Wong model as well as the ℓ-summed Wong model has also been employed. Here also, the role of deformation in formation of 122Xe* nucleus has been examined and the calculated cross-sections find decent agreement with the experimental data.

  7. Characterization and Dynamics of Substituted Ruthenacyclobutanes Relevant to the Olefin Cross-Metathesis Reaction

    Science.gov (United States)

    Blake, Garrett; VanderVelde, David G.; Grubbs, Robert H.

    2011-01-01

    The reaction of the phosphonium alkylidene [(H2IMes)RuCl2=CHP(Cy)3)]+ BF4– with propene, 1-butene, and 1-hexene at –45 °C affords various substituted, metathesis-active ruthenacycles. These metallacycles were found to equilibrate over extended reaction times in response to decreases in ethylene concentrations, which favored increased populations of α-monosubstituted and α,α’-disubstituted (both cis and trans) ruthenacycles. On an NMR timescale, rapid chemical exchange was found to preferentially occur between the β-hydrogens of the cis and trans stereoisomers prior to olefin exchange. Exchange on an NMR timescale was also observed between the α- and β-methylene groups of the monosubstituted ruthenacycle (H2IMes)Cl2Ru(CHRCH2CH2) (R = CH3, CH2CH3, (CH2)3CH3). EXSY NMR experiments at –87 °C were used to determine the activation energies for both of these exchange processes. In addition, new methods have been developed for the direct preparation of metathesis-active ruthenacyclobutanes via the protonolysis of dichloro(1,3-bis(2,4,6-trimethylphenyl)-2-imidazolidinylidene)(benzylidene) bis(pyridine)ruthenium(II) and its 3-bromopyridine analog. Using either trifluoroacetic acid or silica-bound toluenesulfonic acid as the proton source, the ethylene-derived ruthenacyclobutane (H2IMes)Cl2Ru(CH2CH2CH2) was observed in up to 98% yield via NMR at –40 °C. On the basis of these studies, mechanisms accounting for the positional and stereochemical exchange within ruthenacyclobutanes are proposed, as well as the implications of these dynamics towards olefin metathesis catalyst and reaction design are described. PMID:21452876

  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+.

  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.

  10. Bifurcations of Normally Hyperbolic Invariant Manifolds and Consequences for Reaction Dynamics

    CERN Document Server

    Mauguiere, F A L; Ezra, G S; Wiggins, S

    2013-01-01

    In this paper we study the breakdown of normal hyperbolicity and its consequences for reaction dynamics; in particular, the dividing surface, the flux through the dividing surface (DS), and the gap time distribution. Our approach is to study these questions using simple, two degree-of-freedom Hamiltonian models where calculations for the different geometrical and dynamical quantities can be carried out exactly. For our examples, we show that resonances within the normally hyperbolic invariant manifold may, or may not, lead to a `loss of normal hyperbolicity'. Moreover, we show that the onset of such resonances results in a change in topology of the dividing surface, but does not affect our ability to define a DS. The flux through the DS varies continuously with energy, even as the energy is varied in such a way that normal hyperbolicity is lost. For our examples the gap time distributions exhibit singularities at energies corresponding to the existence of homoclinic orbits in the DS, but these singularities a...

  11. A protein dynamics study of photosystem II: the effects of protein conformation on reaction center function.

    Science.gov (United States)

    Vasil'ev, Sergej; Bruce, Doug

    2006-05-01

    Molecular dynamics simulations have been performed to study photosystem II structure and function. Structural information obtained from simulations was combined with ab initio computations of chromophore excited states. In contrast to calculations based on the x-ray structure, the molecular-dynamics-based calculations accurately predicted the experimental absorbance spectrum. In addition, our calculations correctly assigned the energy levels of reaction-center (RC) chromophores, as well as the lowest-energy antenna chlorophyll. The primary and secondary quinone electron acceptors, Q(A) and Q(B), exhibited independent changes in position over the duration of the simulation. Q(B) fluctuated between two binding sites similar to the proximal and distal sites previously observed in light- and dark-adapted RC from purple bacteria. Kinetic models were used to characterize the relative influence of chromophore geometry, site energies, and electron transport rates on RC efficiency. The fluctuating energy levels of antenna chromophores had a larger impact on quantum yield than did their relative positions. Variations in electron transport rates had the most significant effect and were sufficient to explain the experimentally observed multi-component decay of excitation in photosystem II. The implications of our results are discussed in the context of competing evolutionary selection pressures for RC structure and function.

  12. The unified equation for the evaluation of degenerated first-order reactions in dynamic electrophoresis.

    Science.gov (United States)

    Trapp, Oliver

    2006-08-01

    An analytical solution for the unified equation for degenerated (pseudo-) first-order reactions, e.g., enantiomerization processes, in dynamic CE is presented, and validated with a dataset of 31 250 elution profiles covering typical experimental parameters. The unified equation was applied to determine the enantiomerization barrier of the hypnotic glutarimide derivative thalidomide (Contergan(R)) by dynamic capillary electrokinetic chromatography (DEKC). The enantiomer separation of thalidomide was performed in an aqueous 50 mM sodium borate buffer at pH 9.3 in the presence of the chiral mobile phase additive carboxymethyl-beta-CD. Interconversion profiles featuring pronounced plateau formation were observed. Activation parameters DeltaH( not equal) and DeltaS( not equal) were obtained from temperature-dependent measurements between 20.0 and 37.5 degrees C in 2.5K steps. From the activation parameters the enantiomerization barrier of thalidomide at 37 degrees C under basic conditions were calculated to be DeltaG( not equal) = 93.2 kJ/mol. Comparison of the kinetic data with results obtained at pH 8.0 reveals the catalytic influence of the base on the enantiomerization barrier.

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

    Science.gov (United States)

    Mackeprang, Kasper; Kjaergaard, Henrik G.

    2017-04-01

    The local mode perturbation theory (LMPT) model was developed to improve the description of hydrogen bonded XH-stretching transitions, where X is typically O or N. We present a modified version of the LMPT model to extend its application from hydrated bimolecular complexes to hydrogen bonded bimolecular complexes with donors such as alcohols, amines and acids. We have applied the modified model to a series of complexes of different hydrogen bond type and complex energy. We found that the differences between local mode (LM) and LMPT calculated fundamental XH-stretching transition wavenumbers and oscillator strengths were correlated with the strength of the hydrogen bond. Overall, we have found that the LMPT model in most cases predicts transition wavenumbers within 20 cm-1 of the experimental values.

  14. Formations of Bacteria-like Textures by dynamic reactions in Meteorite and Syntheses

    Science.gov (United States)

    Miura, Y.

    2009-05-01

    1. Introduction Spherule texture can be formed in dynamic reaction during meteoritic impact in air. However, there are no reports on nano-bacteria-like (i.e. spherule-chained) textures with iron (and Nickel) oxides (with chlorine) in composition and micro-texture with 100nm order [1] in meteorite and synthetic experiment. The purpose of the present study is to elucidate spherule-chained texture with micro-texture of 100nm in order found in the Kuga iron meteorite, Iwakuni, Yamaguchi, Japan, and its first artificial synthesis in laboratory. 2. Two textures in the Kuga meteorite: The Kuga iron meteorite found in Kuga, Iwakuni, Yamaguchi, Japan reveals spherule-chained texture with Fe, Ni-rich composition with 10μm in size, where each spherule contained "long micro-texture in 100nm in size"[1,2]. The complex texture of flow and chained shapes can be found only in the fusion crust of the meteorite formed by quenched and random processes with vapor-melting process in air of the Earth. The FE-ASEM with EDX analyses by an in-situ observation indicate that the matrix of the spherule-chained texture with Fe, Ni, O-rich (with minor Cl) composition is carbon-rich composition formed by impact reactions in air. 3. Comparison with Martian meteorite Remnant of life in ocean can be found by mineralized fossil, which can be found in the Martian meteorite ALH84001 as bacteria-like chained texture of magnetite in composition (in 100nm order) around carbonate spherules [3]. Similarity of bacteria-like texture of the ALH84001 compared with the Kuga meteorites in this study are composition of Fe-rich, C-bearing, and chained texture of small size replaced by Fe and O-rich composition in air. Major difference of these textures is no carbonates minerals in the Kuga meteorite at dynamic reaction in air [1, 2, 3]. 4. First synthesis of bacteria- like akaganeite: A bacteria-like texture with Fe oxides (with minor chlorine as akaganeite-like compositions) is synthesized by chlorine and water

  15. Bimolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts.

    Science.gov (United States)

    Pattanaik, Sitakanta; Werkman, Joshua R; Yuan, Ling

    2011-01-01

    Protein-protein interactions are an important aspect of the gene regulation process. The expression of a gene in response to certain stimuli, within a specific cell type or at a particular developmental stage, involves a complex network of interactions between different regulatory proteins and the cis-regulatory elements present in the promoter of the gene. A number of methods have been developed to study protein-protein interactions in vitro and in vivo in plant cells, one of which is bimolecular fluorescence complementation (BiFC). BiFC is a relatively simple technique based upon the reconstitution of a fluorescent protein. The interacting protein complex can be visualized directly in a living plant cell when two non-fluorescent fragments, of an otherwise fluorescent protein, are fused to proteins found within that complex. Interaction of tagged proteins brings the two non-fluorescent fragments into close proximity and reconstitutes the fluorescent protein. In addition, the subcellular location of an interacting protein complex in the cell can be simultaneously determined. Using this approach, we have successfully demonstrated a protein-protein interaction between a R2R3 MYB and a basic helix-loop-helix MYC transcription factor related to flavonoid biosynthetic pathway in tobacco protoplasts.

  16. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

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

    KAUST Repository

    Alsam, Amani Abdu

    2015-09-02

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

  19. 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.

  20. Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches.

    Science.gov (United States)

    Schluttig, Jakob; Alamanova, Denitsa; Helms, Volkhard; Schwarz, Ulrich S

    2008-10-21

    We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric, and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c-cytochrome c peroxidase, and p53:MDM2. In each case, proteins are modeled either as spherical particles, as dipolar spheres, or as collection of several small beads with one dipole. Spherical reaction patches are placed on the model proteins according to the known experimental structures of the protein complexes. In the computer simulations, concentration is varied by changing box size. Encounter is defined as overlap of the reaction patches and the corresponding first passage times are recorded together with the number of unsuccessful contacts before encounter. We find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20 to 9000. For all three models, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. Electrostatic steering enhances association up to 50-fold. If diffusional encounter is dominant (p53:MDM2) or similarly important as electrostatic steering (barnase:barstar), then encounter rate decreases with decreasing patch radius. More detailed modeling of protein shapes decreases encounter rates by 5%-95%. Our study shows how generic principles of protein-protein association are modulated by molecular features of the systems under consideration. Moreover it allows us to assess different coarse-graining strategies for the future modeling of the dynamics of large protein complexes.

  1. Effect of the geometric phase on the dynamics of the hydrogen-exchange reaction.

    Science.gov (United States)

    Juanes-Marcos, Juan Carlos; Althorpe, Stuart C; Wrede, Eckart

    2007-01-28

    A recent puzzle in nonadiabatic quantum dynamics is that geometric phase (GP) effects are present in the state-to-state opacity functions of the hydrogen-exchange reaction, but cancel out in the state-to-state integral cross sections (ICSs). Here the authors explain this result by using topology to separate the scattering amplitudes into contributions from Feynman paths that loop in opposite senses around the conical intersection. The clockwise-looping paths pass over one transition state (1-TS) and scatter into positive deflection angles; the counterclockwise-looping paths pass over two transition states (2-TS) and scatter into negative deflection angles. The interference between the 1-TS and 2-TS paths thus integrates to a very small value, which cancels the GP effects in the ICS. Quasiclassical trajectory (QCT) calculations reproduce the scattering of the 1-TS and 2-TS paths into positive and negative deflection angles and show that the 2-TS paths describe a direct insertion mechanism. The inserting atom follows a highly constrained "S-bend" path, which allows it to avoid both the other atoms and the conical intersection and forces the product diatom to scatter into high rotational states. By contrast, the quantum 2-TS paths scatter into a mainly statistical distribution of rotational states, so that the quantum 2-TS total ICS is roughly twice the QCT ICS at 2.3 eV total energy. This suggests that the S-bend constraint is relaxed by tunneling in the quantum system. These findings on H+H(2) suggest that similar cancellations or reductions in GP effects are likely in many other reactions.

  2. Proton-transfer reaction dynamics and energetics in calcification and decalcification.

    Science.gov (United States)

    Suwa, Ryota; Hatta, Masayuki; Ichikawa, Kazuhiko

    2014-10-13

    CaCO3 -saturated saline waters at pH values below 8.5 are characterized by two stationary equilibrium states: reversible chemical calcification/decalcification associated with acid dissociation, Ca(2+) +HCO3 (-) ⇌CaCO3 +H(+) ; and reversible static physical precipitation/dissolution, Ca(2+) +CO3 (2-) ⇌CaCO3 . The former reversible reaction was determined using a strong base and acid titration. The saturation state described by the pH/PCO2 -independent solubility product, [Ca(2+) ][CO3 (2-) ], may not be observed at pH below 8.5 because [Ca(2+) ][CO3 (2-) ]/([Ca(2+) ][HCO3 (-) ]) ≪1. Since proton transfer dynamics controls all reversible acid dissociation reactions in saline waters, the concentrations of calcium ion and dissolved inorganic carbon (DIC) were expressed as a function of dual variables, pH and PCO2 . The negative impact of ocean acidification on marine calcifying organisms was confirmed by applying the experimental culture data of each PCO2 /pH-dependent coral polyp skeleton weight (Wskel) to the proton transfer idea. The skeleton formation of each coral polyp was performed in microspaces beneath its aboral ectoderm. This resulted in a decalcification of 14 weight %, a normalized CaCO3 saturation state Λ of 1.3 at PCO2 ≈400 ppm and pH ≈8.0, and serious decalcification of 45 % and Λ 2.5 at PCO2 ≈1000 ppm and pH ≈7.8.

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

    Science.gov (United States)

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

    2017-02-22

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

  4. Femtosecond Dynamics of Fundamental Reaction Processes in Liquids: Proton Transfer, Geminate Recombination, Isomerization and Vibrational Relaxation.

    Science.gov (United States)

    Schwartz, Benjamin Joel

    Femtosecond and picosecond transient absorption spectroscopy are used to probe several fundamental aspects of chemical reactivity in the condensed phase including proton transfer, germinate recombination, isomerization and vibrational relaxation. The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured for the first time, and the effects of external hydrogen-bonding interactions on the proton transfer are studied in detail. The proton transfer takes place in ~240 fsec in non-polar environments, but becomes faster than the instrumental resolution of 110 fsec in methanol solutions. A simple model is proposed to explain these results. The dynamics following photodissociation of CH _2I_2 and other small molecules provide the first direct observations of germinate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results also show that recombination yields but not rates depend on the molecular details of the solvent environment and suggest that recombination kinetics are dominated by a single collision with the surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. The data show no simple correlation between the hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes. This strongly implies that the isomerization of these systems does not provide a suitable testing ground 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 the 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

  5. Dynamic Influences of Non-Stationary Liquid Flows in Fluid Drives of Heavy Metallurgical Machines on System Dynamics and Reaction for Surroundings

    Directory of Open Access Journals (Sweden)

    Michalczyk J.

    2015-04-01

    Full Text Available The influence of liquids contained in hydraulic pipes of drives of heavy metallurgical machines, e.g. forging hammers and presses, on reduced mass and system dynamics and forces and moments of reaction for surroundings, was investigated in the paper.

  6. Dynamics of the gas-liquid interfacial reaction of O(1D) with a liquid hydrocarbon.

    Science.gov (United States)

    Waring, Carla; King, Kerry L; Costen, Matthew L; McKendrick, Kenneth G

    2011-06-30

    The dynamics of the gas-liquid interfacial reaction of the first electronically excited state of the oxygen atom, O((1)D), with the surface of a liquid hydrocarbon, squalane (C(30)H(62); 2,6,10,15,19,23-hexamethyltetracosane) has been studied experimentally. Translationally hot O((1)D) atoms were generated by 193 nm photolysis of a low pressure (nominally 1 mTorr) of N(2)O a short distance (mean = 6 mm) above a continually refreshed liquid squalane surface. Nascent OH (X(2)Π, v' = 0) reaction products were detected by laser-induced fluorescence (LIF) on the OH A(2)Σ(+)-X(2)Π (1,0) band at the same distance above the surface. The speed distribution of the recoiling OH was characterized by measuring the appearance profiles as a function of photolysis-probe delay for selected rotational levels, N'. The rotational (and, partially, fine-structure) state distributions were also measured by recording LIF excitation spectra at selected photolysis-probe delays. The OH v' = 0 rotational distribution is bimodal and can be empirically decomposed into near thermal (~300 K) and much hotter (~6000 K) Boltzmann-temperature components. There is a strong positive correlation between rotational excitation and translation energy. However, the colder rotational component still represents a significant fraction (~30%) of the fastest products, which have substantially superthermal speeds. We estimate an approximate upper limit of 3% for the quantum yield of OH per O((1)D) atom that collides with the surface. By comparison with established mechanisms for the corresponding reactions in the gas phase, we conclude that the rotationally and translationally hot products are formed via a nonstatistical insertion mechanism. The rotationally cold but translationally hot component is most likely produced by direct abstraction. Secondary collisions at the liquid surface of products of either of the previous two mechanisms are most likely responsible for the rotationally and translationally cold

  7. Development of a new molecular dynamics method for tribochemical reaction and its application to formation dynamics of MoS 2 tribofilm

    Science.gov (United States)

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

    2008-09-01

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

  8. The Reaction Dynamics of the Reactions Ba+CmH2m+1Br(m=1,2,3,4,5)

    Institute of Scientific and Technical Information of China (English)

    韩克利; 郑锡光; 张瑞勤; 孙本繁; 何国钟; 楼南泉

    1994-01-01

    The internal energy distributions of the nascent BaBr products formed in the reactions ofBa+BrR(R=CH3,C2H5,C3H7,C4H9,C5H11) under the single collision condition have been first studied bylaser-induced fluorescence method.With computer simulations of the experimental spectra,we obtained thevibrational distributions of the BaBr products,and found that the vibrational excitation and reaction cross-section increase with the number of the carbon atoms in the alkyl radical R.The quasitriatomic LEPS poten-tial of the Ba+CH3 reaction has been deduced reversely from the experimental results.The dynamics of thereactions Ba+BrR have been studied by the classical trajectory calculations based on the model LEPS poten-tials.It is concluded that the mass factor and the C-Br bond strength are the major factors affecting the rela-tionship between vibrational excitation and reaction cross-section with the number of the carbon atoms in thealkyl radical R.Furthermore,we obtained all the LEPS potentials of the reactive systems Ba+CmH2m+1 andconfirmed its reliability with ab initio calculations.

  9. Coriolis coupling effects in the dynamics of deep well reactions: application to the H(+) + D2 reaction.

    Science.gov (United States)

    Hankel, M

    2011-05-01

    We present exact and estimated quantum differential and integral cross sections as well as product state distributions for the title reaction. We employ a time-dependent wavepacket method including all Coriolis couplings and also an adapted code where the helicity quantum number and with this the Coriolis couplings have been truncated. Results from helicity truncated as well as helicity conserving (HC) calculation are presented. The HC calculations fail to reproduce the exact results due to the influence of the centrifugal barrier. While the truncated calculation overestimate the exact integral cross sections they reproduce the features of the integral cross section very well. We also find that the product rotational state distributions are well reproduced if the maximum helicity state is chosen carefully. The helicity truncated calculations fail to give a good approximation of differential cross sections.

  10. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions.

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  11. Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

    Science.gov (United States)

    Bellesia, Giovanni; Bales, Benjamin B.

    2016-10-01

    We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

  12. Revealing a double-inversion mechanism for the F⁻+CH₃Cl SN2 reaction.

    Science.gov (United States)

    Szabó, István; Czakó, Gábor

    2015-01-19

    Stereo-specific reaction mechanisms play a fundamental role in chemistry. The back-side attack inversion and front-side attack retention pathways of the bimolecular nucleophilic substitution (SN2) reactions are the textbook examples for stereo-specific chemical processes. Here, we report an accurate global analytic potential energy surface (PES) for the F(-)+CH₃Cl SN2 reaction, which describes both the back-side and front-side attack substitution pathways as well as the proton-abstraction channel. Moreover, reaction dynamics simulations on this surface reveal a novel double-inversion mechanism, in which an abstraction-induced inversion via a FH···CH₂Cl(-) transition state is followed by a second inversion via the usual [F···CH₃···Cl](-) saddle point, thereby opening a lower energy reaction path for retention than the front-side attack. Quasi-classical trajectory computations for the F(-)+CH₃Cl(ν1=0, 1) reactions show that the front-side attack is a fast direct, whereas the double inversion is a slow indirect process.

  13. Coherent-states dynamics of the H + + HF reaction at ELab = 30 eV: A complete electron nuclear dynamics investigation

    Science.gov (United States)

    Maiti, Buddhadev; Sadeghi, Raymond; Austin, Anthony; Morales, Jorge A.

    2007-11-01

    Results of a complete investigation of the H + + HF reaction at ELab = 30 eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END-CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of ℏ → 0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H-F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results.

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

    Science.gov (United States)

    Sen, Seema; Lake, Markus; Kroppen, Norman; Farber, Peter; Wilden, Johannes; Schaaf, Peter

    2017-02-01

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

  15. 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...

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

    Science.gov (United States)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

    2014-03-14

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

  17. 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.

  18. Investigating the phase-dependent photochemical reaction dynamics of chlorine dioxide using resonance Raman spectroscopy

    Science.gov (United States)

    Hayes, Sophia C.; Wallace, Paul M.; Bolinger, Josh C.; Reid, Philip J.

    Recent progress in understanding the phase-dependent reactivity demonstrated by halooxides is outlined. Specifically, resonance Raman intensity analysis (RRIA) and time-resolved resonance Raman (TRRR) studies of chlorine dioxide (OClO) photochemistry in solution are presented. Using RRIA, it has been determined that the excited-state structural evolution that occurs along the asymmetric-stretch coordinate in the gas phase is restricted in solution. The absence of evolution along this coordinate results in the preservation of groundstate symmetry in the excited state. The role of symmetry in defining the reaction coordinate and the solvent-solute interactions responsible for modification of the excited-state potential energy surface are discussed. TRRR studies are presented which demonstrate that geminate recombination of the primary photoproducts resulting in the reformation of ground-state OClO is a central feature of OClO photochemistry in solution. These studies also demonstrate that a fraction of photoexcited OClO undergoes photoisomerization to form ClOO, with the ground-state thermal decomposition of this species resulting in Cl production on the subnanosecond timescale. Finally, time-resolved anti-Stokes experiments are presented which demonstrate that the OClO vibrational-relaxation dynamics are solvent dependent. The current picture of OClO photochemistry derived from these studies is discussed, and future directions for study are outlined.

  19. 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.

  20. The unified equation for the evaluation of first order reactions in dynamic electrophoresis.

    Science.gov (United States)

    Trapp, Oliver

    2006-02-01

    The unified equation was validated for first order reactions in dynamic CE with a data set of 31 250 elution profiles. Comparison with the results from conventional iterative computer simulation revealed that the unified equation is superior in terms of success rate and precision. The unified equation was applied to determine the cis-trans isomerization rate constants of the angiotensin converting enzyme inhibitor captopril. The separation of the rotational cis-trans isomeric drug has been performed in an aqueous 66 mM citric acid/Tris buffer at pH 3.0 in a 50 cm polyacrylamide-coated fused-silica capillary. Interconversion profiles featuring pronounced plateau formation and peak broadening were observed. Activation parameters DeltaH not equal and DeltaS not equal were obtained from temperature-dependent measurements between 10 and 25 degrees C in 2.5 K steps. From the activation parameters the isomerization barriers of captopril at 37 degrees C under acidic conditions were calculated to be DeltaG not equal trans-->cis=90.6 kJ/mol and DeltaG not equal cis-->trans=84.6 kJ/mol. By comparison of the kinetic data with the results obtained under basic conditions (pH 9.3) a mechanism of isomerization could be proposed.

  1. Protein-protein interactions visualized by bimolecular fluorescence complementation in tobacco protoplasts and leaves.

    Science.gov (United States)

    Schweiger, Regina; Schwenkert, Serena

    2014-03-09

    Many proteins interact transiently with other proteins or are integrated into multi-protein complexes to perform their biological function. Bimolecular fluorescence complementation (BiFC) is an in vivo method to monitor such interactions in plant cells. In the presented protocol the investigated candidate proteins are fused to complementary halves of fluorescent proteins and the respective constructs are introduced into plant cells via agrobacterium-mediated transformation. Subsequently, the proteins are transiently expressed in tobacco leaves and the restored fluorescent signals can be detected with a confocal laser scanning microscope in the intact cells. This allows not only visualization of the interaction itself, but also the subcellular localization of the protein complexes can be determined. For this purpose, marker genes containing a fluorescent tag can be coexpressed along with the BiFC constructs, thus visualizing cellular structures such as the endoplasmic reticulum, mitochondria, the Golgi apparatus or the plasma membrane. The fluorescent signal can be monitored either directly in epidermal leaf cells or in single protoplasts, which can be easily isolated from the transformed tobacco leaves. BiFC is ideally suited to study protein-protein interactions in their natural surroundings within the living cell. However, it has to be considered that the expression has to be driven by strong promoters and that the interaction partners are modified due to fusion of the relatively large fluorescence tags, which might interfere with the interaction mechanism. Nevertheless, BiFC is an excellent complementary approach to other commonly applied methods investigating protein-protein interactions, such as coimmunoprecipitation, in vitro pull-down assays or yeast-two-hybrid experiments.

  2. Visualization of molecular interactions using bimolecular fluorescence complementation analysis: characteristics of protein fragment complementation.

    Science.gov (United States)

    Kerppola, Tom K

    2009-10-01

    Investigations of the molecular processes that sustain life must include studies of these processes in their normal cellular environment. The bimolecular fluorescence complementation (BiFC) assay provides an approach for the visualization of protein interactions and modifications in living cells. This assay is based on the facilitated association of complementary fragments of a fluorescent protein that are fused to interaction partners. Complex formation by the interaction partners tethers the fluorescent protein fragments in proximity to each other, which can facilitate their association. The BiFC assay enables sensitive visualization of protein complexes with high spatial resolution. The temporal resolution of BiFC analysis is limited by the time required for fluorophore formation, as well as the stabilization of complexes by association of the fluorescent protein fragments. Many modifications and enhancements to the BiFC assay have been developed. The multicolor BiFC assay enables simultaneous visualization of multiple protein complexes in the same cell, and can be used to investigate competition among mutually exclusive interaction partners for complex formation in cells. The ubiquitin-mediated fluorescence complementation (UbFC) assay enables visualization of covalent ubiquitin family peptide conjugation to substrate proteins in cells. The BiFC assay can also be used to visualize protein binding to specific chromatin domains, as well as other molecular scaffolds in cells. BiFC analysis therefore provides a powerful approach for the visualization of a variety of processes that affect molecular proximity in living cells. The visualization of macromolecular interactions and modifications is of great importance owing to the central roles of proteins, nucleic acids and other macromolecular complexes in the regulation of cellular functions. This tutorial review describes the BiFC assay, and discusses the advantages and disadvantages of this experimental approach

  3. New GATEWAY vectors for High Throughput Analyses of Protein-Protein Interactions by Bimolecular Fluorescence Complementation

    Institute of Scientific and Technical Information of China (English)

    Christian Gehl; Rainer Waadt; J(o)rg Kudla; Ralf-R. Mendel; Robert Hansch

    2009-01-01

    Complex protein interaction networks constitute plant metabolic and signaling systems. Bimolecular fluores-cence complementation (BiFC) is a suitable technique to investigate the formation of protein complexes and the locali-zation of protein-protein interactions in planta. However, the generation of large plasmid collections to facilitate the exploration of complex interaction networks is often limited by the need for conventional cloning techniques. Here, we report the implementation of a GATEWAY vector system enabling large-scale combination and investigation of can-didate proteins in BiFC studies. We describe a set of 12 GATEWAY-compatible BiFC vectors that efficiently permit the com-bination of candidate protein pairs with every possible N-or C-terminal sub-fragment of S(CFP)3A or Venus, respectively, and enable the performance of multicolor BiFC (mcBiFC). We used proteins of the plant molybdenum metabolism, in that more than 20 potentially interacting proteins are assumed to form the cellular molybdenum network, as a case study to establish the functionality of the new vectors. Using these vectors, we report the formation of the molybdopterin synthase complex by interaction of Arabidopsis proteins Cnx6 and Cnx7 detected by BiFC as well as the simultaneous formation of Cn×6/Cn×6 and Cn×6/Cn×7 complexes revealed by mcBiFC. Consequently, these GATEWAY-based BiFC vector systems should significantly facilitate the large-scale investigation of complex regulatory networks in plant cells.

  4. Detection of protein-protein interactions in plants using bimolecular fluorescence complementation.

    Science.gov (United States)

    Bracha-Drori, Keren; Shichrur, Keren; Katz, Aviva; Oliva, Moran; Angelovici, Ruthie; Yalovsky, Shaul; Ohad, Nir

    2004-11-01

    Protein function is often mediated via formation of stable or transient complexes. Here we report the determination of protein-protein interactions in plants using bimolecular fluorescence complementation (BiFC). The yellow fluorescent protein (YFP) was split into two non-overlapping N-terminal (YN) and C-terminal (YC) fragments. Each fragment was cloned in-frame to a gene of interest, enabling expression of fusion proteins. To demonstrate the feasibility of BiFC in plants, two pairs of interacting proteins were utilized: (i) the alpha and beta subunits of the Arabidopsis protein farnesyltransferase (PFT), and (ii) the polycomb proteins, FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) and MEDEA (MEA). Members of each protein pair were transiently co-expressed in leaf epidermal cells of Nicotiana benthamiana or Arabidopsis. Reconstitution of a fluorescing YFP chromophore occurred only when the inquest proteins interacted. No fluorescence was detected following co-expression of free non-fused YN and YC or non-interacting protein pairs. Yellow fluorescence was detected in the cytoplasm of cells that expressed PFT alpha and beta subunits, or in nuclei and cytoplasm of cells that expressed FIE and MEA. In vivo measurements of fluorescence spectra emitted from reconstituted YFPs were identical to that of a non-split YFP, confirming reconstitution of the chromophore. Expression of the inquest proteins was verified by immunoblot analysis using monoclonal antibodies directed against tags within the hybrid proteins. In addition, protein interactions were confirmed by immunoprecipitations. These results demonstrate that plant BiFC is a simple, reliable and relatively fast method for determining protein-protein interactions in plants.

  5. Manifestation of macroscopic correlations in elementary reaction kinetics. I. Irreversible reaction A +A→product

    Science.gov (United States)

    Doktorov, Alexander B.; Kipriyanov, Alexander A.; Kipriyanov, Alexey A.

    2010-05-01

    Using an modern many-particle method for the derivation of non-Markovian binary kinetic equations, we have treated theoretically the applicability of the encounter theory (ET) (the prototype of the collision theory) concepts to the widely known diffusion assisted irreversible bulk reaction A +A→product (for example, radical reaction) in dilute solutions. The method shows that the agreement with the ET is observed when the familiar integral ET is employed which in this method is just a step in the derivation of kinetic equations. It allows for two-particle correlations only, but fails to take account of correlation of reactant simultaneously with the partner of the encounter and the reactant in the bulk. However, the next step leading to the modified ET under transformation of equations to the regular form both extends the time range of the applicability of ET rate equation (as it was for reactions proceeding with one of the reactants in excess), and gives the equation of the generalized ET. In full agreement with physical considerations, this theory reveals macroscopic correlations induced by the encounters in the reservoir of free walks. This means that the encounters of reactants in solution are correlated on a rather large time interval of the reaction. Though any nonstationary (non-Markovian) effects manifest themselves rather weakly in the kinetics of the bimolecular reaction in question, just the existence of the revealed macroscopic correlations in the binary theory is of primary importance. In particular, it means that the well-known phenomena which are generally considered to be associated solely with correlation of particles on the encounter (for example, chemically induced dynamic nuclear polarization) may be induced by correlation in the reservoir of free random walks of radicals in solution.

  6. Manifestation of macroscopic correlations in elementary reaction kinetics. I. Irreversible reaction A+A-->product.

    Science.gov (United States)

    Doktorov, Alexander B; Kipriyanov, Alexander A; Kipriyanov, Alexey A

    2010-05-28

    Using an modern many-particle method for the derivation of non-Markovian binary kinetic equations, we have treated theoretically the applicability of the encounter theory (ET) (the prototype of the collision theory) concepts to the widely known diffusion assisted irreversible bulk reaction A+A-->product (for example, radical reaction) in dilute solutions. The method shows that the agreement with the ET is observed when the familiar integral ET is employed which in this method is just a step in the derivation of kinetic equations. It allows for two-particle correlations only, but fails to take account of correlation of reactant simultaneously with the partner of the encounter and the reactant in the bulk. However, the next step leading to the modified ET under transformation of equations to the regular form both extends the time range of the applicability of ET rate equation (as it was for reactions proceeding with one of the reactants in excess), and gives the equation of the generalized ET. In full agreement with physical considerations, this theory reveals macroscopic correlations induced by the encounters in the reservoir of free walks. This means that the encounters of reactants in solution are correlated on a rather large time interval of the reaction. Though any nonstationary (non-Markovian) effects manifest themselves rather weakly in the kinetics of the bimolecular reaction in question, just the existence of the revealed macroscopic correlations in the binary theory is of primary importance. In particular, it means that the well-known phenomena which are generally considered to be associated solely with correlation of particles on the encounter (for example, chemically induced dynamic nuclear polarization) may be induced by correlation in the reservoir of free random walks of radicals in solution.

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

    Science.gov (United States)

    Valero, Rosendo; Truhlar, Donald G

    2007-09-06

    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

  8. 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...

  9. Direct dynamics simulations of the product channels and atomistic mechanisms for the OH(-) + CH3I reaction. Comparison with experiment.

    Science.gov (United States)

    Xie, Jing; Sun, Rui; Siebert, Matthew R; Otto, Rico; Wester, Roland; Hase, William L

    2013-08-15

    Electronic structure and direct dynamics calculations were used to study the potential energy surface and atomic-level dynamics for the OH(-) + CH3I reactions. The results are compared with crossed molecular beam, ion imaging experiments. The DFT/B97-1/ECP/d level of theory gives reaction energetics in good agreement with experiment and higher level calculations, and it was used for the direct dynamics simulations that were performed for reactant collision energies of 2.0, 1.0, 0.5, and 0.05 eV. Five different pathways are observed in the simulations, forming CH3OH + I(-), CH2I(-) + H2O, CH2 + I(-) + H2O, IOH(-) + CH3, and [CH3--I--OH](-). The SN2 first pathway and the proton-transfer second pathway dominate the reaction dynamics. Though the reaction energetics favor the SN2 pathway, the proton-transfer pathway is more important except for the lowest collision energy. The relative ion yield determined from the simulations is in overall good agreement with experiment. Both the SN2 and proton-transfer pathways occur via direct rebound, direct stripping, and indirect mechanisms. Except for the highest collision energy, 70-90% of the indirect reaction for the SN2 pathway occurs via formation of the hydrogen-bonded OH(-)---HCH2I prereaction complex. For the proton-transfer pathway the indirect reaction is more complex with the roundabout mechanism and formation of the OH(-)---HCH2I and CH2I(-)---HOH complexes contributing to the reaction. The majority of the SN2 reaction is direct at 2.0, 1.0, and 0.5 eV, dominated by stripping. At 0.05 eV the two direct mechanisms and the indirect mechanisms have nearly equal contributions. The majority of the proton-transfer pathway is direct stripping at 2.0, 1.0, and 0.5 eV, but the majority of the reaction is indirect at 0.05 eV. The product relative translational energy distributions are in good agreement with experiment for both the SN2 and proton-transfer pathways. For both, direct reaction preferentially transfers the product

  10. 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.

  11. 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.

  12. SN2 and SN2' reaction dynamics of cyclopropenyl chloride with halide ion : A direct ab initio molecular dynamics (MD) study

    OpenAIRE

    Tachikawa, Hiroto

    2005-01-01

    Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F–) (F– + (CH)3Cl → F(CH)3 + Cl–) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F– to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom lead...

  13. 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.

  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. Radiation reaction dynamics in an electromagnetic wave and constant electric field

    Science.gov (United States)

    Atlee Jackson, E.

    1984-05-01

    The relativistic motion of a charged particle is studied when it is acted on simultaneously by a constant electric field and a plane electromagnetic wave, propagating in the direction of the electric field (x axis). The dynamics includes the radiation reaction (self-force) on the particle through a standard approximation of the Lorentz-Dirac equation. The interest is to determine the result of the competition between the average acceleration due to the electromagnetic wave (``radiation pressure'') and the acceleration due to the constant force of the static field. Each of these actions alone of course produce an unbounded particle energy asymptotically in time. However, it is proved first that, when the ``forces'' are in opposite directions, the particle can never accelerate (on the average) indefinitely in the x direction, regardless how weak the electric field (E0) is compared to the amplitude of the wave (A). It is then proved that all solutions converge to a region of zero area in a suitable velocity phase space and, if there exists a periodic solution [in the phase ξ=ω (t-x/c)] in a specified region of this phase space, then all solutions must converge to this solution asymptotically (ξ→+∞). In the case when (E0A2/ω2) has a specified bound (ω: wave frequency), an iterative method is developed which explicitly yields such a periodic solution, showing that the energy remains bounded. The direction of the average drift is determined in terms of (A,E0,ω). When the parameter (E0A2/ω2) is above this bound, a combination of numerical and analytic results are obtained which indicate that this periodic solution persists. These results indicate that all motions tend to states with bounded energy, regardless of the field strengths.

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

    Science.gov (United States)

    Pagano, Jason John

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

  17. 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.

  18. Visualization and quantification of APP intracellular domain-mediated nuclear signaling by bimolecular fluorescence complementation.

    Directory of Open Access Journals (Sweden)

    Florian Riese

    Full Text Available BACKGROUND: The amyloid precursor protein (APP intracellular domain (AICD is released from full-length APP upon sequential cleavage by either α- or β-secretase followed by γ-secretase. Together with the adaptor protein Fe65 and the histone acetyltransferase Tip60, AICD forms nuclear multiprotein complexes (AFT complexes that function in transcriptional regulation. OBJECTIVE: To develop a medium-throughput machine-based assay for visualization and quantification of AFT complex formation in cultured cells. METHODS: We used cotransfection of bimolecular fluorescence complementation (BiFC fusion constructs of APP and Tip60 for analysis of subcellular localization by confocal microscopy and quantification by flow cytometry (FC. RESULTS: Our novel BiFC-constructs show a nuclear localization of AFT complexes that is identical to conventional fluorescence-tagged constructs. Production of the BiFC signal is dependent on the adaptor protein Fe65 resulting in fluorescence complementation only after Fe65-mediated nuclear translocation of AICD and interaction with Tip60. We applied the AFT-BiFC system to show that the Swedish APP familial Alzheimer's disease mutation increases AFT complex formation, consistent with the notion that AICD mediated nuclear signaling mainly occurs following APP processing through the amyloidogenic β-secretase pathway. Next, we studied the impact of posttranslational modifications of AICD on AFT complex formation. Mutation of tyrosine 682 in the YENPTY motif of AICD to phenylalanine prevents phosphorylation resulting in increased nuclear AFT-BiFC signals. This is consistent with the negative impact of tyrosine phosphorylation on Fe65 binding to AICD. Finally, we studied the effect of oxidative stress. Our data shows that oxidative stress, at a level that also causes cell death, leads to a reduction in AFT-BiFC signals. CONCLUSION: We established a new method for visualization and FC quantification of the interaction between

  19. Quantum dynamics of the Walden inversion reaction Cl - +CH3Cl --> ClCH3+Cl -

    Science.gov (United States)

    Clary, David C.; Palma, Juliana

    1997-01-01

    Quantum scattering calculations on the SN2 reaction Cl-+CH3Cl→ClCH3+Cl- are reported. The rotating bond approximation (RBA) has been adapted so that three degrees of freedom including the C-Cl stretching vibration and the CH3 umbrella mode are treated explicitly. The calculations have been done with minor modifications of a potential due to Vande Linde and Hase. It is found that initial excitation of the C-Cl vibration has a large effect on the reaction probabilities, while excitation of the CH3 umbrella vibration is less significant. The reaction is dominated by scattering resonances with lifetimes ranging from 0.1 to 10 ps. It is found that the length of the C-Cl bond at the transition state of the reaction has a particularly pronounced effect on the reaction probabilities. The magnitude of the quantum reaction probabilities compares quite well with those calculated using the quasiclassical trajectory method.

  20. Untangling the Energetics and Dynamics of Boron Monoxide Radical Reactions (11BO; X2Sigma+)

    Science.gov (United States)

    2015-04-15

    Crossed Beam Reaction of Boron Monoxide with Benzene (P6) Organyl oxoboranes (RBO) are valuable reagents in organic synthesis due to their role in... silicon nitride (SiN), and ethynyl (C2H), and their reactions with simple prototype hydrocarbons acetylene (C2H2) and ethylene (C2H4). The fact...Reaction products of isoelectronic boron monoxide (BO), cyano (CN), ethynyl (CCH), and silicon nitride (SiN) radicals with acetylene and ethylene. 3.10

  1. 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.

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

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-01

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

  3. Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates

    Science.gov (United States)

    García-Meseguer, Rafael; Martí, Sergio; Ruiz-Pernía, J. Javier; Moliner, Vicent; Tuñón, Iñaki

    2013-07-01

    Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We show that the structure of the protein provides an adequate environment for the progress of the reaction, although a certain degree of flexibility is needed to attain the full catalytic effect. However, these motions do not introduce significant dynamical corrections to the rate constant and can be described as equilibrium fluctuations.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    Dubey R.

    2016-01-01

    Full Text Available 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.

  10. 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.

  11. 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...

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    , represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis–Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action...... 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......., convenience kinetics, lin-log and power-law). Using the mechanistic model for Escherichia coli central carbon metabolism as a benchmark, we investigate the alternative modeling approaches through comparative simulations analyses. The good dynamic behavior and the powerful predictive capabilities obtained...

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

    Science.gov (United States)

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

    2012-02-16

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

  14. A full-dimensional quantum dynamics study of the mode specificity in the H + HOD abstraction reaction

    Science.gov (United States)

    Fu, Bina; Zhang, Dong H.

    2015-02-01

    We employ the initial state-selected time-dependent wave packet approach to an atom-triatom reaction to study the H + HOD → OH + HD/OD + H2 reaction without the centrifugal sudden approximation, based on an accurate potential energy surface which was recently developed by neural network fitting to high level ab initio energy points. The total reaction probabilities and integral cross sections, which are the exact coupled-channel results, are calculated for the HOD reactant initially in the ground and several vibrationally excited states, including the bending excited state, OD stretching excited states, OH stretching excited states, and combined excitations of them. The reactivity enhancements from different initial states of HOD are presented, which feature strong bond-selective effects of the reaction dynamics. The current results for the product branching ratios, reactivity enhancements, and relative cross sections are largely improved over the previous calculations, in quantitatively good agreement with experiment. The thermal rate constant for the title reaction and the contributions from individual vibrational states of HOD are also obtained.

  15. The Unimolecular Decomposition and H Abstraction Reactions by HO and HO2 from n-Butanol

    Science.gov (United States)

    Moc, Jerzy; Black, Gráinne; Simmie, John M.; Curran, Henry J.

    2009-08-01

    By using correlated ab initio (MP2, CCSD(T)) and multi-level (G3, CBS-QB3) methods we have studied unimolecular and bimolecular reactions of n-butanol in the gas phase. The specific processes investigated include H2O elimination and hydrogen abstraction by the hydroxy (HO) and hydroperoxy (HO2) radicals from this alcohol.

  16. Theoretical Study on the Dynamics of the Reaction of HNO((1)A') with HO2((2)A″).

    Science.gov (United States)

    Mousavipour, S Hosein; Asemani, S Somayeh

    2015-06-04

    We used stochastic one-dimensional chemical master equation (CME) simulation to gain insight into the dynamics of the reaction of HNO((1)A') with HO2((2)A″). The reaction takes place over a multiwell, multichannel potential energy surface that is based on the computations at the CBS-QB3 level of theory. The calculated multipath potential energy surface consists of three potential wells and three van der Waals complexes. In solving the master equation, the Lennard-Jones potential is used to model the collision between the collider gases. The fractional population of different intermediates and products in the early stages of the reaction is examined to determine the role of the energized intermediates and van der Waals complexes on the kinetics of the title reaction. The major products of the title reaction at lower temperatures are OH, HNO2, HNOH, and O2(X(3)Σg(-)). The temperature- and pressure-dependence of the reaction over a wide range of temperature (300-3000 K) and pressure (0.1-2000 Torr) are studied. No sign of pressure dependence was being observed for the title reaction over the stated range of pressure. The calculated rate constants from the CME simulation are compared with those obtained from the RRKM-SSA method that is based on strong collision assumption. Our results indicate that the strong collision assumption increases the calculated rate constant for the formation of the main products (HNO2 + OH) by a factor of 2 at 300 K and 1 atm pressure, compared to the results of CME simulation, although the results are in good agreement at higher temperatures.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schnell, Sondre K. [Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720 (United States); Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Skorpa, Ragnhild; Bedeaux, Dick [Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Kjelstrup, Signe [Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim (Norway); Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Vlugt, Thijs J. H. [Process and Energy Laboratory, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft (Netherlands); Simon, Jean-Marc, E-mail: jmsimon@u-bourgogne.fr [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS-Université de Bourgogne, 9, av. Savary, 21000 Dijon (France)

    2014-10-14

    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.

  18. Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

    Science.gov (United States)

    Xie, Jing; Kohale, Swapnil C; Hase, William L; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A

    2013-12-27

    Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of

  19. Mapping the dynamics of adverse drug reactions in subsequent time periods using INDSCAL

    NARCIS (Netherlands)

    Rikken, F.; Kiers, H.A.L.; Vos, R.

    1995-01-01

    In this study we have focused on the problem of mapping the dynamics of co-word-matrices from subsequent time periods. Methods for mapping dynamics are important for following trends in research. We have explored the possibilities of a three way multidimensional scaling method, INDSCAL. We are espec

  20. Coherent-states dynamics of the H{sup +} + HF reaction at E{sub Lab} = 30 eV: A complete electron nuclear dynamics investigation

    Energy Technology Data Exchange (ETDEWEB)

    Maiti, Buddhadev [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States); Sadeghi, Raymond [Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249-0698 (United States); Austin, Anthony [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States); Morales, Jorge A. [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, TX 79409-1061 (United States)], E-mail: jorge.morales@ttu.edu

    2007-11-09

    Results of a complete investigation of the H{sup +} + HF reaction at E{sub Lab} = 30 eV with the electron nuclear dynamics (END) and the coherent-states dynamics (CSD) theories are herein presented. Current END-CSD methodology employs frozen Gaussian wave packet in the semiclassical limit of h {yields} 0 for the nuclei, and a single-determinantal Thouless coherent state (CS) for the electrons. The simulated 400 CS trajectories from five independent HF target orientations provide a complete description of the reactive processes in this system, including: non-charge-transfer scattering (NCTS), charge-transfer scattering (CTS), hydrogen fluoride dissociation (H-F D), and hydrogen rearrangement (HR). Several aspects of the reactions dynamics, such as mechanistic details and rainbow angles effects, are discussed. Differential and integral cross sections are evaluated via a novel CS formulation of those properties in conjunction with semiclassical techniques. The calculated total differential cross section shows an excellent agreement with available experimental results.

  1. Dynamics of surface-migration: Electron-induced reaction of 1,2-dihaloethanes on Si(100)

    Science.gov (United States)

    Huang, Kai; MacLean, Oliver; Guo, Si Yue; McNab, Iain R.; Ning, Zhanyu; Wang, Chen-Guang; Ji, Wei; Polanyi, John C.

    2016-10-01

    Scanning Tunneling Microscopy was used to investigate the electron-induced reaction of 1,2-dibromoethane (DBE) and 1,2-dichloroethane (DCE) on Si(100).We observed a long-lived physisorbed molecular state of DBE at 75 K and of DCE at 110 K. As a result we were able to characterize by experiment and also by ab initio theory the dynamics of ethylene production in the electron-induced surface-reaction of these physisorbed species. For both DBE and DCE the ethylene product was observed to migrate across the surface. In the case of DBE the recoil of the ethylene favored the silicon rows, migrating by an average distance of 22 Å, and up to 100 Å. Trajectory calculations were performed for this electron-induced reaction, using an 'Impulsive Two-State' model involving an anionic excited state and a neutral ground-potential. The model agreed with experiment in reproducing both migration and desorption of the ethylene product. The computed migration exhibited a 'ballistic' launch and subsequent 'bounces', thereby accounting for the observed long-range migratory dynamics.

  2. Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study.

    Science.gov (United States)

    Tachikawa, Hiroto

    2006-01-12

    Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

  3. Revealing structural dynamics in catalytic reactions using ultrafast transient x-ray absorption spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Chen, L. X.; Liu, D.; Chemical Sciences and Engineering Division; Northwestern Univ.

    2009-03-02

    Progression of a typical heterogeneous catalytic process as a function of a reaction parameter such as temperature can often be segmented, according to Fig. 1. Reactants first bind to active sites to form reaction intermediates with increases in temperature and kinetic energy (Region I). Further temperature increase leads to a full 'light-off' of the catalytic conversion and the reaction is dominated by the intra-particulate diffusion (Region II). The characteristic 'light-off' temperature at the boundary of region I and II often defines the activity of the catalyst. At even higher temperature enters the bulk diffusion region (III), where the catalytic reaction is limited mainly by mass transport between different phases. Significant efforts in practical catalyst design involve improving catalytic activities in the kinetic region (I) and reducing the 'light-off' temperature. Reaction rates at the kinetic region are defined by potential saddle points on top of which a series of 'transitional state' complexes are formed between the active sites and the adsorbed reactants (Fig. 2). Capturing structures of the 'transition state complexes' from the active center's perspective will provide ultimate understanding of catalytic mechanisms and insight into new catalyst design. Experimentally, however, it is a very challenging proposition.

  4. 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.

  5. Model reduction and parameter estimation of non-linear dynamical biochemical reaction networks.

    Science.gov (United States)

    Sun, Xiaodian; Medvedovic, Mario

    2016-02-01

    Parameter estimation for high dimension complex dynamic system is a hot topic. However, the current statistical model and inference approach is known as a large p small n problem. How to reduce the dimension of the dynamic model and improve the accuracy of estimation is more important. To address this question, the authors take some known parameters and structure of system as priori knowledge and incorporate it into dynamic model. At the same time, they decompose the whole dynamic model into subset network modules, based on different modules, and then they apply different estimation approaches. This technique is called Rao-Blackwellised particle filters decomposition methods. To evaluate the performance of this method, the authors apply it to synthetic data generated from repressilator model and experimental data of the JAK-STAT pathway, but this method can be easily extended to large-scale cases.

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

    Science.gov (United States)

    Liu, Na; Yang, Minghui

    2015-10-01

    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.

  7. Dynamics of reaction-diffusion patterns controlled by asymmetric nonlocal coupling as a limiting case of differential advection.

    Science.gov (United States)

    Siebert, Julien; Alonso, Sergio; Bär, Markus; Schöll, Eckehard

    2014-05-01

    A one-component bistable reaction-diffusion system with asymmetric nonlocal coupling is derived as a limiting case of a two-component activator-inhibitor reaction-diffusion model with differential advection. The effects of asymmetric nonlocal couplings in such a bistable reaction-diffusion system are then compared to the previously studied case of a system with symmetric nonlocal coupling. We carry out a linear stability analysis of the spatially homogeneous steady states of the model and numerical simulations of the model to show how the asymmetric nonlocal coupling controls and alters the steady states and the front dynamics in the system. In a second step, a third fast reaction-diffusion equation is included which induces the formation of more complex patterns. A linear stability analysis predicts traveling waves for asymmetric nonlocal coupling, in contrast to a stationary Turing patterns for a system with symmetric nonlocal coupling. These findings are verified by direct numerical integration of the full equations with nonlocal coupling.

  8. Applications of dynamic nuclear polarization to the study of reactions and reagents in organic and biomolecular chemistry.

    Science.gov (United States)

    Hilty, Christian; Bowen, Sean

    2010-08-07

    Nuclear Magnetic Resonance (NMR) is an important spectroscopic tool for the identification and structural characterization of molecules in chemistry and biochemistry. The most significant limitation of NMR compared to other spectroscopies is its relatively low sensitivity, which thus often requires long measurement times or large amounts of sample. A way of increasing sensitivity of single scan NMR spectra by several orders of magnitude is through hyperpolarization of nuclear spins. Dynamic nuclear polarization allows hyperpolarization of most spins in small molecules encountered in chemistry and biochemistry. NMR spectra of small amounts of samples from natural source, or from chemical synthesis can readily be acquired. Perhaps more interestingly, the availability of the entire hyperpolarized NMR signal in one single scan allows the measurement of transient processes in real time, if applied together with a stopped-flow technique. Through observation of chemical shift, different reactant and product species can be distinguished, and kinetics and mechanisms, for example in enzyme catalyzed reactions, can be elucidated. Real-time hyperpolarization-enhanced NMR is uniquely amenable to correlating atomic positions not only through space, but also over time between reactant and product species. Such correlations carry mechanistic information about a reaction, and can prove reaction pathways. Applications of this technique are emerging in different areas of chemistry concerned with rapid reactions, including not only enzymatic processes, but also chemical catalysis and protein folding.

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

    NARCIS (Netherlands)

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

    1997-01-01

    The adduct of the Diels-Alder reaction of nitrosobenzene with cyclopentadiene is not stable in solution. The equilibrium constant for the reaction depends strongly on the medium and water induces a spectacular shift to the adduct. Comparison with the bimolecular addition of nitrosobenzene to 1,3-cyc

  10. 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.

  11. 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.

  12. Modeling and finite difference numerical analysis of reaction-diffusion dynamics in a microreactor.

    Science.gov (United States)

    Plazl, Igor; Lakner, Mitja

    2010-03-01

    A theoretical description with numerical experiments and analysis of the reaction-diffusion processes of homogeneous and non-homogeneous reactions in a microreactor is presented considering the velocity profile for laminar flows of miscible and immiscible fluids in a microchannel at steady-state conditions. A Mathematical model in dimensionless form, containing convection, diffusion, and reaction terms are developed to analyze and to forecast the reactor performance. To examine the performance of different types of reactors, the outlet concentrations for the plug-flow reactor (PFR), and the continuous stirred-tank reactor (CSTR) are also calculated for the case of an irreversible homogeneous reaction of two components. The comparison of efficiency between ideal conventional macroscale reactors and the microreactor is presented for a wide range of operating conditions, expressed as different Pe numbers (0.01 < Pe < 10). The numerical procedure of complex non-linear systems based on an implicit finite-difference method improved by non-equidistant differences is proposed.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  14. Systematic Studies of the Three-nucleon System Dynamics in the Deutron–Proton Breakup Reaction

    NARCIS (Netherlands)

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

    2013-01-01

    Precise and large sets of data for cross section, vector and tensor analyzing powers for the H-1((d) over right arrow ,pp)n breakup reaction were obtained in experiments carried out at KVI Groningen and FZ-Julich at deuteron beam energies of 100 MeV, 13 MeV and 160 MeV (cross sections only). These p

  15. Weakly nonlinear dynamics in reaction-diffusion systems with Levy flights

    Energy Technology Data Exchange (ETDEWEB)

    Nec, Y; Nepomnyashchy, A A [Department of Mathematics, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Golovin, A A [Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208 (United States)], E-mail: flyby@techunix.technion.ac.il

    2008-12-15

    Reaction-diffusion equations with a fractional Laplacian are reduced near a long wave Hopf bifurcation. The obtained amplitude equation is shown to be the complex Ginzburg-Landau equation with a fractional Laplacian. Some of the properties of the normal complex Ginzburg-Landau equation are generalized for the fractional analogue. In particular, an analogue of the Kuramoto-Sivashinsky equation is derived.

  16. 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.

  17. Analytical Solution of Nonlinear Dynamics of a Self-Igniting Reaction-Diffusion System Using Modified Adomian Decomposition Method

    Directory of Open Access Journals (Sweden)

    Felicia Shirly Peace

    2014-01-01

    Full Text Available A mathematical model of the dynamics of the self-ignition of a reaction-diffusion system is studied in this paper. An approximate analytical method (modified Adomian decomposition method is used to solve nonlinear differential equations under steady-state condition. Analytical expressions for concentrations of the gas reactant and the temperature have been derived for Lewis number (Le and parameters β, γ, and ϕ2. Furthermore, in this work, the numerical simulation of the problem is also reported using MATLAB program. An agreement between analytical and numerical results is noted.

  18. 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.

  19. Determination of total selenium and Se-77 in isotopically enriched human samples by ICP-dynamic reaction cell-MS

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt; Bügel, Susanne H.;

    2003-01-01

    This paper describes an analytical method for the simultaneous quantitative determination of total selenium (Se) and Se-77 in isotopically enriched human plasma, urine and faeces by inductively coupled plasma- dynamic reaction cell- mass spectrometry ( ICP- DRC- MS). The samples originated from...... and the digested faecal samples were diluted using an aqueous diluent containing 0.5% Triton X-100, 2% nitric acid and 3% methanol. Selenium was detected as Se-76, Se-77 and Se-80 by ICP- DRC- MS. Selenium originating from the natural isotope abundance yeast and other selenium sources from the diet was determined...

  20. 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.

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

    Science.gov (United States)

    Slobodyan, O. V.; Danielson, E. L.; Moench, S. J.; Dinser, J. A.; Gutierrez, M.; Vanden Bout, D. A.; Holliday, B. J.; Dodabalapur, A.

    2015-06-01

    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.

  2. Communication: Energy transfer and reaction dynamics for DCl scattering on Au(111): An ab initio molecular dynamics study

    Science.gov (United States)

    Kolb, Brian; Guo, Hua

    2016-07-01

    Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.

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

    CERN Document Server

    Balasi, K G; Martínez-Pinedo, G

    2015-01-01

    The description of nuclear reactions induced by supernova neutrinos has witnessed significant progress during the recent years. 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 could be derived from charge-exchange reactions and from inelastic electron scattering data. Importantly the diagonalization shell model has been proven to accurately describe 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. This manuscript reviews the recent progress achieved in calculating su...

  4. Electron-beam dynamics in a strong laser field including quantum radiation reaction

    CERN Document Server

    Neitz, Norman

    2014-01-01

    The evolution of an electron beam colliding head-on with a strong plane-wave field is investigated in the framework of strong-field QED including radiation-reaction effects due to photon emission. Employing a kinetic approach to describe the electron and the photon distribution it is shown that at a given total laser fluence the final electron distribution depends on the shape of the laser envelope and on the pulse duration, in contrast to the classical predictions of radiation reaction based on the Landau-Lifshitz equation. Finally, it is investigated how the pair-creation process leads to a nonlinear coupled evolution of the electrons in the beam, of the produced charged particles, and of the emitted photons.

  5. Electron-beam dynamics in a strong laser field including quantum radiation reaction

    Science.gov (United States)

    Neitz, N.; Di Piazza, A.

    2014-08-01

    The evolution of an electron beam colliding head on with a strong plane-wave field is investigated in the framework of strong-field QED including radiation-reaction effects due to photon emission. Employing a kinetic approach to describe the electron and the photon distribution it is shown that at a given total laser fluence the final electron distribution depends on the shape of the laser envelope and on the pulse duration, in contrast to the classical predictions of radiation reaction based on the Landau-Lifshitz equation. Finally, it is investigated how the pair-creation process leads to a nonlinear coupled evolution of the electrons in the beam, of the produced charged particles, and of the emitted photons.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-11-15

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

  7. 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.

  8. State-to-state quantum dynamics of N(2D) + HD (υ = 0, j = 0) reaction

    Science.gov (United States)

    Zhang, Yong

    2016-12-01

    The N(2D) + HD (v = 0, j = 0) reaction has been studied by a quantum time-dependent wave packet approach with a second-order split operator on the potential energy surface of Li et al. (Li Y, Yuan J, Chen M, Ma F and Sun M J. Comput. Chem. 34 1686). The rovibrationally resolved reaction probability, vibrationally integral cross section, and differential cross section of the NH + D and ND + H channel are investigated at the state-to-state level of theory. The experimental data of the thermal rate constant of two output channels is very scare, but the sum of the two output channels is in excellent agreement with the experimental data which was reported by Umemoto et al. It may imply that the thermal rate constants of the two output channels are accurate and reliable.

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

    Science.gov (United States)

    Windus, Alastair; Jensen, Henrik J.

    2008-11-01

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

  10. 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.

  11. Dynamic Solvent Effects in Alcohol Solutions for Electron Transfer Reactions Involving the Metallocenes

    Science.gov (United States)

    1990-05-15

    Transfer Reactions Involving the Metallocenes by W.R. Fawcett and C.A. Foss, Jr. Prepared for Presentation at The Electrochemical Society Meeting...Technical 800 N. Quincy Arlington, VA 22217-5000 &UL OWaep "W" Prepared for presentation at The" Electrochemical Society Meeting, Montreal Canada, tlay...Extended Abstract must be submitted with the 75-Ward Abstract by December 1, 1969 Montreal, Quebec, Canada-May 6-11, 1990 Submit to: The Electrochemical

  12. Excited State Dynamics of Protonated Phenylalanine and Tyrosine: Photo-Induced Reactions Following Electronic Excitation.

    Science.gov (United States)

    Féraud, Géraldine; Broquier, Michel; Dedonder, Claude; Jouvet, Christophe; Grégoire, Gilles; Soorkia, Satchin

    2015-06-11

    The electronic spectroscopy and the electronic excited state properties of cold protonated phenylalanine and protonated tyrosine have been revisited on a large spectral domain and interpreted by comparison with ab initio calculations. The protonated species are stored in a cryogenically cooled Paul trap, maintained at ∼10 K, and the parent and all the photofragment ions are mass-analyzed in a time-of-flight mass spectrometer, which allows detecting the ionic species with an improved mass resolution compared to what is routinely achieved with a quadrupole mass spectrometer. These new results emphasize the competition around the band origin between two proton transfer reactions from the ammonium group toward either the aromatic chromophore or the carboxylic acid group. These reactions are initiated by the coupling of the locally excited ππ* state with higher charge transfer states, the positions and coupling of which depend on the conformation of the protonated molecules. Each of these reaction processes gives rise to specific fragmentation channels that supports the conformer selectivity observed in the photofragmentation spectra of protonated tyrosine and phenylalanine.

  13. Isotope effects in photodissociation: Chemical reaction dynamics and implications for atmospheres

    DEFF Research Database (Denmark)

    Jørgensen, Solvejg; Grage, Mette Marie-Louise; Nyman, Gunnar

    2008-01-01

    and implicitly involve the short time approximation. in the time-dependent methods the time-dependent Schrodinger equation is solved exactly and the method considers the effect of dynamics away from the Franck-Condon region. We illustrate the presented methods using small molecules (HCl, N2O, OCS and HCHO...

  14. Quantum-based Molecular Dynamics Simulations of Shock-induced Reactions with Time-resolved Raman Spectra

    Science.gov (United States)

    Cawkwell, Marc; Sanville, Edward; Coe, Joshua; Niklasson, Anders

    2012-02-01

    Shock-induced reactions in liquid hydrocarbons have been studied using quantum-based, self-consistent tight-binding (SC-TB) molecular dynamics simulations with an accurate and transferable model for interatomic bonding. Our SC-TB code LATTE enables explicit simulations of shock compression using the universal liquid Hugoniot. Furthermore, the effects of adiabatic shock heating are captured precisely using Niklasson's energy conserving extended Lagrangian Born-Oppenheimer Molecular Dynamics formalism. We have been able to perform relatively large-scale SC-TB simulations by either taking advantage of the sparsity of the density matrix to achieve O(N) performance or by using graphics processing units to accelerate O(N^3) algorithms. We have developed the capability for the on-the-fly computation of Raman spectra from the Fourier transform of the polarizability autocorrelation function via the density matrix perturbation theory of Niklasson and Challacombe. These time-resolved Raman spectra enable us compare the results of our simulations with identical diagnostics collected experimentally. We will illustrate these capabilities with a series of simulations of shock-induced reaction paths in a number of simple molecules.

  15. 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.

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

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-06-28

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

  17. 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

  18. 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.

  19. Dynamics of interfacial reactions between O({sup 3} P) atoms and long-chain liquid hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Allan, Mhairi [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Bagot, Paul A J [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Koehler, Sven P K [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Reed, Stewart K [Department of Physics and Astronomy, University of Edinburgh, The King' s Buildings, Edinburgh EH9 3JZ (United Kingdom); Westacott, Robin E [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Costen, Matthew L [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); McKendrick, Kenneth G [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom)

    2007-09-15

    Recent progress that has been made towards understanding the dynamics of collisions at the gas-liquid interface is summarized briefly. We describe in this context a promising new approach to the experimental study of gas-liquid interfacial reactions that we have introduced. This is based on laser-photolytic production of reactive gas-phase atoms above the liquid surface and laser-spectroscopic probing of the resulting nascent products. This technique is illustrated for reaction of O({sup 3}P) atoms at the surface of the long-chain liquid hydrocarbon squalane (2,6,10,15,19,23-hexamethyltetracosane). Laser-induced fluorescence detection of the nascent OH has revealed mechanistically diagnostic correlations between its internal and translational energy distributions. Vibrationally excited OH molecules are able to escape the surface. At least two contributions to the product rotational distributions are identified, confirming and extending previous hypotheses of the participation of both direct and trapping-desorption mechanisms. We speculate briefly on future experimental and theoretical developments that might be necessary to address the many currently unanswered mechanistic questions for this, and other, classes of gas-liquid interfacial reaction.

  20. Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

    Science.gov (United States)

    Glowacki, David R; Rodgers, W J; Shannon, Robin; Robertson, Struan H; Harvey, Jeremy N

    2017-04-28

    The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of

  1. Effect of osmolytes on protein dynamics in the lactate dehydrogenase-catalyzed reaction.

    Science.gov (United States)

    Zhadin, Nickolay; Callender, Robert

    2011-03-15

    Laser-induced temperature jump relaxation spectroscopy was used to probe the effect of osmolytes on the microscopic rate constants of the lactate dehydrogenase-catalyzed reaction. NADH fluorescence and absorption relaxation kinetics were measured for the lactate dehydrogenase (LDH) reaction system in the presence of varying amounts of trimethylamine N-oxide (TMAO), a protein-stabilizing osmolyte, or urea, a protein-destabilizing osmolyte. Trimethylamine N-oxide (TMAO) at a concentration of 1 M strongly increases the rate of hydride transfer, nearly nullifies its activation energy, and also slightly increases the enthalpy of hydride transfer. In 1 M urea, the hydride transfer enthalpy is almost nullified, but the activation energy of the step is not affected significantly. TMAO increases the preference of the closed conformation of the active site loop in the LDH·NAD(+)·lactate complex; urea decreases it. The loop opening rate in the LDH·NADH·pyruvate complex changes its temperature dependence to inverse Arrhenius with TMAO. In this complex, urea accelerates the loop motion, without changing the loop opening enthalpy. A strong, non-Arrhenius decrease in the pyruvate binding rate in the presence of TMAO offers a decrease in the fraction of the open loop, pyruvate binding competent form at higher temperatures. The pyruvate off rate is not affected by urea but decreases with TMAO. Thus, the osmolytes strongly affect the rates and thermodynamics of specific events along the LDH-catalyzed reaction: binding of substrates, loop closure, and the chemical event. Qualitatively, these results can be understood as an osmolyte-induced change in the energy landscape of the protein complexes, shifting the conformational nature of functional substates within the protein ensemble.

  2. Molecular Dynamics Simulations of Polymer Networks Undergoing Sequential Cross-Linking and Scission Reactions

    DEFF Research Database (Denmark)

    Rottach, Dana R.; Curro, John G.; Budzien, Joanne;

    2007-01-01

    The effects of sequential cross-linking and scission of polymer networks formed in two states of strain are investigated using molecular dynamics simulations. Two-stage networks are studied in which a network formed in the unstrained state (stage 1) undergoes additional cross-linking in a uniaxia......The effects of sequential cross-linking and scission of polymer networks formed in two states of strain are investigated using molecular dynamics simulations. Two-stage networks are studied in which a network formed in the unstrained state (stage 1) undergoes additional cross...... good agreement with the predictions of Flory and Fricker. It was found that the fractional stress reduction upon removal of the first-stage cross-links could be accurately calculated from the slip tube model of Rubinstein and Panyukov modified to use the theoretical transfer functions of Fricker.  ...

  3. Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

    CERN Document Server

    Sushko, Gennady B; Verkhovtsev, Alexey V; Volkov, Sergey N; Solov'yov, Andrey V

    2015-01-01

    The concept of molecular mechanics force field has nowadays been widely accepted for studying various processes in biomolecular systems. In this paper we suggest a modification for the standard CHARMM force field, that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, in this paper we provide several case studies where dynamical topology is necessary. In particular, it is shown, that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation or collision induced damage, transformation and fragmentation processes involving biomolecular systems.

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

    Science.gov (United States)

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

    2011-12-01

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

  5. Charge recombination kinetics and protein dynamics in wild type and carotenoid-less bacterial reaction centers: studies in trehalose glasses.

    Science.gov (United States)

    Francia, Francesco; Malferrari, Marco; Sacquin-Mora, Sophie; Venturoli, Giovanni

    2009-07-30

    The coupling between electron transfer and protein dynamics has been investigated in reaction centers (RCs) from the wild type (wt) and the carotenoid-less strain R26 of the photosynthetic bacterium Rhodobacter sphaeroides. Recombination kinetics between the primary photoreduced quinone acceptor (QA-) and photoxidized donor (P+) have been analyzed at room temperature in RCs incorporated into glassy trehalose matrices of different water/sugar ratios. As previously found in R26 RCs, also in the wt RC, upon matrix dehydration, P+QA- recombination accelerates and becomes broadly distributed, reflecting the inhibition of protein relaxation from the dark-adapted to the light-adapted conformation and the hindrance of interconversion between conformational substates. While in wet trehalose matrices (down to approximately one water per trehalose molecule) P+QA- recombination kinetics are essentially coincident in wt and R26 RCs, more extensive dehydration leads to two-times faster and more distributed kinetics in the carotenoid-containing RC, indicating a stronger inhibition of the internal protein dynamics in the wt RC. Coarse-grained Brownian dynamics simulations performed on the two RC structures reveal a markedly larger flexibility of the R26 RC, showing that a rigid core of residues, close to the quinone acceptors, is specifically softened in the absence of the carotenoid. These experimental and computational results concur to indicate that removal of the carotenoid molecule has long-range effects on protein dynamics and that the structural/dynamical coupling between the protein and the glassy matrix depends strongly upon the local mechanical properties of the protein interior. The data also suggest that the conformational change stabilizing P+QA- is localized around the QA binding pocket.

  6. 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.

  7. Dynamics of the gas-liquid interfacial reaction of O(3P) atoms with hydrocarbons

    Science.gov (United States)

    Kelso, Hailey; Köhler, Sven P. K.; Henderson, David A.; McKendrick, Kenneth G.

    2003-11-01

    We describe an experimental approach to the determination of the nascent internal state distribution of gas-phase products of a gas-liquid interfacial reaction. The system chosen for study is O(3P) atoms with the surface of liquid deuterated squalane, a partially branched long-chain saturated hydrocarbon, C30D62. The nascent OD products are detected by laser-induced fluorescence. Both OD (v'=0) and (v'=1) were observed in significant yield. The rotational distributions in both vibrational levels are essentially the same, and are characteristic of a Boltzmann distribution at a temperature close to that of the liquid surface. This contrasts with the distributions in the corresponding homogeneous gas-phase reactions. We propose a preliminary interpretation in terms of a dominant trapping-desorption mechanism, in which the OD molecules are retained at the surface sufficiently long to cause rotational equilibration but not complete vibrational relaxation. The significant yield of vibrationally excited OD also suggests that the surface is not composed entirely of -CD3 endgroups, but that secondary and/or tertiary units along the backbone are exposed.

  8. QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics.

    Science.gov (United States)

    Monge-Palacios, M; Yang, M; Espinosa-García, J

    2012-04-14

    A detailed dynamics study, using both quasi-classical trajectory (QCT) and reduced-dimensional quantum mechanical (QM) calculations, was carried out to understand the reactivity and mechanism of the Cl((2)P) + NH(3)→ HCl + NH(2) gas-phase reaction, which evolves through deep wells in the entry and exit channels. The calculations were performed on an analytical potential energy surface recently developed by our group, PES-2010 [M. Monge-Palacios, C. Rangel, J. C. Corchado and J. Espinosa-Garcia, Int. J. Quantum. Chem., 2011], together with a simplified model surface, mod-PES, in which the reactant well is removed to analyze its influence. The main finding was that the QCT and QM methods show a change of the reaction probability with collision energy, suggesting a change of the atomic-level mechanism of reaction with energy. This change disappeared when the mod-PES was used, showing that the behaviour at low energies is a direct consequence of the existence of the reactant well. Analysis of the trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) > 5 kcal mol(-1)) practically all trajectories are direct, at low energies (E(coll) cross section results reinforce this change of mechanism, showing also the influence of the reactant well on this reaction. Thus, the PES-2010 surface yields a forward-backward symmetry in the scattering, while when the reactant well is removed with the mod-PES the shape is more isotropic.

  9. A Classical Approach in Simple Nuclear Fusion Reaction 1H2 + 1H3 using Two-Dimension Granular Molecular Dynamics Model

    CERN Document Server

    Viridi, Sparisoma; Waris, Abdul; Perkasa, Yudha Satya

    2011-01-01

    Molecular dynamics in 2-D accompanied by granular model provides an opportunity to investigate binding between nuclei particles and its properties that arises during collision in a fusion reaction. A fully classical approach is used to observe the influence of initial angle of nucleus orientation to the product yielded by the reaction. As an example, a simplest fusion reaction between 1H2 and 1H3 is observed. Several products of the fusion reaction have been obtained, even the unreported ones, including temporary 2He4 nucleus.

  10. 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.

  11. Flex Dynamics Avoidance Control of the NEA Scout Solar Sail Spacecraft's Reaction Control System

    Science.gov (United States)

    Heaton Andrew; Stiltner, Brandon; Diedrich, Benjamin; Becker, Christopher; Orphee, Juan

    2017-01-01

    The Attitude Control System (ACS) is developed for a Near Earth Asteroid (NEA) Scout mission using a solar sail. The NEA-Scout spacecraft is a 6U cubesat with an 86 square-meter solar sail. NEA Scout will launch on Space Launch System (SLS) Exploration Mission 1 (EM-1), currently scheduled to launch in 2018. The spacecraft will rendezvous with a target asteroid after a two year journey, and will conduct science imagery. The solar sail spacecraft ACS consists of three major actuating subsystems: a Reaction Wheel (RW) control system, a Reaction Control System (RCS), and an Adjustable Mass Translator (AMT) system. The three subsystems allow for a wide range of spacecraft attitude control capabilities, needed for the different phases of the NEA-Scout mission. Because the sail is a flexible structure, care must be taken in designing a control system to avoid exciting the structural modes of the sail. This is especially true for the RCS, which uses pulse actuated, cold-gas jets to control the spacecraft's attitude. While the reaction wheels can be commanded smoothly, the RCS jets are simple on-off actuators. Long duration firing of the RCS jets - firings greater than one second - can be thought of as step inputs to the spacecraft's torque. On the other hand, short duration firings - pulses on the order of 0.1 seconds - can be thought of as impulses in the spacecraft's torque. These types of inputs will excite the structural modes of the spacecraft, causing the sail to oscillate. Sail oscillations are undesirable for many reasons. Mainly, these oscillations will feed into the spacecraft attitude sensors and pointing accuracy, and long term oscillations may be undesirable over the lifetime of the solar sail. In order to limit the sail oscillations, an RCS control scheme is being developed to minimize sail excitations. Specifically, an input shaping scheme similar to the method described in Reference 1 will be employed. A detailed description of the RCS control scheme will

  12. 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.

  13. Dynamical Behavior of Delayed Reaction-Diffusion Hopfield Neural Networks Driven by Infinite Dimensional Wiener Processes.

    Science.gov (United States)

    Liang, Xiao; Wang, Linshan; Wang, Yangfan; Wang, Ruili

    2016-09-01

    In this paper, we focus on the long time behavior of the mild solution to delayed reaction-diffusion Hopfield neural networks (DRDHNNs) driven by infinite dimensional Wiener processes. We analyze the existence, uniqueness, and stability of this system under the local Lipschitz function by constructing an appropriate Lyapunov-Krasovskii function and utilizing the semigroup theory. Some easy-to-test criteria affecting the well-posedness and stability of the networks, such as infinite dimensional noise and diffusion effect, are obtained. The criteria can be used as theoretic guidance to stabilize DRDHNNs in practical applications when infinite dimensional noise is taken into consideration. Meanwhile, considering the fact that the standard Brownian motion is a special case of infinite dimensional Wiener process, we undertake an analysis of the local Lipschitz condition, which has a wider range than the global Lipschitz condition. Two samples are given to examine the availability of the results in this paper. Simulations are also given using the MATLAB.

  14. Accurate Test of Chiral Dynamics in the \\boldmath$\\gamma p \\rightarrow \\pi^0p$ Reaction

    CERN Document Server

    Hornidge, D; Annand, J R M; Arends, H J; Beck, R; Bekrenev, V; Berghaeuser, H; Bernstein, A M; Braghieri, A; Briscoe, W J; Cherepnya, S; Dieterle, M; Downie, E J; Drexler, P; Fernandez-Ramirez, C; Filkov, L V; Glazier, D I; Barrientos, P Hall; Heid, E; Hilt, M; Jaegle, I; Jahn, O; Jude, T C; Kashevarov, V L; Keshelashvili, I; Kondratiev, R; Korolija, M; Koulbardis, A; Krambrich, D; Kruglov, S; Krusche, B; Laffoley, A T; Lisin, V; Livingston, K; MacGregor, I J D; Mancell, J; Manley, D M; McNicoll, E F; Mekterovic, D; Metag, V; Micanovic, S; Middleton, D G; Moores, K W; Mushkarenkov, A; Nefkens, B M K; Oberle, M; Ostrick, M; Otte, P B; Oussena, B; Pedroni, P; Pheron, F; Polonski, A; Prakhov, S; Robinson, J; Rostomyan, T; Scherer, S; Schumann, S; Sikora, M H; Starostin, A; Supek, I; Thiel, M; Thomas, A; Tiator, L; Unverzagt, M; Watts, D P; Werthmueller, D; Witthauer, L

    2013-01-01

    A precision measurement of the photon asymmetry $\\Sigma$ and differential cross sections $d\\sigma/d\\Omega$ for the $\\gamma p \\rightarrow \\pi^0p$ reaction in the near-threshold region has been performed with a tagged photon beam and almost $4\\pi$ detector at the Mainz Microtron. The Glasgow-Mainz photon tagging facility along with the Crystal Ball/TAPS multi-photon detector system and a cryogenic liquid hydrogen target were used. These data allowed for a precise determination of the energy dependence of the real parts of the $S$- and all three $P$-wave amplitudes for the first time and provide the most stringent test to date of the predictions of Chiral Perturbation Theory and its energy region of convergence. The upper limit of agreement is between 165 and 175 MeV incident photon lab energy, $\\simeq25$ MeV above threshold.

  15. 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...

  16. Investigations into the role of oxacarbenium ions in glycosylation reactions by ab initio molecular dynamics.

    Science.gov (United States)

    Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo

    2006-12-29

    We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.

  17. 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

  18. Excited states in electron-transfer reaction products: ultrafast relaxation dynamics of an isolated acceptor radical anion.

    Science.gov (United States)

    Horke, Daniel A; Roberts, Gareth M; Verlet, Jan R R

    2011-08-04

    The spectroscopy and ultrafast relaxation dynamics of excited states of the radical anion of a representative charge-transfer acceptor molecule, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, have been studied in the gas phase using time-resolved photoelectron spectroscopy. The photoelectron spectra reveal that at least two anion excited states are bound. Time-resolved studies show that both excited states are very short-lived and internally convert to the anion ground state, with the lower energy state relaxing within 200 fs and a near-threshold valence-excited state relaxing on a 60 fs time scale. These excited states, and in particular the valence-excited state, present efficient pathways for electron-transfer reactions in the highly exergonic inverted region which commonly displays rates exceeding predictions from electron-transfer theory.

  19. Static and dynamic headspace analysis of instant coffee blends by proton-transfer-reaction mass spectrometry.

    Science.gov (United States)

    Romano, Andrea; Gaysinsky, Sylvia; Czepa, Andreas; Del Pulgar, José Sanchez; Cappellin, Luca; Biasioli, Franco

    2015-09-01

    Instant coffee is a widespread product, generally related to a high consumer acceptability, also because of its ease of preparation. The present work addresses the characterization of the headspace of freshly brewed instant coffees resulting from different blends, during and immediately after preparation. The sample set consisted of 10 coffees, obtained by mixing three different blends in different proportions. The employment of Proton Transfer Reaction-Mass Spectrometry (PTR-MS) allowed for direct and real-time sampling from the headspace, under conditions that mimic those that are encountered above the cup during and right after brewing. Different coffee brews were separated on the basis of the respective volatile profiles, and data showed good consistency with the respective blend compositions. When the headspace evolution was monitored during preparation, similar results were obtained in terms of blend separation; moreover, different blends displayed different and reproducible 'signatures' in terms of time evolution. A straightforward method for the prediction of headspace composition is proposed, allowing to predict the volatile profiles of two-component and three-component blends on the basis of the respective parent components. Overall, the results constitute a successful example of the applicability of PTR-MS as a tool for product development in food science. Copyright © 2015 John Wiley & Sons, Ltd.

  20. Compound nucleus formation probability PCN determined within the dynamical cluster-decay model for various "hot" fusion reactions

    Science.gov (United States)

    Kaur, Arshdeep; Chopra, Sahila; Gupta, Raj K.

    2014-08-01

    The compound nucleus (CN) fusion/formation probability PCN is defined and its detailed variations with the CN excitation energy E*, center-of-mass energy Ec .m., fissility parameter χ, CN mass number ACN, and Coulomb interaction parameter Z1Z2 are studied for the first time within the dynamical cluster-decay model (DCM). The model is a nonstatistical description of the decay of a CN to all possible processes. The (total) fusion cross section σfusion is the sum of the CN and noncompound nucleus (nCN) decay cross sections, each calculated as the dynamical fragmentation process. The CN cross section σCN is constituted of evaporation residues and fusion-fission, including intermediate-mass fragments, each calculated for all contributing decay fragments (A1, A2) in terms of their formation and barrier penetration probabilities P0 and P. The nCN cross section σnCN is determined as the quasi-fission (qf) process, where P0=1 and P is calculated for the entrance-channel nuclei. The DCM, with effects of deformations and orientations of nuclei included in it, is used to study the PCN for about a dozen "hot" fusion reactions forming a CN of mass number A ˜100 to superheavy nuclei and for various different nuclear interaction potentials. Interesting results are that PCN=1 for complete fusion, but PCNPCN≪1 due to the nCN contribution, depending strongly on different parameters of the entrance-channel reaction but found to be independent of the nuclear interaction potentials used.

  1. Photoisomerization among ring-open merocyanines. I. Reaction dynamics and wave-packet oscillations induced by tunable femtosecond pulses

    Science.gov (United States)

    Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Walter, Christof; Engels, Bernd; Brixner, Tobias

    2014-06-01

    Upon ultraviolet excitation, photochromic spiropyran compounds can be converted by a ring-opening reaction into merocyanine molecules, which in turn can form several isomers differing by cis and trans configurations in the methine bridge. Whereas the spiropyran-merocyanine conversion reaction of the nitro-substituted indolinobenzopyran 6-nitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-indoline] (6-nitro BIPS) has been studied extensively in theory and experiments, little is known about photoisomerization among the merocyanine isomers. In this article, we employ femtosecond transient absorption spectroscopy with variable excitation wavelengths to investigate the excited-state dynamics of the merocyanine in acetonitrile at room temperature, where exclusively the trans-trans-cis (TTC) and trans-trans-trans (TTT) isomers contribute. No photochemical ring-closure pathways exist for the two isomers. Instead, we found that (18±4)% of excited TTC isomers undergo an ultrafast excited-state cis→trans photoisomerization to TTT within 200 fs, while the excited-state lifetime of TTC molecules that do not isomerize is 35 ps. No photoisomerization was detected for the TTT isomer, which relaxes to the ground state with a lifetime of roughly 160 ps. Moreover, signal oscillations at 170 cm-1 and 360 cm-1 were observed, which can be ascribed to excited-state wave-packet dynamics occurring in the course of the TTC→TTT isomerization. The results of high-level time-dependent density functional theory in conjunction with polarizable continuum models are presented in the subsequent article [C. Walter, S. Ruetzel, M. Diekmann, P. Nuernberger, T. Brixner, and B. Engels, J. Chem. Phys. 140, 224311 (2014)].

  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. Modeling dual-scale epidemic dynamics on complex networks with reaction diffusion processes

    Institute of Scientific and Technical Information of China (English)

    Xiao-gang JIN; Yong MIN

    2014-01-01

    The frequent outbreak of severe foodborne diseases (e.g., haemolytic uraemic syndrome and Listeriosis) in 2011 warns of a potential threat that world trade could spread fatal pathogens (e.g., enterohemorrhagic Escherichia coli). The epidemic potential from trade involves both intra-proliferation and inter-diffusion. Here, we present a worldwide vegetable trade network and a stochastic computational model to simulate global trade-mediated epidemics by considering the weighted nodes and edges of the network and the dual-scale dynamics of epidemics. We address two basic issues of network structural impact in global epi-demic patterns:(1) in contrast to the prediction of heterogeneous network models, the broad variability of node degree and edge weights of the vegetable trade network do not determine the threshold of global epidemics;(2) a‘penetration effect’, by which community structures do not restrict propagation at the global scale, quickly facilitates bridging the edges between communities, and leads to synchronized diffusion throughout the entire network. We have also defined an appropriate metric that combines dual-scale behavior and enables quantification of the critical role of bridging edges in disease diffusion from widespread trading. The unusual structure mechanisms of the trade network model may be useful in producing strategies for adaptive immunity and reducing international trade frictions.

  4. Dynamic alterations in wellbore cement integrity due to geochemical reactions in CO2-rich environments

    Science.gov (United States)

    Cao, Peilin; Karpyn, Zuleima T.; Li, Li

    2013-07-01

    The interaction between wellbore cement and CO2 has the potential to alter cement properties and form preferential leakage pathways during geological carbon sequestration. This work investigates changes in wellbore cement integrity during continuous flooding of CO2-saturated brine. We created composite cement-sandstone core samples with a continuous gap in the cement zone in order to represent defects such as fractures and voids in wellbore cement. Volumetric and structural changes in the cement zone were monitored and quantified using X-ray Micro-Computed Tomography imaging. During an 8 day dynamic flow-through period, the fracture/void aperture increased significantly, whereas the host sandstone remained unaltered. The void volume increased at a faster rate in the early stage of the flow-through period than it did toward the end of the period. Compared to the apertures close to the core outlet, those located near the core inlet experienced more severe cement degradation, accompanied by a decrease in specific surface area, constituting evidence of a smoothing effect. Contrary to previous observations of the self-healing behavior of cement fractures, the in situ permeability on a parallel experiment increased by a factor of 8 after 10 days of flooding. Findings from this work will provide valuable insights applicable to the development of predictive models and for risk assessment under conditions relevant to CO2 sequestration.

  5. 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.

  6. An individual and dynamic Body Segment Inertial Parameter validation method using ground reaction forces.

    Science.gov (United States)

    Hansen, Clint; Venture, Gentiane; Rezzoug, Nasser; Gorce, Philippe; Isableu, Brice

    2014-05-01

    Over the last decades a variety of research has been conducted with the goal to improve the Body Segment Inertial Parameters (BSIP) estimations but to our knowledge a real validation has never been completely successful, because no ground truth is available. The aim of this paper is to propose a validation method for a BSIP identification method (IM) and to confirm the results by comparing them with recalculated contact forces using inverse dynamics to those obtained by a force plate. Furthermore, the results are compared with the recently proposed estimation method by Dumas et al. (2007). Additionally, the results are cross validated with a high velocity overarm throwing movement. Throughout conditions higher correlations, smaller metrics and smaller RMSE can be found for the proposed BSIP estimation (IM) which shows its advantage compared to recently proposed methods as of Dumas et al. (2007). The purpose of the paper is to validate an already proposed method and to show that this method can be of significant advantage compared to conventional methods.

  7. 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)

  8. Monitoring dynamic reactions of red blood cells to UHF electromagnetic waves radiation using a novel micro-imaging technology.

    Science.gov (United States)

    Ruan, Ping; Yong, Junguang; Shen, Hongtao; Zheng, Xianrong

    2012-12-01

    Multiple state-of-the-art techniques, such as multi-dimensional micro-imaging, fast multi-channel micro-spetrophotometry, and dynamic micro-imaging analysis, were used to dynamically investigate various effects of cell under the 900 MHz electromagnetic radiation. Cell changes in shape, size, and parameters of Hb absorption spectrum under different power density electromagnetic waves radiation were presented in this article. Experimental results indicated that the isolated human red blood cells (RBCs) do not have obviously real-time responses to the ultra-low density (15 μW/cm(2), 31 μW/cm(2)) electromagnetic wave radiation when the radiation time is not more than 30 min; however, the cells do have significant reactions in shape, size, and the like, to the electromagnetic waves radiation with power densities of 1 mW/cm(2) and 5 mW/cm(2). The data also reveal the possible influences and statistical relationships among living human cell functions, radiation amount, and exposure time with high-frequency electromagnetic waves. The results of this study may be significant on protection of human being and other living organisms against possible radiation affections of the high-frequency electromagnetic waves.

  9. 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.

  10. 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.

  11. 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.

  12. Interception of excited vibrational quantum states by O2 in atmospheric association reactions.

    Science.gov (United States)

    Glowacki, David R; Lockhart, James; Blitz, Mark A; Klippenstein, Stephen J; Pilling, Michael J; Robertson, Struan H; Seakins, Paul W

    2012-08-31

    Bimolecular reactions in Earth's atmosphere are generally assumed to proceed between reactants whose internal quantum states are fully thermally relaxed. Here, we highlight a dramatic role for vibrationally excited bimolecular reactants in the oxidation of acetylene. The reaction proceeds by preliminary adduct formation between the alkyne and OH radical, with subsequent O(2) addition. Using a detailed theoretical model, we show that the product-branching ratio is determined by the excited vibrational quantum-state distribution of the adduct at the moment it reacts with O(2). Experimentally, we found that under the simulated atmospheric conditions O(2) intercepts ~25% of the excited adducts before their vibrational quantum states have fully relaxed. Analogous interception of excited-state radicals by O(2) is likely common to a range of atmospheric reactions that proceed through peroxy complexes.

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

    Science.gov (United States)

    Parascandolo, C.; Pierroutsakou, D.; Alba, R.; Del Zoppo, A.; Maiolino, C.; Santonocito, D.; Agodi, C.; Baran, V.; Boiano, A.; Colonna, M.; Coniglione, R.; De Filippo, E.; Di Toro, M.; Emanuele, U.; Farinon, F.; Guglielmetti, A.; La Commara, M.; Martin, B.; Mazzocchi, C.; Mazzocco, M.; Rizzo, C.; Romoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Strano, E.; Torresi, D.; Trifirò, A.; Trimarchi, M.

    2016-05-01

    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. 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.

  15. Quantum dynamics of {sup 16}O + {sup 36}O{sub 2} and {sup 18}O + {sup 32}O{sub 2} exchange reactions

    Energy Technology Data Exchange (ETDEWEB)

    Rajagopala Rao, T.; Mahapatra, S., E-mail: smsc@uohyd.ernet.in [School of Chemistry, University of Hyderabad, Hyderabad 500 046 (India); Guillon, G. [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS-Université de Bourgogne, 21078 Dijon Cedex (France); Honvault, P., E-mail: pascal.honvault@univ-fcomte.fr [Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS-Université de Bourgogne, 21078 Dijon Cedex (France); UFR Sciences et Techniques, Université de Franche-Comté, 25030 Besançon Cedex (France)

    2015-05-07

    We present quantum dynamical investigations of {sup 16}O + {sup 36}O{sub 2} and {sup 18}O + {sup 32}O{sub 2} exchange reactions using a time-independent quantum mechanical method and an accurate global potential energy surface of ozone [Dawes et al., J. Chem. Phys. 135, 081102 (2011)]. Initial state-selected integral cross sections, rate constants, and Boltzmann averaged thermal rate constants are obtained and compared with earlier experimental and theoretical results. The computed thermal rate constants for the oxygen exchange reactions exhibit a negative temperature dependence, as found experimentally. They are in better agreement with the experiments than the previous studies on the same reactions.

  16. Direct dynamics trajectory study of the reaction of formaldehyde cation with D2: vibrational and zero-point energy effects on quasiclassical trajectories.

    Science.gov (United States)

    Liu, Jianbo; Song, Kihyung; Hase, William L; Anderson, Scott L

    2005-12-22

    Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.

  17. 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

    2016-03-21

    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

  18. Molecular dynamical studies of the dissociation of a diatomic molecular crystal. I. Energy exchange in rapid exothermic reactions

    Science.gov (United States)

    Tsai, D. H.; Trevino, S. F.

    1983-08-01

    We discuss the results of a study of the exothermic dissociation of a model diatomic molecular crystal. Our main purpose is to investigate the dynamics of energy transport and energy sharing in this system during the dissociation process. The crystal was prepared in a metastable molecular form, in thermal equilibrium at a low initial temperature and pressure. When we heated the system to a higher temperature, at constant volume, we observed thermally initiated dissociations which progressed rapidly to completion. During the dissociation process, we found that the sharing of the potential energy released by the metastable molecules with the rest of the system, and the sharing of the kinetic energy of the dissociated fragments with the kinetic energy of the molecules in the translational degrees of freedom, were rather efficient. But the intra- and intermolecular exchange of the kinetic energy among the various degrees of freedom, viz., translation-rotation, translation-vibration, and rotation-vibration was inefficient. Dissociation would occur in one of the regions of high local kinetic energy density, after a molecule in that region had acquired sufficient vibrational energy to break apart, and when the ``caging'' effect was favorable to allow the molecule to dissociate. From such a reaction site, and there may be others, the reaction would spread to a neighboring site, and continue this way until all the molecules became dissociated. The induction time showed an approximately logarithmic dependence on the inverse of the temperature of the system after heating. But during the process of rapid dissociation, both the potential energy and the kinetic energy of the system underwent rapid changes, and thermal equilibrium was not reached until the end of the process.

  19. The cardiac cycle time effect revisited: Temporal dynamics of the central-vagal modulation of heart rate in human reaction time tasks.

    NARCIS (Netherlands)

    R.J.M. Somsen; J.R. Jennings; M.W. van der Molen

    2004-01-01

    Lacey and Lacey (1974) suggested that during reaction time tasks higher brain centers dynamically adjust efferent vagal nerve pulses to the sino-atrial node of the heart, inducing phase-dependent heart rate changes. Since then, animal and human neuro-physiological results have provided evidence for

  20. Prevalence of Bimolecular Routes in the Activation of Diatomic Molecules with Strong Chemical Bonds (O2, NO, CO, N2) on Catalytic Surfaces.

    Science.gov (United States)

    Hibbitts, David; Iglesia, Enrique

    2015-05-19

    sites that are scarce on such surfaces. N-O bonds cleave instead via H*-assistance to form *HNOH* intermediates, with barriers much lower than for direct NO* dissociation. CO hydrogenation on Co and Ru occurs on crowded surfaces saturated with CO*; rates increase with increasing Co and Ru cluster size, indicating that low-index surfaces on large clusters can activate CO*. Direct CO*dissociation, however, occurs with high activation barriers on low-index Co and Ru surfaces, and even on defect sites (step-edge, corner sites) at high CO* coverages. CO* dissociation proceeds instead with H*-assistance to form *HCOH* species that cleave C-O bonds with lower barriers than direct CO* dissociation, irrespective of surface coordination. H2O increases CO activation rates by assisting H-additions to form *HCOH*, as in the case of peroxide formation in Au-catalyzed oxidations. N2 dissociation steps in NH3 synthesis on Ru and Fe are thought to also require defect sites; yet, barriers on Ru(0001) indicate that H*-assisted N2 activation - unlike O2, CO, and NO - is not significantly more facile than direct N2 dissociation, suggesting that defects and low-index planes may both contribute to NH3 synthesis rates. The activation of strong chemical bonds often occurs via bimolecular reactions. These steps weaken such bonds before cleavage on crowded low-index surfaces, thus avoiding the ubiquitous kinetic hurdles of direct dissociations without requiring defect sites.

  1. In situ dimerization of multiple wild type and mutant zinc transporters in live cells using bimolecular fluorescence complementation.

    Science.gov (United States)

    Lasry, Inbal; Golan, Yarden; Berman, Bluma; Amram, Noy; Glaser, Fabian; Assaraf, Yehuda G

    2014-03-14

    Zinc transporters (ZnTs) facilitate zinc efflux and zinc compartmentalization, thereby playing a key role in multiple physiological processes and pathological disorders, presumed to be modulated by transporter dimerization. We recently proposed that ZnT2 homodimerization is the underlying basis for the dominant negative effect of a novel heterozygous G87R mutation identified in women producing zinc-deficient milk. To provide direct visual evidence for the in situ dimerization and function of multiple normal and mutant ZnTs, we applied here the bimolecular fluorescence complementation (BiFC) technique, which enables direct visualization of specific protein-protein interactions. BiFC is based upon reconstitution of an intact fluorescent protein including YFP when its two complementary, non-fluorescent N- and C-terminal fragments (termed YN and YC) are brought together by a pair of specifically interacting proteins. Homodimerization of ZnT1, -2, -3, -4, and -7 was revealed by high subcellular fluorescence observed upon co-transfection of non-fluorescent ZnT-YC and ZnT-YN; this homodimer fluorescence localized in the characteristic compartments of each ZnT. The validity of the BiFC assay in ZnT dimerization was further corroborated when high fluorescence was obtained upon co-transfection of ZnT5-YC and ZnT6-YN, which are known to form heterodimers. We further show that BiFC recapitulated the pathogenic role that ZnT mutations play in transient neonatal zinc deficiency. Zinquin, a fluorescent zinc probe applied along with BiFC, revealed the in situ functionality of ZnT dimers. Hence, the current BiFC-Zinquin technique provides the first in situ evidence for the dimerization and function of wild type and mutant ZnTs in live cells.

  2. 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.

  3. 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.

    2016-05-01

    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.

  4. Preliminary Comparison of Reaction Rate theory and Object Kinetic Monte Carlo Simulations of Defect Cluster Dynamics under Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Stoller, Roger E [ORNL; Golubov, Stanislav I [ORNL; Becquart, C. S. [Universite de Lille; Domain, C. [EDF R& D, Clamart, France

    2006-09-01

    The multiscale modeling scheme encompasses models from the atomistic to the continuum scale. Phenomena at the mesoscale are typically simulated using reaction rate theory (RT), Monte Carlo (MC), or phase field models. These mesoscale models are appropriate for application to problems that involve intermediate length scales ( m to >mm), and timescales from diffusion (~ s) to long-term microstructural evolution (~years). Phenomena at this scale have the most direct impact on mechanical properties in structural materials of interest to nuclear energy systems, and are also the most accessible to direct comparison between the results of simulations and experiments. Recent advances in computational power have substantially expanded the range of application for MC models. Although the RT and MC models can be used simulate the same phenomena, many of the details are handled quite differently in the two approaches. A direct comparison of the RT and MC descriptions has been made in the domain of point defect cluster dynamics modeling, which is relevant to both the nucleation and evolution of radiation-induced defect structures. The relative merits and limitations of the two approaches are discussed, and the predictions of the two approaches are compared for specific irradiation conditions.

  5. 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.

  6. Rapid determination of parabens in personal care products by stable isotope GC-MS/MS with dynamic selected reaction monitoring.

    Science.gov (United States)

    Wang, Perry G; Zhou, Wanlong

    2013-06-01

    In this study, a rapid and sensitive analytical method for the determination of methyl-, ethyl-, propyl-, and butyl esters of para-hydroxy benzoic acid (parabens) in personal care products was developed and fully validated. Test portions were extracted with methanol followed by vortexing, sonication, centrifugation, and filtration without derivatization. The four parabens were quantified by GC-MS/MS in the electron ionization mode. Four corresponding isotopically labeled parabens were selected as internal standards, which were added at the beginning of the sample preparation and used to correct for recovery and matrix effects. Sensitivity, extraction efficiency, and recovery of the respective analytes were evaluated. The coefficients of determination (r(2)) were all greater than 0.995 for the four parabens investigated. The recoveries ranged from 97 to 107% at three spiked levels and a one-time (single) extraction efficiency greater than 97% was obtained. This method has been applied to screen 26 personal care products. This is the first time that a unique GC-MS/MS method with dynamic selected reaction monitoring and confirmation of analytes has been used to determine these parabens in cosmetic personal care products.

  7. Dilepton production and reaction dynamics in heavy-ion collisions at SIS energies from coarse-grained transport simulations

    CERN Document Server

    Endres, Stephan; Weil, Janus; Bleicher, Marcus

    2015-01-01

    Dilepton invariant-mass spectra for heavy-ion collisions at SIS 18 and BEVALAC energies are calculated using a coarse-grained time evolution from the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model. The coarse-graining of the microscopic simulations enables to calculate thermal dilepton emission rates by application of in-medium spectral functions from equilibrium quantum-field theoretical calculations. The results show that extremely high baryon chemical potentials dominate the evolution of the created hot and dense fireball. Consequently, a significant modification of the $\\rho$ spectral shape becomes visible in the dilepton invariant-mass spectrum, resulting in an enhancement in the low-mass region $M_{ee} = 200$ to 600 MeV/$c^{2}$. This enhancement, mainly caused by baryonic effects on the $\\rho$ spectral shape, can fully describe the experimentally observed excess above the hadronic cocktail contributions in Ar+KCl ($E_{\\mathrm{lab}}=1.76$ $A$GeV) reactions as measured by the HADES collaborat...

  8. 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.

    Science.gov (United States)

    Song, Hui; Dai, Dongxu; Wu, Guorong; Wang, Chia Chen; Harich, Steven A; Hayes, Michael Y; Wang, Xiuyan; Gerlich, Dieter; Yang, Xueming; Skodje, Rex T

    2005-08-15

    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.

  9. Probing the interplay between factors determining reaction rates on silica gel using termolecular systems.

    Science.gov (United States)

    Kirkpatrick, Iain; Worrall, David R; Williams, Siân L; Buck, Craig J T; Meseguer, Rafael G

    2012-10-01

    In this study we have compared energy and electron transfer reactions in termolecular systems using a nanosecond diffuse reflectance laser flash photolysis technique. We have previously investigated these processes on silica gel surfaces for bimolecular systems and electron transfer in termolecular systems. The latter systems involved electron transfer between three arene molecules with azulene acting as a molecular shuttle. In this study we present an alternative electron transfer system using trans β-carotene as an electron donor in order to effectively immobilise all species except the shuttle, providing the first unambiguous evidence for radical ion mobility. In the energy transfer system we use naphthalene, a structural isomer of azulene, as the shuttle, facilitating energy transfer from a selectively excited benzophenone sensitiser to 9-cyanoanthracene. Bimolecular rate constants for all of these processes have been measured and new insights into the factors determining the rates of these reactions on silica gel have been obtained.

  10. 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.

  11. Chemical dynamics simulations of the monohydrated OH(-)(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment.

    Science.gov (United States)

    Xie, Jing; Otto, Rico; Wester, Roland; Hase, William L

    2015-06-28

    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.

  12. 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

  13. 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 ...

  14. 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.

  15. Charge transfer reactions at interfaces between neutral gas and plasma: Dynamical effects and X-ray emission

    Science.gov (United States)

    Provornikova, E.; Izmodenov, V. V.; Lallement, R.

    2012-04-01

    Charge-transfer is the main process linking neutrals and charged particles in the interaction regions of neutral (or partly ionized) gas with a plasma. In this paper we illustrate the importance of charge-transfer with respect to the dynamics and the structure of neutral gas-plasma interfaces. We consider the following phenomena: (1) the heliospheric interface - region where the solar wind plasma interacts with the partly-ionized local interstellar medium (LISM) and (2) neutral interstellar clouds embedded in a hot, tenuous plasma such as the million degree gas that fills the so-called ``Local Bubble". In (1), we discuss several effects in the outer heliosphere caused by charge exchange of interstellar neutral atoms and plasma protons. In (2) we describe the role of charge exchange in the formation of a transition region between the cloud and the surrounding plasma based on a two-component model of the cloud-plasma interaction. In the model the cloud consists of relatively cold and dense atomic hydrogen gas, surrounded by hot, low density, fully ionized plasma. We discuss the structure of the cloud-plasma interface and the effect of charge exchange on the lifetime of interstellar clouds. Charge transfer between neutral atoms and minor ions in the plasma produces X-ray emission. Assuming standard abundances of minor ions in the hot gas surrounding the cold interstellar cloud, we estimate the X-ray emissivity consecutive to the charge transfer reactions. Our model shows that the charge-transfer X-ray emission from the neutral cloud-plasma interface may be comparable to the diffuse thermal X-ray emission from the million degree gas cavity itself.

  16. Crossed beam reaction of cyano radicals with hydrocarbon molecules. IV. Chemical dynamics of cyanoacetylene (HCCCN; X 1Σ+) formation from reaction of CN(X 2Σ+) with acetylene, C2H2(X 1Σg+)

    Science.gov (United States)

    Huang, L. C. L.; Asvany, O.; Chang, A. H. H.; Balucani, N.; Lin, S. H.; Lee, Y. T.; Kaiser, R. I.; Osamura, Y.

    2000-11-01

    The chemical reaction dynamics to form cyanoacetylene, HCCCN (X 1Σ+), via the radical-neutral reaction of cyano radicals, CN(X 2Σ+;ν=0), with acetylene, C2H2(X 1Σg+), are unraveled in crossed molecular beam experiments at two collision energies of 21.1 and 27.0 kJ mol-1. Laboratory angular distributions and time-of-flight spectra of the HCCCN product are recorded at m/e=51 and 50. Experiments were supplemented by electronic structure calculations on the doublet C3H2N potential energy surface and RRKM investigations. Forward-convolution fitting of the crossed beam data combined with our theoretical investigations shows that the reaction has no entrance barrier and is initiated by an attack of the CN radical to the π electron density of the acetylene molecule to form a doublet cis/trans HCCHCN collision complex on the 2A' surface via indirect reactive scattering dynamics. Here 85% of the collision complexes undergo C-H bond rupture through a tight transition state located 22 kJ mol-1 above the cyanoacetylene, HCCCN (X 1Σ+) and H(2S1/2) products (microchannel 1). To a minor amount (15%) trans HCCHCN shows a 1,2-H shift via a 177 kJ mol-1 barrier to form a doublet H2CCCN radical, which is 46 kJ mol-1 more stable than the initial reaction intermediate (microchannel 2). The H2CCCN complex decomposes via a rather loose exit transition state situated only 7 kJ mol-1 above the reaction products HCCCN (X 1Σ+) and H(2S1/2). In both cases the geometry of the exit transition states is reflected in the observed center-of-mass angular distributions showing a mild forward/sideways peaking. The explicit identification of the cyanoacetylene as the only reaction product represents a solid background for the title reaction to be included in reaction networks modeling the chemistry in dark, molecular clouds, outflow of dying carbon stars, hot molecular cores, as well as the atmosphere of hydrocarbon rich planets and satellites such as the Saturnian moon Titan.

  17. 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.

  18. 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

  19. 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.

  20. 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.

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

    Science.gov (United States)

    Costa, Rafael S; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C

    2010-05-01

    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, 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, convenience kinetics, lin-log and power-law). Using the mechanistic model for Escherichia coli central carbon metabolism as a benchmark, we investigate the alternative modeling approaches through comparative simulations analyses. The good dynamic behavior and the powerful predictive capabilities obtained 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.

  2. Dynamic pathways to mediate reactions buried in thermal fluctuations. I. Time-dependent normal form theory for multidimensional Langevin equation.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2009-12-14

    We present a novel theory which enables us to explore the mechanism of reaction selectivity and robust functions in complex systems persisting under thermal fluctuation. The theory constructs a nonlinear coordinate transformation so that the equation of motion for the new reaction coordinate is independent of the other nonreactive coordinates in the presence of thermal fluctuation. In this article we suppose that reacting systems subject to thermal noise are described by a multidimensional Langevin equation without a priori assumption for the form of potential. The reaction coordinate is composed not only of all the coordinates and velocities associated with the system (solute) but also of the random force exerted by the environment (solvent) with friction constants. The sign of the reaction coordinate at any instantaneous moment in the region of a saddle determines the fate of the reaction, i.e., whether the reaction will proceed through to the products or go back to the reactants. By assuming the statistical properties of the random force, one can know a priori a well-defined boundary of the reaction which separates the full position-velocity space in the saddle region into mainly reactive and mainly nonreactive regions even under thermal fluctuation. The analytical expression of the reaction coordinate provides the firm foundation on the mechanism of how and why reaction proceeds in thermal fluctuating environments.

  3. Discrete approximations of detonation flows with structured detonation reaction zones by discontinuous front models: A program burn algorithm based on detonation shock dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bdzil, J.B. [Los Alamos National Lab., NM (United States); Jackson, T.L. [Univ. of Illinois, Urbana, IL (United States). Center for Simulation of Advanced Rockets; Stewart, D.S. [Univ. of Illinois, Urbana, IL (United States). Theoretical and Applied Mechanics

    1999-02-02

    In the design of explosive systems the generic problem that one must consider is the propagation of a well-developed detonation wave sweeping through an explosive charge with a complex shape. At a given instant of time the lead detonation shock is a surface that occupies a region of the explosive and has a dimension that is characteristic of the explosive device, typically on the scale of meters. The detonation shock is powered by a detonation reaction zone, sitting immediately behind the shock, which is on the scale of 1 millimeter or less. Thus, the ratio of the reaction zone thickness to the device dimension is of the order of 1/1,000 or less. This scale disparity can lead to great difficulties in computing three-dimensional detonation dynamics. An attack on the dilemma for the computation of detonation systems has lead to the invention of sub-scale models for a propagating detonation front that they refer to herein as program burn models. The program burn model seeks not to resolve the fine scale of the reaction zone in the sense of a DNS simulation. The goal of a program burn simulation is to resolve the hydrodynamics in the inert product gases on a grid much coarser than that required to resolve a physical reaction zone. The authors first show that traditional program burn algorithms for detonation hydrocodes used for explosive design are inconsistent and yield incorrect shock dynamic behavior. To overcome these inconsistencies, they are developing a new class of program burn models based on detonation shock dynamic (DSD) theory. It is hoped that this new class will yield a consistent and robust algorithm which reflects the correct shock dynamic behavior.

  4. Untangling the reaction dynamics of the silylidyne radical (SiH; X2Π) with acetylene (C2H2; X1Σg+)

    Science.gov (United States)

    Yang, Tao; Dangi, Beni B.; Thomas, Aaron M.; Kaiser, Ralf I.

    2016-06-01

    The chemical reaction dynamics of silylidyne (SiH; X2Π) with acetylene (C2H2; X1Σg+) were studied exploiting the crossed molecular beam approach, and compared with previous studies on D1-silylidyne with acetylene. The reaction is initiated by a barrierless addition of silylidyne to one or both carbons of acetylene leading to 1-sila-1-propene-1,3-diylidene and/or the cyclic 1-silacyclopropenyl with the former isomerizing to the latter. 1-Silacyclopropenyl eventually loses atomic hydrogen yielding silacyclopropenylidene (c-SiC2H2) in an overall exoergic reaction (experiment: -14.7 ± 8.5 kJ mol-1; theory: -13 ± 3 kJ mol-1). The enthalpy of formation for silacyclopropenylidene is determined to be 421.4 ± 9.3 kJ mol-1.

  5. Does the breakup process affect the reaction dynamics for the systems 17O, 17F + 58Ni at Coulomb barrier energies?

    Directory of Open Access Journals (Sweden)

    Parascandolo C.

    2011-10-01

    Full Text Available The scattering processes of two mirror projectiles, the well bound 17O (Sn = 4.143 MeV and the loosely bound radioactive 17F (Sp = 0.600 MeV, on the proton closed shell target 58Ni were measured at several energies around the Coulomb barrier. The experimental data were analyzed within the framework of the optical model to extract the reaction cross section and to investigate the role played by direct reaction channels at near-barrier energies. The comparison shows a similar behaviour for the two A = 17 projectiles despite their very different binding energies and suggests a rather small effect of the 17F breakup channel on the reaction dynamics.

  6. Quantum dynamics study of energy requirement on reactivity for the HBr + OH reaction with a negative-energy barrier

    Science.gov (United States)

    Wang, Yuping; Li, Yida; Wang, Dunyou

    2017-01-01

    A time-dependent, quantum reaction dynamics approach in full dimensional, six degrees of freedom was carried out to study the energy requirement on reactivity for the HBr + OH reaction with an early, negative energy barrier. The calculation shows both the HBr and OH vibrational excitations enhance the reactivity. However, even this reaction has a negative energy barrier, the calculation shows not all forms of energy are equally effective in promoting the reactivity. On the basis of equal amount of total energy, the vibrational energies of both the HBr and OH are more effective in enhancing the reactivity than the translational energy, whereas the rotational excitations of both the HBr and OH hinder the reactivity. The rate constants were also calculated for the temperature range between 5 to 500 K. The quantal rate constants have a better slope agreement with the experimental data than quasi-classical trajectory results.

  7. Effect of CH stretching excitation on the reaction dynamics of F + CHD{sub 3} → DF + CHD{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiayue; Zhang, Dong; Chen, Zhen; Jiang, Bo [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, Liaoning 116023 (China); Blauert, Florian [Dynamics at Surfaces, Faculty of Chemistry, Georg-August-Universität Göttingen, 37077 Göttingen (Germany); Dai, Dongxu; Wu, Guorong, E-mail: wugr@dicp.ac.cn, E-mail: xmyang@dicp.ac.cn; Zhang, Donghui; Yang, Xueming, E-mail: wugr@dicp.ac.cn, E-mail: xmyang@dicp.ac.cn [State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, 457 Zhongshan Road, Dalian, Liaoning 116023 (China); Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-07-28

    The vibrationally excited reaction of F + CHD{sub 3}(ν{sub 1} = 1) → DF + CHD{sub 2} at a collision energy of 9.0 kcal/mol is investigated using the crossed-beams and time-sliced velocity map imaging techniques. Detailed and quantitative information of the CH stretching excitation effects on the reactivity and dynamics of the title reaction is extracted with the help of an accurate determination of the fraction of the excited CHD{sub 3} reagent in the crossed-beam region. It is found that all vibrational states of the CHD{sub 2} products observed in the ground-state reaction, which mainly involve the excitation of the umbrella mode of the CHD{sub 2} products, are severely suppressed by the CH stretching excitation. However, there are four additional vibrational states of the CHD{sub 2} products appearing in the excited-state reaction which are not presented in the ground-state reaction. These vibrational states either have the CH stretching excitation retained or involve one quantum excitation in the CH stretching and the excitation of the umbrella mode. Including all observed vibrational states, the overall cross section of the excited-state reaction is estimated to be 66.6% of that of the ground-state one. Experimental results also show that when the energy of CH stretching excitation is released during the reaction, it is deposited almost exclusively as the rovibrational energy of the DF products, with little portion in the translational degree of freedom. For vibrational states of the CHD{sub 2} products observed in both ground- and excited-state reactions, the CH stretching excitation greatly suppresses the forward scattered products, causing a noticeable change in the product angular distributions.

  8. Microscopic approach of molecular dynamics. Applications to reactions near the barrier; Approches microscopiques de la dynamique nucleaire. Applications aux reactions autour de la barriere

    Energy Technology Data Exchange (ETDEWEB)

    Simenel, C.; Avez, B. [CEA Saclay, Dept. d' Astrophysique, de Physique des Particules de Physique Nucleaire et de l' Instrumentation Associee (DSM/DAPNIA/SPhN), 91- Gif sur Yvette (France); Lacroix, D. [GANIL, 14 - Caen (France)

    2007-07-01

    This lecture introduces several microscopic approaches to nuclear dynamics. Our goal is to provide a good description of low energy heavy ions collisions. We study both the formalism and the practical application of the time-dependent Hartree-Fock (TDHF) theory. The TDHF approach gives a mean field dynamics of the system under the assumption of independent particles. As an example, we study the fusion of both spherical and deformed nuclei with TDHF. We also show that nucleon transfer may occur between nuclei below the barrier. These studies allow us to specify the field of applications of TDHF in one hand, and, in the other hand, its intrinsic limitations, as for instance the fact that there is no fusion by tunnel effect with TDHF. It is then important to get rid of the independent particle assumption. We finally present some approaches to go beyond TDHF, including for instance pairing and/or collision term between nucleons, though only few realistic applications have been performed so far. (authors)

  9. Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl

    Science.gov (United States)

    Tachikawa, Hiroto

    2006-10-01

    Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl-+H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH ⋯H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.

  10. 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.

  11. Influence of collision energy and vibrational excitation on the dynamics for the H+HBr → H2 + Br reaction

    Indian Academy of Sciences (India)

    Yanhua Wang; Min Peng; Jianying Tong; Yuliang Wang

    2015-08-01

    Quasi-classical trajectory (QCT) calculations of H+HBr → H2 + Br reaction have been performed on a recently proposed ab initio potential energy surface. The reaction probability and integral cross section are found to be in fairly good agreement with the available quantum mechanical (QM) results on this surface. The behavior of reactivity is well consistent with properties of exothermic reaction. Once the energy of vibrational excited HBr is larger than the barrier height, the integral cross sections for the reaction diverge at very low collision energies close to the threshold, similarly to capture reaction. In addition, differential cross sections show that scattering of the product H2 shift from backward to forward directions as the collision energy and vibrational quantum number increase. All the theoretical findings are reasonably explained by the properties of the surface, as well as reactive mechanisms.

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

    Science.gov (United States)

    Zhu, Jian-Zhuo; Qi, Ling-Hui; Du, Hui-Jing; Chai, Ying-Chun

    2015-10-01

    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. Project supported by the Natural Science Foundation of Hebei Province, China (Grant No. A2012203016), the Science Fund from the Education Department of Hebei Province, China (Grant Nos. QN20131103 and Z2009114), the Doctor Foundation of Yanshan University, China (Grant No. B580), and the Young Teachers' Research Project of Yanshan University, China (Grant No. 13LGB028).

  13. The dynamics of the H(+) + D(2) reaction: a comparison of quantum mechanical wavepacket, quasi-classical and statistical-quasi-classical results.

    Science.gov (United States)

    Jambrina, P G; Aoiz, F J; Bulut, N; Smith, Sean C; Balint-Kurti, G G; Hankel, M

    2010-02-01

    A detailed study of the proton exchange reaction H(+) + D(2)(v = 0, j = 0) --> HD + D(+) on its ground 1(1)A' potential energy surface has been carried out using 'exact' close-coupled quantum mechanical wavepacket (WP-EQM), quasi-classical trajectory (QCT), and statistical quasi-classical trajectory (SQCT) calculations for a range of collision energies starting from the reaction threshold to 1.3 eV. The WP-EQM calculations include all total angular momenta up to J(max) = 50, and therefore the various dynamical observables are converged up to 0.6 eV. It has been found that it is necessary to include all Coriolis couplings to obtain reliable converged results. Reaction probabilities obtained using the different methods are thoroughly compared as a function of the total energy for a series of J values. Comparisons are also made of total reaction cross sections as function of the collision energy, and rate constants. In addition, opacity functions, integral cross sections (ICS) and differential cross sections (DCS) are presented at 102 meV, 201.3 meV and 524.6 meV collision energy. The agreement between the three sets of results is only qualitative. The QCT calculations fail to describe the overall reactivity and most of the dynamical observables correctly. At low collision energies, the QCT method is plagued by the lack of conservation of zero point energy, whilst at higher collision energies and/or total angular momenta, the appearance of an effective repulsive potential associated with the centrifugal motion "over" the well causes a substantial decrease of the reactivity. In turn, the statistical models overestimate the reactivity over the whole range of collision energies as compared with the WP-EQM method. Specifically, at sufficiently high collision energies the reaction cannot be deemed to be statistical and important dynamical effects seem to be present. In general the WP-EQM results lie in between those obtained using the QCT and SQCT methods. One of the main

  14. 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.

  15. Effects of incomplete mixing on chemical reactions under flow heterogeneities.

    Science.gov (United States)

    Perez, Lazaro; Hidalgo, Juan J.; Dentz, Marco

    2016-04-01

    Evaluation of the mixing process in aquifers is of primary importance when assessing attenuation of pollutants. In aquifers different hydraulic and chemical properties can increase mixing and spreading of the transported species. Mixing processes control biogeochemical transformations such as precipitation/dissolution reactions or degradation reactions that are fast compared to mass transfer processes. Reactions are local phenomena that fluctuate at the pore scale, but predictions are often made at much larger scales. However, aquifer heterogeities are found at all scales and generates flow heterogeneities which creates complex concentration distributions that enhances mixing. In order to assess the impact of spatial flow heterogeneities at pore scale we study concentration profiles, gradients and reaction rates using a random walk particle tracking (RWPT) method and kernel density estimators to reconstruct concentrations and gradients in two setups. First, we focus on a irreversible bimolecular reaction A+B → C under homogeneous flow to distinguish phenomena of incomplete mixing of reactants from finite-size sampling effects. Second, we analise a fast reversible bimolecular chemical reaction A+B rightleftharpoons C in a laminar Poiseuille flow reactor to determine the difference between local and global reaction rates caused by the incomplete mixing under flow heterogeneities. Simulation results for the first setup differ from the analytical solution of the continuum scale advection-dispersion-reaction equation studied by Gramling et al. (2002), which results in an overstimation quantity of reaction product (C). In the second setup, results show that actual reaction rates are bigger than the obtained from artificially mixing the system by averaging the concentration vertically. - LITERATURE Gramling, C. M.,Harvey, C. F., Meigs, and L. C., (2002). Reactive transport in porous media: A comparison of model prediction with laboratory visualization, Environ. Sci

  16. 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.

  17. REACTION MECHANISM AND DYNAMICS OF H2O2-BASED CHLORINE DIOXIDE PRODUCTION%过氧化氢法制备二氧化氯的反应机理及动力学

    Institute of Scientific and Technical Information of China (English)

    钱宇; 陈赟; 江燕斌; 纪红兵

    2004-01-01

    To develop a cleaner production process of H2O2-based chlorine dioxide, this paper presents a study on reaction mechanism and dynamics of the process. It is shown that a complex H2ClO2-ClO3 exists as an intermediate in the process. A rational reaction process is proposed, which unifies several reaction mechanisms reported by different researchers in a wider range of reaction temperature. A theoretical model of the dynamics is presented, and parameters of the model are experimentally estimated and verified.

  18. Fusion and quasifission dynamics in the reactions 48Ca+249Bk and 50Ti+249Bk using a time-dependent Hartree-Fock approach

    Science.gov (United States)

    Umar, A. S.; Oberacker, V. E.; Simenel, C.

    2016-08-01

    Background: Synthesis of superheavy elements (SHEs) 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 SHEs have been recently produced with doubly-magic 48Ca beams. However, SHE synthesis experiments with single-magic 50Ti 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 48Ca,50Ti+249Bk 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: Nucleus-nucleus potentials, nuclear contact times, masses and charges of the fragments, as well as their kinetic and excitation energies strongly depend on the orientation of the prolate 249Bk nucleus. Long contact times associated with fusion are observed in collisions of both projectiles with the side of the 249Bk nucleus, but not on collisions with its tip. The energy and impact parameter dependencies of the fragment properties, as well as their mass-angle and mass-total kinetic energy correlations are investigated. Conclusions: Entrance channel reaction dynamics are similar with both 48Ca and 50Ti projectiles. Both are expected to lead to the formation of a compound nucleus by fusion if they have enough energy to get in contact with the side of the 249Bk target.

  19. Modelling of gas-liquid reactors - stability and dynamic behaviour of gas-liquid mass transfer accompanied by irreversible reaction

    NARCIS (Netherlands)

    Elk, E.P. van; Borman, P.C.; Kuipers, J.A.M.; Versteeg, G.F.

    1999-01-01

    The dynamic behaviour and stability of single-phase reacting systems has been investigated thoroughly in the past and design rules for stable operation are available from literature. The dynamic behaviour of gas-liquid processes is considerably more complex and has received relatively little attenti

  20. Hydrogen release reactions of Al-based complex hydrides enhanced by vibrational dynamics and valences of metal cations.

    Science.gov (United States)

    Sato, T; Ramirez-Cuesta, A J; Daemen, L; Cheng, Y-Q; Tomiyasu, K; Takagi, S; Orimo, S

    2016-09-27

    Hydrogen release from Al-based complex hydrides composed of metal cation(s) and [AlH4](-) was investigated using inelastic neutron scattering viewed from vibrational dynamics. The hydrogen release followed the softening of translational and [AlH4](-) librational modes, which was enhanced by vibrational dynamics and the valence(s) of the metal cation(s).

  1. Theoretical studies on dynamics and thermochemistry of the reactions CHClFCHO, CHF 2CHO and CClF 2CHO with the Cl atom

    Science.gov (United States)

    Wang, Ying; Liu, Jing-Yao; Li, Ze-Sheng; Wang, Li; Wu, Jia-Yan; Sun, Chia-Chung

    2006-05-01

    The theoretical investigations are performed on the reaction mechanisms, including hydrogen abstraction and addition reaction channels for the three reactions CHClFCHO + Cl → products (R1), CHF 2CHO + Cl → products (R2), and CClF 2CHO + Cl → products (R3) by ab initio direct dynamics approach. The electronic structure information for the stationary points is obtained at the MP2 level of theory using the cc-pVDZ and aug-cc-pVDZ basis sets. The classical energy profile is refined by multi-coefficient correlation method based on quadratic configuration interaction with single and double excitation (MC-QCISD) using the MP2 optimized geometries. The enthalpies of formation for the reactants and product radicals involved in the three reactions are estimated at the MC-QCISD//MP2 level via isodesmic reactions. We find that each addition reaction pathway has a much higher potential energy barrier, and therefore its contribution to the total rate constants can be neglected. The rate constants for the H-abstraction reactions, which are evaluated by canonical variational transition state theory with the small-curvature tunneling correction over a range of temperatures from 220 to 2000 K, are in good agreement with the available experimental values. The Arrhenius expressions are fitted to be (in cm 3 molecule -1 s -1) k1 = 5.08 × 10 -160 T1.60 exp (244.6/ T), k2 = 4.80 × 10 -17 T1.86 exp (274.9/ T), and k3 = 2.34 × 10 -16 T1.67 exp (37.1/ T), respectively. Our conclusions show that for reaction CHClFCHO + Cl → products (R1), the channel of hydrogen abstraction from the formyl (-CHO) position is the primary pathway at low temperature, but as the temperature increases the hydrogen abstraction from the -CHClF group is more probable. While for reaction CHF 2CHO + Cl → products (R2), the pathway of hydrogen abstraction from the formyl position is always the primary channel over the whole temperature range. We also find that the halogen substitute (F or Cl

  2. Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions.

    Directory of Open Access Journals (Sweden)

    Niamh M C Connolly

    Full Text Available Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK, re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult.

  3. Theoretical and Experimental Studies on the Reaction Mechanism of Cl2+I2=2ICl

    Institute of Scientific and Technical Information of China (English)

    YANG Guo-Ying; YUAN Li-Xia; SUN De-Sheng; WANG Zun-Yao; JIANG Tao

    2006-01-01

    The gas phase reaction mechanism of Cl2 + I2 = 2ICI has been theoretically investigated by DFT method at the B3LYP/3-21G* level. Transition states of three reaction channels were consequently given. The results indicate that in the title reaction the least activation energy of bi-molecular reaction was smaller than the dissociation energies of I2 and Cl2, and thus the reaction mechanism was the course of molecule-molecule interaction at low reaction rate. If other factors such as illumination were taken into account, I2 could dissociate into I atoms and then react with Cl2,or Cl2 dissociates into Cl atoms and reacts with I2. These were photochemical reactions with high reaction speed. The theoretical results were further validated with absorbance measurement at 516 nm.

  4. Processes in regulatory systems during development of various adaptational reactions and evaluation of functional state dynamics in the organism

    Directory of Open Access Journals (Sweden)

    Galina V. Zhukova

    2015-11-01

    Full Text Available The paper describes some concepts on processes occurring in the neuroendocrine and immune systems during development of general unspecific adaptational reactions. The concepts are based on the known evidence on the changes in the regulatory systems and the previously identified peculiarities in correlations between the levels of biogenic amines in blood and the organs, respectively, under various adaptational reactions, as well as the known effects of biogenic amines. A number of practical consequences significant for the correct evaluation of the functional state in humans and animals are also considered herein.

  5. An eight-dimensional quantum dynamics study of the Cl + CH{sub 4}→ HCl + CH{sub 3} reaction

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Na; Yang, Minghui, E-mail: yangmh@wipm.ac.cn [State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China)

    2015-10-07

    In this work, the later-barrier reaction Cl + CH{sub 4} → HCl + CH{sub 3} 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 CH{sub 4} 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.

  6. Mode-specific multi-channel dynamics of the F- + CHD2Cl reaction on a global ab initio potential energy surface

    Science.gov (United States)

    Szabó, István; Czakó, Gábor

    2016-10-01

    We report a detailed quasiclassical trajectory study for the dynamics of the ground-state and CH/CD stretching-excited F- + CHD2Cl(vCH/CD = 0, 1) → Cl- + CHD2F, HF + CD2Cl-, and DF + CHDCl- SN2, proton-, and deuteron-abstraction reactions using a full-dimensional global ab initio analytical potential energy surface. The simulations show that (a) CHD2Cl(vCH/CD = 1), especially for vCH = 1, maintains its mode-specific excited character prior to interaction, (b) the SN2 reaction is vibrationally mode-specific, (c) double inversion can occur and is enhanced upon CH/CD stretching excitations, (d) in the abstraction reactions the HF channel is preferred and the vCH/CD = 1 excitations significantly promote the HF/DF channels, (e) back-side rebound, back-side stripping, and front-side stripping are the dominant direct abstraction mechanisms based on correlated scattering- and attack-angle distributions, (f) the exact classical vibrational energy-based Gaussian binning (1GB) provides realistic mode-specific polyatomic product state distributions, (g) in the abstraction reactions CH and CD stretchings are not pure spectator modes and mainly ground-state products are produced, thus most of the initial energy transfers into product translation, and (h) the HF and DF product molecules are rotationally cold without any significant dependence on the reactant's and HF/DF vibrational states.

  7. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    Science.gov (United States)

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-08

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. 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. As an example of the application of this approach, we also 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.

  8. Theoretical Studies of the Role of Vibrational Excitation on the Dynamics of the Hydrogen-Transfer Reaction of F(^2P) + HCl → FH + Cl({^2}P)

    Science.gov (United States)

    Ray, Sara E.; Vissers, Gé W. M.; McCoy, Anne B.

    2009-06-01

    Hydrogen-transfer reactions are probed through vibrational excitation of the HCl bond in the pre-reactive F\\cdotsHCl complex. Such open-shell species provide a challenge for quantum dynamical calculations due to the need to take into account multiple potential energy surfaces to accurately describe the system.A three-dimensional, fully-coupled potential energy surface has been constructed based on electronic energies calculated at the multireference configuration interaction+Davidson correction (MRCI+Q) level of theory with an aug-cc-pVnZ (n=2,3,4) basis. Spin orbit calculations have also been included. Here we present the results of time-dependent quantum wave packet calculations on the asymmetric hydrogen-transfer reaction of F(^2P) + HCl. In these calculations, the reaction is initiated by vibrationally exciting the HCl stretching motion in the pre-reactive F\\cdotsHCl complex. The wave packet is propagated on the coupled potential energy surfaces. Product state distributions were calculated for reactions initiated in the first three vibrationally excited states of HCl, v=1-3. M. P. Deskevich, M. Y. Hayes, K. Takahashi, R. T. Skodje, and D. J. Nesbitt J. Chem. Phys. 124 (22) 224303 (2006) M. P. Deskevich and D. J. Nesbitt private communication(2007)

  9. Reaction dynamics in the combustion synthesis system of Al-CrO3-Al2O3-NaF-N2-O2

    Institute of Scientific and Technical Information of China (English)

    Dazheng Yang; Yue Zhang; Degang Li; Dianwei Qi; Wei Deng; Dayong Xun

    2007-01-01

    A new material with heat-resistant and adiabatic characteristics and high strength was prepared using the combustion synthesis method by mixed powders of CrO3, Al, Al2O3, and NaF in atmospheric gas. The reaction dynamic process of the Al-CrO3-NaF-Al2O3-N2-O2 new material system by the combustion synthesis method was discussed based on the observation results by SEM,EDS, and XRD in combination with the combustion front quenching method (CFQM) and the relation curves between reaction free enthalpies and the corresponding temperatures. The combustion synthesis mechanism and the formation reasons of the phase in the combustion product were analyzed.

  10. A comprehensive interpretation of mixing effects on stationary states and dynamical behavior of the bistable ClO - 2-I - reaction in a flow reactor

    Science.gov (United States)

    Boissonade, J.; De Kepper, P.

    1987-07-01

    We propose an interpretation of mixing effects on temporal dissipative structures in CSTR in terms of micromixing. The bistability of the ClO-2 -I- reaction is extensively discussed. The micromixing process is successively represented by a mean field model and a coalescence redispersion model, together with a realistic kinetic scheme of the reaction. The latter was found more suited to the problem. The results are in good agreement with experimental observations previously reported, accounting for shifts in the transitions from thermodynamic branch to flow branch both in premixed and nonpremixed mode. It also accounts for dynamical behavior in the vicinity of the transition, including oscillatory fluctuations. It is finally suggested that micromixing processes could induce oscillations in otherwise nonoscillating conditions if the system was perfectly homogeneous.

  11. Effects of reactant rotation on the dynamics of the OH + CH4 → H2O + CH3 reaction: A six-dimensional study

    Science.gov (United States)

    Song, Hongwei; Li, Jun; Jiang, Bin; Yang, Minghui; Lu, Yunpeng; Guo, Hua

    2014-02-01

    The dynamics of the hydrogen abstraction reaction between methane and hydroxyl radical is investigated using an initial state selected time-dependent wave packet method within a six-dimensional model. The ab initio calibrated global potential energy surface of Espinosa-García and Corchado was used. Integral cross sections from several low-lying rotational states of both reactants have been obtained using the centrifugal sudden and J-shifting approximations. On the empirical potential energy surface, the rotational excitation of methane has little effect on the reaction cross section, but excited rotational states of OH inhibit the reactivity slightly. These results are rationalized with the newly proposed sudden vector projection model.

  12. Stereodirectional Origin of anti-Arrhenius Kinetics for a Tetraatomic Hydrogen Exchange Reaction: Born-Oppenheimer Molecular Dynamics for OH + HBr.

    Science.gov (United States)

    Coutinho, Nayara D; Aquilanti, Vincenzo; Silva, Valter H C; Camargo, Ademir J; Mundim, Kleber C; de Oliveira, Heibbe C B

    2016-07-14

    Among four-atom processes, the reaction OH + HBr → H2O + Br is one of the most studied experimentally: its kinetics has manifested an unusual anti-Arrhenius behavior, namely, a marked decrease of the rate constant as the temperature increases, which has intrigued theoreticians for a long time. Recently, salient features of the potential energy surface have been characterized and most kinetic aspects can be considered as satisfactorily reproduced by classical trajectory simulations. Motivation of the work reported in this paper is the investigation of the stereodirectional dynamics of this reaction as the prominent reason for the peculiar kinetics: we started in a previous Letter ( J. Phys. Chem. Lett. 2015 , 6 , 1553 - 1558 ) a first-principles Born-Oppenheimer "canonical" molecular dynamics approach. Trajectories are step-by-step generated on a potential energy surface quantum mechanically calculated on-the-fly and are thermostatically equilibrated to correspond to a specific temperature. Here, refinements of the method permitted a major increase of the number of trajectories and the consideration of four temperatures -50, +200, +350, and +500 K, for which the sampling of initial conditions allowed us to characterize the stereodynamical effect. The role is documented of the adjustment of the reactants' mutual orientation to encounter the entrance into the "cone of acceptance" for reactivity. The aperture angle of this cone is dictated by a range of directions of approach compatible with the formation of the specific HOH angle of the product water molecule; and consistently the adjustment is progressively less effective the higher the kinetic energy. Qualitatively, this emerging picture corroborates experiments on this reaction, involving collisions of aligned and oriented molecular beams, and covering a range of energies higher than the thermal ones. The extraction of thermal rate constants from this molecular dynamics approach is discussed and the systematic

  13. Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

    Science.gov (United States)

    Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

    2011-05-14

    We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

  14. The acute effects of a warm-up including static or dynamic stretching on countermovement jump height, reaction time, and flexibility.

    Science.gov (United States)

    Perrier, Erica T; Pavol, Michael J; Hoffman, Mark A

    2011-07-01

    The purpose of this research was to compare the effects of a warm-up with static vs. dynamic stretching on countermovement jump (CMJ) height, reaction time, and low-back and hamstring flexibility and to determine whether any observed performance deficits would persist throughout a series of CMJs. Twenty-one recreationally active men (24.4 ± 4.5 years) completed 3 data collection sessions. Each session included a 5-minute treadmill jog followed by 1 of the stretch treatments: no stretching (NS), static stretching (SS), or dynamic stretching (DS). After the jog and stretch treatment, the participant performed a sit-and-reach test. Next, the participant completed a series of 10 maximal-effort CMJs, during which he was asked to jump as quickly as possible after seeing a visual stimulus (light). The CMJ height and reaction time were determined from measured ground reaction forces. A treatment × jump repeated-measures analysis of variance for CMJ height revealed a significant main effect of treatment (p = 0.004). The CMJ height was greater for DS (43.0 cm) than for NS (41.4 cm) and SS (41.9 cm) and was not less for SS than for NS. Analysis also revealed a significant main effect of jump (p = 0.005) on CMJ height: Jump height decreased from the early to the late jumps. The analysis of reaction time showed no significant effect of treatment. Treatment had a main effect (p < 0.001) on flexibility, however. Flexibility was greater after both SS and DS compared to after NS, with no difference in flexibility between SS and DS. Athletes in sports requiring lower-extremity power should use DS techniques in warm-up to enhance flexibility while improving performance.

  15. Applied reaction dynamics: Efficient synthesis gas production via single collision partial oxidation of methane to CO on Rh(111)

    Science.gov (United States)

    Gibson, K. D.; Viste, M.; Sibener, S. J.

    2006-10-01

    Supersonic molecular beams have been used to determine the yield of CO from the partial oxidation of CH4 on a Rh(111) catalytic substrate, CH4+(1/2)O2→CO +2H2, as a function of beam kinetic energy. These experiments were done under ultrahigh vacuum conditions with concurrent molecular beams of O2 and CH4, ensuring that there was only a single collision for the CH4 to react with the surface. The fraction of CH4 converted is strongly dependent on the normal component of the incident beam's translational energy, and approaches unity for energies greater than ˜1.3eV. Comparison with a simplified model of the methane-Rh(111) reactive potential gives insight into the barrier for methane dissociation. These results demonstrate the efficient conversion of methane to synthesis gas, CO +2H2, are of interest in hydrogen generation, and have the optimal stoichiometry for subsequent utilization in synthetic fuel production (Fischer-Tropsch or methanol synthesis). Moreover, under the reaction conditions explored, no CO2 was detected, i.e., the reaction proceeded with the production of very little, if any, unwanted greenhouse gas by-products. These findings demonstrate the efficacy of overcoming the limitations of purely thermal reaction mechanisms by coupling nonthermal mechanistic steps, leading to efficient C-H bond activation with subsequent thermal heterogeneous reactions.

  16. Probing the Energy Transfer Dynamics of Photosynthetic Reaction Center Complexes Through Hole-Burning and Single-Complex Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Kerry Joseph [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Photosynthesis is the process by which light energy is used to drive reactions that generate sugars to supply energy for cellular processes. It is one of the most important fundamental biological reactions and occurs in both prokaryotic (e.g. bacteria) and eukaryotic (e.g. plants and algae) organisms. Photosynthesis is also remarkably intricate, requiring the coordination of many different steps and reactions in order to successfully transform absorbed solar energy into a biochemical usable form of energy. However, the net reaction for all photosynthetic organisms can be reduced to the following, deceptively general, equation developed by Van Niel[1] H2 - D + Aimplieshv A - H2 + D where H2-D is the electron donor, e.g. H2O, H2S. A is the electron acceptor, e.g. CO2, and A-H2 is the synthesized sugar. Amazingly, this simple net equation is responsible for creating the oxidizing atmosphere of Earth and the recycling of CO2, both of which are necessary for the sustainment of the global ecosystem.

  17. Intersystem crossing and dynamics in O(3P) + C2H4 multichannel reaction: experiment validates theory.

    Science.gov (United States)

    Fu, Bina; Han, Yong-Chang; Bowman, Joel M; Angelucci, Luca; Balucani, Nadia; Leonori, Francesca; Casavecchia, Piergiorgio

    2012-06-19

    The O((3)P) + C(2)H(4) reaction, of importance in combustion and atmospheric chemistry, stands out as a paradigm reaction involving triplet- and singlet-state potential energy surfaces (PESs) interconnected by intersystem crossing (ISC). This reaction poses challenges for theory and experiments owing to the ruggedness and high dimensionality of these potentials, as well as the long lifetimes of the collision complexes. Primary products from five competing channels (H + CH(2)CHO, H + CH(3)CO, H(2) + CH(2)CO, CH(3) + HCO, CH(2) + CH(2)O) and branching ratios (BRs) are determined in crossed molecular beam experiments with soft electron-ionization mass-spectrometric detection at a collision energy of 8.4 kcal/mol. As some of the observed products can only be formed via ISC from triplet to singlet PESs, from the product BRs the extent of ISC is inferred. A new full-dimensional PES for the triplet state as well as spin-orbit coupling to the singlet PES are reported, and roughly half a million surface hopping trajectories are run on the coupled singlet-triplet PESs to compare with the experimental BRs and differential cross-sections. Both theory and experiment find almost equal contributions from the two PESs to the reaction, posing the question of how important is it to consider the ISC as one of the nonadiabatic effects for this and similar systems involved in combustion chemistry. Detailed comparisons at the level of angular and translational energy distributions between theory and experiment are presented for the two primary channel products, CH(3) + HCO and H + CH(2)CHO. The agreement between experimental and theoretical functions is excellent, implying that theory has reached the capability of describing complex multichannel nonadiabatic reactions.

  18. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations.

    Science.gov (United States)

    Ardèvol, Albert; Rovira, Carme

    2015-06-24

    Carbohydrate-active enzymes such as glycoside hydrolases (GHs) and glycosyltransferases (GTs) are of growing importance as drug targets. The development of efficient competitive inhibitors and chaperones to treat diseases related to these enzymes requires a detailed knowledge of their mechanisms of action. In recent years, sophisticated first-principles modeling approaches have significantly advanced in our understanding of the catalytic mechanisms of GHs and GTs, not only the molecular details of chemical reactions but also the significant implications that just the conformational dynamics of a sugar ring can have on these mechanisms. Here we provide an overview of the progress that has been made in the past decade, combining molecular dynamics simulations with density functional theory to solve these sweet mysteries of nature.

  19. A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions

    Science.gov (United States)

    Chevalier, Michael W.; El-Samad, Hana

    2014-12-01

    Noise and stochasticity are fundamental to biology and derive from the very nature of biochemical reactions where thermal motion of molecules translates into randomness in the sequence and timing of reactions. This randomness leads to cell-to-cell variability even in clonal populations. Stochastic biochemical networks have been traditionally modeled as continuous-time discrete-state Markov processes whose probability density functions evolve according to a chemical master equation (CME). In diffusion reaction systems on membranes, the Markov formalism, which assumes constant reaction propensities is not directly appropriate. This is because the instantaneous propensity for a diffusion reaction to occur depends on the creation times of the molecules involved. In this work, we develop a chemical master equation for systems of this type. While this new CME is computationally intractable, we make rational dimensional reductions to form an approximate equation, whose moments are also derived and are shown to yield efficient, accurate results. This new framework forms a more general approach than the Markov CME and expands upon the realm of possible stochastic biochemical systems that can be efficiently modeled.

  20. Mass-dependent dynamics of the luminescent exchange reactions C+(2P), P+(3P) + H2, D2, HD

    Science.gov (United States)

    Glenewinkel-Meyer, Th; Hoppe, U.; Kowalski, A.; Ottinger, Ch; Rabenda, D.

    1995-06-01

    Chemiluminescent ion/molecule reactions of ground state C+ and P+ ions with H2, D2 and HD have been studied in an ion beam/target gas cell arrangement. Emission spectra of CH+, CD+ (A 1II) and of PH+, PD+ (A 2[Delta]) were observed with up to 1 Å FWHM resolution and at collision energies from threshold ([approximate] 3 eV) to 8 eVc.m. (centre-of-mass) and 15eVc.m., respectively. Very detailed computer simulations of the spectral contours were done, including ab initio transition moments and, in the case of PH+/PD+, the effects of predissociation. In simulating the spectra obtained with HD, the overlapped hydride and deuteride product ion spectra could be isolated by varying the respective weighting factors to achieve an optimum overall fit. In the case of C+ + HD, the two components were found to have very similar rovibrational distributions as with the products from C+ + H2 and C+ + D2. In the P+ case, however, the rotational, although not the vibrational, distributions were found to be significantly different for the isotopically mixed and the pure reactions. The cross-sections showed an intermolecular isotope effect only for C+ + H2 vs. C+ + D2 at high energies. However, both with C+ + HD and P+ + HD, a very strong intramolecular isotope effect, i.e. an energy-dependent branching ratio, was observed: at low energies deuteride formation prevails, at high energies hydride. This behaviour is discussed in terms of an impulsive collision model, assuming the "pairwise" relative kinetic energy between the reacting atoms to be the determining factor. On the basis of the measured cross-section curves for the H2 and D2 reactions, the energy-dependent hydride/deuteride ratio in the HD reaction can then be predicted. The agreement with the experimental results is excellent in the P+ case, but only moderate for the C+ reactions. Even the P+ reaction, however, does not occur via the spectator stripping mechanisms. The spectra show an energy-independent vibrational excitation