WorldWideScience

Sample records for bimolecular reaction dynamics

  1. Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

    KAUST Repository

    Lipková, Jana

    2011-01-01

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

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

    KAUST Repository

    Suleimanov, Yu.V.

    2013-03-01

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

  3. 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, D.A.

    1997-08-01

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

  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. Tuning bimolecular chemical reactions by electric fields

    CERN Document Server

    Tscherbul, Timur V

    2014-01-01

    We develop a theoretical method for solving the quantum mechanical reactive scattering problem in the presence of external fields based on a hyperspherical coordinate description of the reaction complex combined with the total angular momentum representation for collisions in external fields. The method allows us to obtain converged results for the chemical reaction LiF + H -> Li + HF in an electric field. Our calculations demonstrate that, by inducing couplings between states of different total angular momenta, electric fields with magnitudes <150 kV/cm give rise to resonant scattering and a significant modification of the total reaction probabilities, product state distributions and the branching ratios for reactive vs inelastic scattering.

  8. Theory of Crowding Effects on Bimolecular Reaction Rates.

    Science.gov (United States)

    Berezhkovskii, Alexander M; Szabo, Attila

    2016-07-01

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

  9. 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.

  10. Improved understanding of bimolecular reactions in deceptively simple homogeneous media: From laboratory experiments to Lagrangian quantification

    Science.gov (United States)

    Zhang, Yong; Qian, Jiazhong; Papelis, Charalambos; Sun, Pengtao; Yu, Zhongbo

    2014-02-01

    Medium heterogeneity affects reaction kinetics by controlling the mixing of reactant particles, but the linkage between medium properties and reaction kinetics is difficult to build, even for simple, relatively homogeneous media. This study aims to explore the dynamics of bimolecular reactions, aniline + 1,2-naphthoquinone-4-sulfonic acid → 1,2-naphthoquinone-4-aminobenzene, in relatively homogeneous flow cells. Laboratory experiments were conducted to monitor the transport of both conservative and reactive tracers through columns packed with silica sand of specific diameters. The measured tracer breakthrough curves exhibit subdiffusive behavior with a late-time tail becoming more pronounced with decreasing sand size, probably due to the segregated flow regions formed more easily in columns packed with smaller size sand. Numerical analysis using a novel Lagrangian model shows that subdiffusion has a twofold effect on bimolecular reactions. While subdiffusion enhances the power-law growth rate of product mass by prolonging the exposure of reactant particles in the depletion zone, the global reaction rate is constrained because subdiffusion constrains the mobility of reactant particles. Reactive kinetics in deceptively simple homogeneous media is therefore controlled by subdiffusion, which is sensitive to the dimensions of packed sand.

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

    Science.gov (United States)

    Arshadi, Masoud; Rajaram, Harihar

    2015-09-01

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

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

    OpenAIRE

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

    2015-01-01

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

  13. 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.

  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. 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.

  16. 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

  17. 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.

  18. 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.

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

    Science.gov (United States)

    Doktorov, Alexander B

    2016-08-28

    Manifestations of the "cage" effect at the encounters of reactants have been theoretically treated on the example of multistage reactions (including bimolecular exchange reactions as elementary stages) proceeding from different active sites in liquid solutions. It is shown that for reactions occurring near the contact of reactants, consistent consideration of quasi-stationary kinetics of such multistage reactions (possible in the framework of the encounter theory only) can be made on the basis of chemical concepts of the "cage complex," just as in the case of one-site model described in the literature. Exactly as in the one-site model, the presence of the "cage" effect gives rise to new channels of reactant transformation that cannot result from elementary event of chemical conversion for the given reaction mechanism. Besides, the multisite model demonstrates new (as compared to one-site model) features of multistage reaction course. PMID:27586911

  20. Luminescence Spectroscopy and Bimolecular Quenching

    Science.gov (United States)

    Demas, J. N.

    1975-01-01

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

  1. Roaming dynamics in radical addition-elimination reactions

    Science.gov (United States)

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

    2014-06-01

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Dynamics of anion-molecule reactions at low energy

    International Nuclear Information System (INIS)

    Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (SN2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of SN2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing SN2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout SN2 mechanism involving CH3-rotation. (orig.)

  7. 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.)

  8. Semiclassical methods in chemical reaction dynamics

    International Nuclear Information System (INIS)

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

  9. Semiclassical methods in chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Keshavamurthy, S.

    1994-12-01

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

  10. 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.

  11. 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…

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

    International Nuclear Information System (INIS)

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

  13. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-12-01

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

  15. 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....

  16. 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...

  17. 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.

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

    OpenAIRE

    Tsintsarska, Stefka

    2007-01-01

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

  19. 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.

  20. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-10

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

  1. 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.

  2. Quantum effects in unimolecular reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Gezelter, J.D.

    1995-12-01

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

  3. 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.

  4. 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

  5. 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.

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

    Science.gov (United States)

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

    2009-06-01

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

  7. 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.

  8. 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.

  9. 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.

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

    Science.gov (United States)

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

    2015-08-01

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

  11. A network dynamics approach to chemical reaction networks

    NARCIS (Netherlands)

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

    2016-01-01

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

  12. 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.

  13. 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.

  14. Mode-coupling theory for reaction dynamics in liquids

    OpenAIRE

    Shental, Nurit; Rabani, Eran

    2003-01-01

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

  15. 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}.

  16. Electromagnetic reactions and few-nucleon dynamics

    International Nuclear Information System (INIS)

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

  17. Electromagnetic Reactions and Few-Nucleon Dynamics

    Directory of Open Access Journals (Sweden)

    Bacca Sonia

    2014-03-01

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

  18. 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.

  19. 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.

  20. 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.

  1. Dynamics of fission and heavy ion reactions

    International Nuclear Information System (INIS)

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

  2. Testing string dynamics in lepton nucleus reactions

    International Nuclear Information System (INIS)

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

  3. 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...

  4. 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.

  5. A network dynamics approach to chemical reaction networks

    Science.gov (United States)

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

    2016-04-01

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

  6. Crossed molecular beam studies of unimolecular reaction dynamics

    International Nuclear Information System (INIS)

    The study of seven radical-molecule reactions using the crossed molecular beam technique with supersonic nozzle beams is reported. Product angular and velocity distributions were obtained and compared with statistical calculations in order to identify dynamical features of the reactions. In the reaction of chlorine and fluorine atoms with vinyl bromide, the product energy distributions are found to deviate from predictions of the statistical model. A similar effect is observed in the reaction of chlorine atoms with 1, 2 and 3-bromopropene. The reaction of oxygen atoms with ICl and CF3I has been used to obtain an improved value of the IO bond energy, 55.0 +- 2.0 kcal mol-1. In all reactions studied, the product energy and angular distributions are found to be coupled, and this is attributed to a kinematic effect of the conservation of angular momentum

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

    Science.gov (United States)

    Takayanagi, Toshiyuki; Tanaka, Tomokazu

    2011-03-01

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

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

    Institute of Scientific and Technical Information of China (English)

    Gao Yongcan; Zhang Jiushun; Xie Chaogang; Long Jun

    2002-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Dasgupta M.

    2014-03-01

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

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

    International Nuclear Information System (INIS)

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

  11. 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...

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

    Science.gov (United States)

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

    2016-07-14

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

  13. 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.

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

    OpenAIRE

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

    2014-01-01

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

  15. 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.

  16. 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

  17. Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions

    Science.gov (United States)

    Menon, Madhu

    1998-01-01

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

  18. Finite temperature amplitudes and reaction rates in Thermofield dynamics

    CERN Document Server

    Rakhimov, A M

    2001-01-01

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

  19. 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.

  20. 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

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

    International Nuclear Information System (INIS)

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

  2. 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.

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

    International Nuclear Information System (INIS)

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

  4. 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...

  5. 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.

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

    Science.gov (United States)

    Zeitler, Todd R.

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

  7. Crossed molecular beam studies of atmospheric chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jingsong

    1993-04-01

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

  8. 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.

  9. 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.

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

    Science.gov (United States)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

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

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

    Science.gov (United States)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

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

  12. 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.

  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. 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.

  15. Fluid dynamic modeling of nano-thermite reactions

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-03-14

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

  16. Fluid dynamic modeling of nano-thermite reactions

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Georgiev Nikola

    2006-01-01

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

  1. 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 ...

  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. 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

  4. The quantum dynamics of electronically nonadiabatic chemical reactions

    Science.gov (United States)

    Truhlar, Donald G.

    1993-04-01

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

  5. Dynamics of GeV light-ion-induced reactions

    International Nuclear Information System (INIS)

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

  6. Dynamics of GeV light-ion-induced reactions

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-09-01

    Recent results from studies of the 1.8 - 4.8 GeV {sup 3}He + {sup nat}Ag, {sup 197}Au reactions at LNS with the ISiS detector array have shown evidence for a saturation in deposition energy and multifragmentation from a low-density source. The collision dynamics have been examined in the context of intranuclear cascade and BUU models, while breakup phenomena have been compared with EES and SMM models. Fragment-fragment correlations and isotope ratios are also investigated. (K.A.). 19 refs.

  7. Adsorption Isotherms and Surface Reaction Kinetics

    Science.gov (United States)

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

    1974-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2013-01-01

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

  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. Dynamical calculations of nuclear fission and heavy-ion reactions

    International Nuclear Information System (INIS)

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

  15. Dynamical Monte Carlo methods for plasma-surface reactions

    Science.gov (United States)

    Guerra, Vasco; Marinov, Daniil

    2016-08-01

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

  16. Femtosecond stimulated Raman spectroscopy of ultrafast biophysical reaction dynamics

    Science.gov (United States)

    McCamant, David William

    2004-12-01

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

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

    International Nuclear Information System (INIS)

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

  18. 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

  19. 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...

  20. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-14

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

  1. 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.

  2. 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…

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

    Directory of Open Access Journals (Sweden)

    Merabet Samir

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    YANG XueMing; XIE DaiQian; ZHANG DongHui

    2007-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. Accelerating chemical reactions: Exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

    Science.gov (United States)

    Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.

    2011-01-01

    A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673

  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. 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.

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

    Science.gov (United States)

    Yu, Hua-Gen

    2011-08-01

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

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

    CERN Document Server

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

    2015-01-01

    Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's u...

  13. 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...

  14. 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.

  15. 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.

  16. A catalyst for an acetal hydrolysis reaction from a dynamic combinatorial library

    NARCIS (Netherlands)

    Vial, Laurent; Sanders, Jeremy K.M.; Otto, Sijbren

    2005-01-01

    A transition-state analogue (TSA) for an acetal hydrolysis reaction was found to select and amplify a macrocycle from a dynamic combinatorial library (DCL) of disulfides in water. This host was able to accelerate the reaction by a factor of two; a similar value was progressively reached when the mac

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

    International Nuclear Information System (INIS)

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

  18. 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.

  19. 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)

  20. Reaction dynamics of molecular hydrogen on silicon surfaces

    DEFF Research Database (Denmark)

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

    1996-01-01

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

  1. Resonances and reactions from mean-field dynamics

    Directory of Open Access Journals (Sweden)

    Stevenson P. D.

    2016-01-01

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

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

    NARCIS (Netherlands)

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

    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

  3. Reaction dynamics for fusion of weakly-bound nuclei

    OpenAIRE

    Hagino, K.; Vitturi, A.

    2004-01-01

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

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

    OpenAIRE

    Radermacher, Tobias; Lübbert, Jan; Weber, Jürgen

    2016-01-01

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

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

    Science.gov (United States)

    Pinnamaneni, M.; Murray, J.

    1987-01-01

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

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

    Science.gov (United States)

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

    2016-05-10

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

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

    CERN Document Server

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

    1999-01-01

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

  8. Reaction dynamics and nuclear structure of moderately neutron-rich Ne isotopes by heavy ion reactions

    Directory of Open Access Journals (Sweden)

    Bottoni S.

    2014-03-01

    Full Text Available The heavy ion reaction 22Ne+208Pb at 128 MeV of bombarding energy has been studied using the PRISMA-CLARA experimental setup at Legnaro National Laboratories. Elastic, inelastic and one nucleon transfer cross sections have been measured. The experimental results are presented in parallel with the analysis on existing data for the unstable 24Ne nucleus, from the reaction 24Ne+208Pb at 182 MeV (measured at SPIRAL with the VAMOS-EXOGAM setup. The β2C charge deformation parameter for both 22Ne and 24Ne has been determined by a DWBA analysis of the experimental angular dis- tributions, showing a strong reduction for 24Ne.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

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

    International Nuclear Information System (INIS)

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

  14. 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).

  15. 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.

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

    Science.gov (United States)

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

    2008-06-01

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

  17. 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.

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

    Science.gov (United States)

    Prakash, S.; Nicolis, G.

    1996-01-01

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

  19. 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.

  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. 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.

  2. 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...

  3. Bimolecular fluorescence complementation analysis of eukaryotic fusion products

    OpenAIRE

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  5. 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.

  6. 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.

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

    Science.gov (United States)

    Ward, Kebra A.; Richman, Brittany R.; Biaggio, Ivan

    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 × 1020 cm-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.

  8. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

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

  11. 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.

  12. 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.

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

    Science.gov (United States)

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

    2015-11-01

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

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

    International Nuclear Information System (INIS)

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

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

    DEFF Research Database (Denmark)

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

    2004-01-01

    A dynamic model describing carbon atom transitions in the central metabolism of Saccharomyces cerevisiae is used to investigate the influence of transamination reactions and protein turnover on the transient behavior of C-13-labeling chemostat experiments. The simulations performed suggest that c...

  16. 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.

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

    Wang, Ning; Li, Zhuxia

    2015-01-01

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

  19. 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.

  20. 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.

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

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

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

  2. 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.

  3. The characteristics of O+HD (v = 0, j = 0)reaction dynamics

    Institute of Scientific and Technical Information of China (English)

    Luo Wen-Lang; Ruan Wen; Zhang Li; Zhu Zheng-He

    2009-01-01

    The analytical potential energy function of HDO is constructed at first using the many-body expansion method. The reaction dynamics of O+HD (v = 0, j = 0) in five product channels are all studied by quasi-classical trajec-tory (QCT) method. The results show that the long-lived complex compound HDO is the dominant product at low collision energy. With increasing collision energy, O+HD → OH+D and O+HD → OD+H exchange reactions will occur with remarkable characteristics, such as near threshold energies, different reaction probabilities, and different reaction cross sections, implying the isotopic effect between H and D. With further increasing collision energy (e.g., up to 502.08 kJ/mol), O+HD → O+H+D will occur and induce the complete dissociation into single O, H, and D atoms.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Kaur Maninder

    2015-01-01

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  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. Reaction Dynamics Following Ionization of Ammonia Dimer Adsorbed on Ice Surface.

    Science.gov (United States)

    Tachikawa, Hiroto

    2016-09-22

    The ice surface provides an effective two-dimensional reaction field in interstellar space. However, how the ice surface affects the reaction mechanism is still unknown. In the present study, the reaction of an ammonia dimer cation adsorbed both on water ice and cluster surface was theoretically investigated using direct ab initio molecular dynamics (AIMD) combined with our own n-layered integrated molecular orbital and molecular mechanics (ONIOM) method, and the results were compared with reactions in the gas phase and on water clusters. A rapid proton transfer (PT) from NH3(+) to NH3 takes place after the ionization and the formation of intermediate complex NH2(NH4(+)) is found. The reaction rate of PT was significantly affected by the media connecting to the ammonia dimer. The time of PT was calculated to be 50 fs (in the gas phase), 38 fs (on ice), and 28-33 fs (on water clusters). The dissociation of NH2(NH4(+)) occurred on an ice surface. The reason behind the reaction acceleration on an ice surface is discussed. PMID:27588552

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

    Science.gov (United States)

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

    2014-03-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Blaszczak, Ewa; Prigent, Claude; Rabut, Gwenaël

    2016-01-01

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

  15. 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.

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

    Science.gov (United States)

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

    2016-07-15

    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. PMID:27255903

  17. 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.

  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. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-22

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

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

    CERN Document Server

    Saito, Seiki; Nakamura, Hiroaki

    2009-01-01

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

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

    International Nuclear Information System (INIS)

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

  3. 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.

  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. 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 ...

  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. 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).

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

    International Nuclear Information System (INIS)

    We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (Hen, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He4 and He5 clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks

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

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-21

    Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid electrodes. The extremely small relaxation time constant of less than 0.15 s indicates a fast redox reaction at the MnO2/CNT hybrid electrodes, securing a stable electrochemical performance for the dynamically stretchable pseudocapacitors. This finding and the fundamental understanding gained from the pseudo-capacitive behavior coupled with mechanical deformation under a dynamic stretching mode would provide guidance to further improve their overall performance including a higher power density than LIBs, a higher energy density than EDLCs, and a long-life cycling stability. Most importantly, these results will potentially accelerate the applications of stretchable pseudocapacitors for flexible and biomedical electronics. PMID:26090617

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Naruemon, Rueangkham; Charin, Modchang

    2016-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-08-01

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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. A new intermediate in the Prins reaction

    Directory of Open Access Journals (Sweden)

    Shinichi Yamabe

    2013-03-01

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

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

    International Nuclear Information System (INIS)

    A new experimental technique for the study of vibrational effects on ion-molecule reaction cross sections is described. Vibrational and collision energy dependent cross sections are presented for proton and H atom transfer, charge transfer and collision induced dissociation reactions in various isotopic H2+ + H2 systems. Charge and proton transfer cross sections are presented for the reactions of H2+ and D2+ with Ar, N2, CO, and O2. All the reactions are shown to be highly influenced by avoided crossings between the ground and first excited potential energy surfaces. Because of the nature of the crossings, vibrational motion of the systems can cause both adiabatic and non-adiabatic behavior of the system. This makes the vibrational dependences of the various cross sections a very sensitive probe of the dynamics of the collisions particularly, their behavior in the region of the crossings. Evidence is seen for charge transfer between reagents as they approach each other, transition to and in some cases reactions on excited potential energy surfaces, competition between different channels, and strong coupling of proton and charge transfer channels which occurs only for two of the systems studied (H2+ + Ar, N2). Oscillatory structure is observed in the collision energy dependence of the endoergic H2+ (v = 0) + Ar charge transfer reaction for the first time, and a simple model which is commonly used for atom-atom charge transfer is used to fit the peaks. Finally a simple model is used to assess the importance of energy resonance and Franck-Condon effects on molecular charge transfer

  1. 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.

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Aono, Masashi; Wakabayashi, Masamitsu

    2015-09-01

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

  4. 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.

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

    International Nuclear Information System (INIS)

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    CERN Document Server

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

    2006-01-01

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

  12. 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.

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

    CERN Document Server

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

    2010-01-01

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

  14. 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

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

    OpenAIRE

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

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Awes, T.C.

    1997-12-01

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

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

    International Nuclear Information System (INIS)

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

  18. 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.

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

    CERN Document Server

    Di Toro, M

    2005-01-01

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

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

    International Nuclear Information System (INIS)

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

  2. 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.

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-21

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

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

    CERN Document Server

    Oberhofer, H

    2009-01-01

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

  6. 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.

  7. 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.

  8. 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.

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

    International Nuclear Information System (INIS)

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

  10. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

    Science.gov (United States)

    Zhou, Y; Wang, S; Li, Y; Zhang, Y

    2016-01-01

    There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Dynamic structural changes at LiMn2O4/electrolyte interface during lithium battery reaction.

    Science.gov (United States)

    Hirayama, Masaaki; Ido, Hedekazu; Kim, KyungSu; Cho, Woosuk; Tamura, Kazuhisa; Mizuki, Jun'ichiro; Kanno, Ryoji

    2010-11-01

    Gaining a thorough understanding of the reactions on the electrode surfaces of lithium batteries is critical for designing new electrode materials suitable for high-power, long-life operation. A technique for directly observing surface structural changes has been developed that employs an epitaxial LiMn(2)O(4) thin-film model electrode and surface X-ray diffraction (SXRD). Epitaxial LiMn(2)O(4) thin films with restricted lattice planes (111) and (110) are grown on SrTiO(3) substrates by pulsed laser deposition. In situ SXRD studies have revealed dynamic structural changes that reduce the atomic symmetry at the electrode surface during the initial electrochemical reaction. The surface structural changes commence with the formation of an electric double layer, which is followed by surface reconstruction when a voltage is applied in the first charge process. Transmission electron microscopy images after 10 cycles confirm the formation of a solid electrolyte interface (SEI) layer on both the (111) and (110) surfaces and Mn dissolution from the (110) surface. The (111) surface is more stable than the (110) surface. The electrode stability of LiMn(2)O(4) depends on the reaction rate of SEI formation and the stability of the reconstructed surface structure. PMID:20939527

  16. 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...

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2014-10-01

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

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

    International Nuclear Information System (INIS)

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

  1. 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

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

    Science.gov (United States)

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

    2015-07-01

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

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

    DEFF Research Database (Denmark)

    Birck, Anders; Labouriau, Rodrigo; Christensen, Preben

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Stamatakis Michail

    2010-04-01

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

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

    Science.gov (United States)

    Lespade, Laure

    2016-08-01

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

  6. 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.

  7. 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...

  8. Ultrafast Dynamics of Plasmon-Exciton Interaction of Ag Nanowire- Graphene Hybrids for Surface Catalytic Reactions.

    Science.gov (United States)

    Ding, Qianqian; Shi, Ying; Chen, Maodu; Li, Hui; Yang, Xianzhong; Qu, Yingqi; Liang, Wenjie; Sun, Mengtao

    2016-01-01

    Using the ultrafast pump-probe transient absorption spectroscopy, the femtosecond-resolved plasmon-exciton interaction of graphene-Ag nanowire hybrids is experimentally investigated, in the VIS-NIR region. The plasmonic lifetime of Ag nanowire is about 150 ± 7 femtosecond (fs). For a single layer of graphene, the fast dynamic process at 275 ± 77 fs is due to the excitation of graphene excitons, and the slow process at 1.4 ± 0.3 picosecond (ps) is due to the plasmonic hot electron interaction with phonons of graphene. For the graphene-Ag nanowire hybrids, the time scale of the plasmon-induced hot electron transferring to graphene is 534 ± 108 fs, and the metal plasmon enhanced graphene plasmon is about 3.2 ± 0.8 ps in the VIS region. The graphene-Ag nanowire hybrids can be used for plasmon-driven chemical reactions. This graphene-mediated surface-enhanced Raman scattering substrate significantly increases the probability and efficiency of surface catalytic reactions co-driven by graphene-Ag nanowire hybridization, in comparison with reactions individually driven by monolayer graphene or single Ag nanowire. This implies that the graphene-Ag nanowire hybrids can not only lead to a significant accumulation of high-density hot electrons, but also significantly increase the plasmon-to-electron conversion efficiency, due to strong plasmon-exciton coupling. PMID:27601199

  9. 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

  10. 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.

  11. 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. PMID:16800031

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

    Science.gov (United States)

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

    2015-11-01

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

  13. 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.

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

    Science.gov (United States)

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

    2011-02-10

    The Norrish Type I reaction in the S(1) (nπ*) state of acetone is a prototype case of ketone photochemistry. On the basis of results from time-resolved mass spectrometry (TRMS) and photoelectron spectroscopy (TRPES) experiments, it was recently suggested that after excitation the wave packet travels toward the S(1) minimum in less than 30 fs and stays there for more than 100 picoseconds [Chem. Phys. Lett.2008, 461, 193]. In this work we present simulated TRMS and TRPES signals based on ab initio multiple spawning simulations of the dynamics during the first 200 fs after excitation, getting quite good agreement with the experimental signals. We can explain the ultrafast decay of the experimental signals in the following manner: the wave packet simply travels, mainly along the deplanarization coordinate, out of the detection window of the ionizing probe. This window is so narrow that subsequent revival of the signal due to the coherent deplanarization vibration is not observed, meaning that from the point of view of the experiment the wave packets travels directly to the S(1) minimum. This result stresses the importance of pursuing a closer link to the experimental signal when using molecular dynamics simulations in interpreting experimental results. PMID:21229990

  15. ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

    Science.gov (United States)

    Birrento, Monica L.; Bryan, Tracy M.; Samosorn, Siritron; Beck, Jennifer L.

    2015-07-01

    Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine ( 1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of ( 1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand ( 1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism.

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

    KAUST Repository

    Alsam, Amani A.

    2015-09-02

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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Christine M Helfer

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

  19. 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.

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  1. 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.

  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. 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.

  4. 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.

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

    Science.gov (United States)

    Harris, Don Ahmasi

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

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

    Directory of Open Access Journals (Sweden)

    Lepomir Čoga

    2009-03-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    Science.gov (United States)

    Feng, Zhao-Qing

    2016-07-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    Trinh, Philippe H.; Ward, Michael J.

    2016-03-01

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

  15. 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.

  16. 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.

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

    CERN Document Server

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

    2014-01-01

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

  18. Time-Dependent Quantum Dynamics of T+CH4 → CH3+HT Reaction

    Institute of Scientific and Technical Information of China (English)

    BAI Li-Hua; ZHANG Jing-Tao; ZHANG Qing-Gang; XU Zhi-Zhan

    2004-01-01

    @@ Reaction probability, cross section and rate constant are studied for polyatomic reaction T+CH4 → CHs+HT using the semirigid vibrating rotor target (SVRT) model. The numerical calculation for the reaction system is carried out using the time-dependent wavepacket method, and the wavepacket is propagated by the splitoperator method. The calculation exhibits a variety of features that can be used for comparison with future experimental investigations. The reaction probability as a function of the translational energy shows slight oscillatory structures, similar to those observed in H abstraction reactions H+H2 and H+CH4. The comparisons with the H+CH4 reaction are described.

  19. 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...

  20. 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.

  1. 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...

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

    Science.gov (United States)

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

    2015-12-01

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

  3. 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.

  4. 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.

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

    Science.gov (United States)

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

    2016-04-21

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

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

    International Nuclear Information System (INIS)

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

  7. 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.

  8. 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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Merritt, Jeremy; Douberly, Gary; Miller, Roger

    2008-03-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

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

    2005-01-01

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

  15. 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.

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

    International Nuclear Information System (INIS)

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

  17. 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

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

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

    Tachikawa, Hiroto; ABE, Shigeaki

    2007-01-01

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

  20. 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...

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

    Directory of Open Access Journals (Sweden)

    Makarova E.V.

    2012-12-01

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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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...

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

    International Nuclear Information System (INIS)

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

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rom, J.; Stricker, J.

    1974-01-01

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

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

    Science.gov (United States)

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

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

  11. Velocity map imaging the dynamics of the reactions of Cl atoms with neopentane and tetramethylsilane

    Science.gov (United States)

    Rose, Rebecca A.; Greaves, Stuart J.; Orr-Ewing, Andrew J.

    2010-06-01

    The reactions of ground state Cl(P23/2) atoms with neopentane and tetramethylsilane have been studied at collision energies of 7.9±2.0 and 8.2±2.0 kcal mol-1, respectively. The nascent HCl(v=0,J) products were probed using resonance enhanced multiphoton ionization spectroscopy combined with velocity map imaging (VMI) to determine the rotational level population distributions, differential cross sections (DCSs), and product translational energy distributions. The outcomes from PHOTOLOC and dual beam methods are compared and are discussed in light of previous studies of the reactions of Cl atoms with other saturated hydrocarbons, including a recent crossed molecular beam and VMI investigation of the reaction of Cl atoms with neopentane [Estillore et al., J. Chem. Phys. 132, 164313 (2010)]. Rotational distributions were observed to be cold, consistent with the reactions proceeding via a transition state with a collinear Cl-H-C moiety. The DCSs for both reactions are forward peaked but show scatter across a broad angular range. Interpretation using a model based on linear dependence of scattering angle on impact parameter indicates that the probability of reaction is approximately constant across all allowed impact parameters. Product translational energy distributions from dual beam experiments have mean values, expressed as fractions of the total available energy, of 0.67 (Cl+neopentane) and 0.64 (Cl+tetramethylsilane) that are consistent with a kinematic model for the reaction in which the translational energy of the reactants is conserved into product translational energy.

  12. 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.

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

    Science.gov (United States)

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

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

  14. 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.

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

    CERN Document Server

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

    2005-01-01

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

  16. 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.

  17. 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.

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

    International Nuclear Information System (INIS)

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

  19. 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.

  20. 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.

  1. 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, Jan W.; Engberts, Jan 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

  2. 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.

  3. 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...

  4. 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.

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

    Science.gov (United States)

    Honvault, Pascal; Launay, Jean-Michel

    2004-05-01

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

  6. 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.

  7. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-05-24

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-02-01

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

  10. Static and dynamic systems in Rickettsia slovaca life cycle evaluated by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Spitalská, E; Sparagano, O; Boldis, V

    2010-04-01

    Quantitative real-time polymerase chain reaction was used to characterize the growth of Rickettsia slovaca, a tick-borne pathogen transmitted by Dermacentor reticulatus and D. marginatus ticks, in static (L929 and Vero cells) and dynamic (D. marginatus and Ixodes ricinus ticks) cultivation systems. The highest points of bacterial multiplication and the time-spans between the inoculum and the maximum of rickettsial copies were increased in consecutive order from eukaryotic cells, I. ricinus to D. marginatus systems. In dynamic system, multiplication maximum of R. slovaca was achieved 9 days earlier in I. ricinus; however, the number of rickettsial DNA copies was approximately 3.6 x 10(6) more in D. marginatus. PMID:20537110

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-01-01

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

  14. 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.

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

    International Nuclear Information System (INIS)

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

  16. 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.

  17. 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...

  18. 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.

  19. 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.

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

    International Nuclear Information System (INIS)

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

  1. 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.

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

    International Nuclear Information System (INIS)

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

  3. 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.

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

    International Nuclear Information System (INIS)

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

  5. 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.

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

    International Nuclear Information System (INIS)

    The title reaction has been studied at collision energies of 0.83 and 2.41 eV. Direct reaction dynamics have been observed at both energies and an increasingly high fraction of the total energy appears in product translation as the collision energy increases. This result is consistent with the concept of induced repulsive energy release, which becomes more effective as trajectories sample the corner of the potential energy surface. At the higher collision energy, the protonated acetone cation undergoes two unimolecular decay channels: C-C bond cleavage to CH3CO+ and CH4, and C-O bond cleavagto C3H5+ (presumably to allyl cation) and H2O. The CH3CO+ channel, endothermic relative to ground state protonated acetone cations by 0.74 eV, appears to liberate 0.4 eV in relative product translation while the C3H5+ channel, endothermic by 2.17 eV, liberates only 0.07 eV in relative translation. These results are discussed in terms of the location on the reaction coordinate and magnitudes of potential energy barriers to 1,3-hydrogen atoms shifts which must precede the bond cleavage processes

  7. 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.

  8. 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

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

    Science.gov (United States)

    Das, Anuradha; Biswas, Ranjit

    2015-08-01

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

  10. 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.

  11. Modeling-gas phase reactions in indoor environments using computational fluid dynamics

    DEFF Research Database (Denmark)

    Sørensen, Dan Nørtoft; Weschler, Charles J.

    2002-01-01

    different terpenes, the scenarios include two air exchange rates (0.5 and 2.0 h(-1)). The terpene is introduced as a floor source with an emission pattern similar to a floor-care product. These four scenarios have been set in a fairly large two-dimensional room (13.6 x 40.6 m) with a supply at the top...... surfaces while the terpenes do not. The results show that for all four scenarios, under steady-state conditions, there are large concentration gradients within the room for both reactants and product. To some extent this is due to imperfect mixing. However. it also reflects that reactions occur...

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

    Science.gov (United States)

    Harris, Leonard A.; Clancy, Paulette

    2006-10-01

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

  13. 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.

  14. 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.

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

    OpenAIRE

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  17. 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.

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

    International Nuclear Information System (INIS)

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

  19. 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.

  20. 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.

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

    Science.gov (United States)

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

    2003-08-01

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

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2016-08-01

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

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

    International Nuclear Information System (INIS)

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

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

    CERN Document Server

    Simenel, Cédric; Lacroix, Denis

    2008-01-01

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

  7. Quantum wavepacket dynamics of the N(4 S) + NO(X2 Π) reaction and its isotopic variants: Integral cross sections and thermal rate constants

    Science.gov (United States)

    Manivannan, V.; Padmanaban, R.

    2016-08-01

    We investigate the initial state-selected dynamics of the title reaction on its ground (1 3A″) and first excited (1 3A‧) triplet potential energy surfaces (PESs) by a time-dependent wavepacket propagation method, employing the ab initio analytical PESs developed by Gamallo et al. (2003). All partial wave contributions up to the total angular momentum J = 140 are found to be necessary for the scattering of NO diatom in its vibrational and rotational ground state up to a collision energy ∼ 0.9 eV. The converged initial state-selected reaction attributes viz., reaction probabilities, integral cross sections and thermal rate constants are obtained within the centrifugal sudden (CS) approximation and the convergence of the results are carefully checked by varying all parameters used in the numerical calculations. The dynamical results are compared with the other reported theoretical and experimental findings. Investigation on the energy-resolved channel-specific reaction probabilities infers that the N2 formation channel is very much favorable than the N-exchange channel. The reaction proceeds via some metastable resonances, observed from the oscillatory probability curves, which is more in the latter channel compared to the former. The effect of rotational and vibrational excitations of the reagent (NO diatom) on the dynamics is examined. We also examine the effect of isotopic substitution of N-atom (14 N by 15 N) on the reaction dynamics.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fokin, A.B

    1998-11-01

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

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

    OpenAIRE

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

    2000-01-01

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

  10. 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

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

    Science.gov (United States)

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

    1975-10-01

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

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

    CERN Document Server

    Vermani, Yogesh K

    2010-01-01

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

  13. 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.

  14. 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...

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2013-03-01

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

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

    Science.gov (United States)

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

    1993-06-01

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

  18. 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.

  19. 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 ...

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

    Science.gov (United States)

    Çetin, Füsun

    2004-07-01

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

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

    Science.gov (United States)

    Liang, Xing; Jiang, Jifa

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

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

    Science.gov (United States)

    Matsubara, Toshiaki; Ito, Tomoyoshi

    2016-05-01

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

  3. 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.

  4. 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.

  5. 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.

  6. Effective reaction rates for diffusion-limited reaction cycles

    Science.gov (United States)

    Nałecz-Jawecki, Paweł; Szymańska, Paulina; Kochańczyk, Marek; Miekisz, Jacek; Lipniacki, Tomasz

    2015-12-01

    Biological signals in cells are transmitted with the use of reaction cycles, such as the phosphorylation-dephosphorylation cycle, in which substrate is modified by antagonistic enzymes. An appreciable share of such reactions takes place in crowded environments of two-dimensional structures, such as plasma membrane or intracellular membranes, and is expected to be diffusion-controlled. In this work, starting from the microscopic bimolecular reaction rate constants and using estimates of the mean first-passage time for an enzyme-substrate encounter, we derive diffusion-dependent effective macroscopic reaction rate coefficients (EMRRC) for a generic reaction cycle. Each EMRRC was found to be half of the harmonic average of the microscopic rate constant (phosphorylation c or dephosphorylation d), and the effective (crowding-dependent) motility divided by a slowly decreasing logarithmic function of the sum of the enzyme concentrations. This implies that when c and d differ, the two EMRRCs scale differently with the motility, rendering the steady-state fraction of phosphorylated substrate molecules diffusion-dependent. Analytical predictions are verified using kinetic Monte Carlo simulations on the two-dimensional triangular lattice at the single-molecule resolution. It is demonstrated that the proposed formulas estimate the steady-state concentrations and effective reaction rates for different sets of microscopic reaction rates and concentrations of reactants, including a non-trivial example where with increasing diffusivity the fraction of phosphorylated substrate molecules changes from 10% to 90%.

  7. 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.

  8. Effect of an organoclay on the reaction-induced phase-separation in a dynamically asymmetric epoxy/PCL system

    Directory of Open Access Journals (Sweden)

    J. Rotrekl

    2013-12-01

    Full Text Available The addition of layered silicates can significantly affect the phase behaviour of both immiscible thermoplastic blends and partially miscible thermoset systems that undergo reaction-induced phase separation (RIPS during curing. This study focuses on the phase behaviour of polycaprolactone (PCL/epoxy in the presence of organically modified montmorillonite (oMMT. Due to the high dynamic asymmetry caused by the differences in the molecular weights and viscosities of the PCL and the uncured epoxy, the critical point is localised at low PCL concentrations, as indicated by the pseudophase diagram. The addition of oMMT to the system led to the marked shift of the critical point towards higher concentrations of PCL, with an increase in the oMMT content occurring as a consequence of the preferential localisation of the clay in the epoxy phase, making this phase more dynamically slow. Significant changes in morphology, including phase inversion of the PCL/epoxy systems caused by the presence of oMMT, were recorded for PCL concentrations ranging from 10 to 30%.

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

    International Nuclear Information System (INIS)

    Iodine photodissociation and recombination was studied as a model for processes common to chemical reaction in the liquid phase. Picosecond transient absorption measurements from 1000 to 295 nm were used to monitor the dynamics in a variety of solvents. Most of the atoms which undergo geminate recombination were found to do so in less than or equal to 15 ps, in agreement with the results of existing molecular dynamics simulations. Vibrational relaxation times vary from approx.15 ps near the middle of the ground state well to approx.150 ps for complete relaxation to v = 0. The prediction of strong resonant vibrational energy transfer to chlorinated methane solvents was not supported, but some evidence for this mechanism was found for alkane solvents. Current theory is unable to explain the large variation (65 to 2700 ps) of the excited A'-state lifetime in various solvents. The 10-Hz amplified, synchronously-pumped dye laser which was used in these studies is described and characterized. SERS (Stimulated Electronic Raman Scattering) and difference frequency mixing were used in the generation of the infrared and far-infrared, respectively. 54 refs., 38 figs., 3 tabs

  10. 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)

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

    International Nuclear Information System (INIS)

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

  12. 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.

  13. Innovative Bimolecular-Based Advanced Logic Operations: A Prime Discriminator and An Odd Parity Checker.

    Science.gov (United States)

    Zhou, Chunyang; Liu, Dali; Dong, Shaojun

    2016-08-17

    Herein, a novel logic operation of prime discriminator is first performed for the function of identifying the prime numbers from natural numbers less than 10. The prime discriminator logic operation is developed by DNA hybridizations and the conjugation of graphene oxide and single-stranded DNA as a reacting platform. On the basis of the similar reaction principle, an odd parity checker is also developed. The odd parity checker logic operation can identify the even numbers and odd numbers from natural numbers less than 10. Such advanced logic operations with digital recognition ability can provide a new field of vision toward prototypical DNA-based logic operations and promote the development of advanced logic circuits. PMID:27459592

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

    International Nuclear Information System (INIS)

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

  16. 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.

  17. 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.

  18. 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.

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

    Science.gov (United States)

    Chiba, Sachie; Yoshida, Fuka; Takayanagi, Toshiyuki

    2014-03-01

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

  20. Decay of 202Pb* formed in 48Ca+154Sm reaction using the dynamical cluster-decay model

    International Nuclear Information System (INIS)

    The decay of compound nucleus 202Pb*, formed in entrance channel reaction 48Ca+154Sm at different incident energies, is studied by using the dynamical cluster-decay model (DCM) where all decay products are calculated as emissions of preformed clusters through the interaction barriers. The calculated results show an excellent agreement with experimental data for the fusion-evaporation residue cross-section σER together with the fusion-fission cross-section σFF (taken as a sum of the energetically favored symmetric ACN*/2 ± 20 and near symmetric A=65–75 plus complementary fragments), and the competing, non-compound-nucleus quasi-fission cross-section σQF where the entrance channel is considered not to lose its identity (and hence with preformation factor P0=1). The interesting feature of this study is that the three decay processes (ER, FF and QF) are quite comparable at low energies, ER being the most dominant, whereas at higher energies FF becomes most probable followed by ER and QF. The prediction of two fission windows, the symmetric fission (SF) and the near symmetric fission (nSF) whose contribution is more at lower incident energies, suggests the presence of a fine structure effect in the fusion-fission of 202Pb*. This result is attributed to the shell effects (magic shells) playing effective role in the fragment preformation yields for 48Ca+154Sm reaction at lower excitation energies, giving rise to shoulders, to an otherwise Gaussian FF mass distribution, responsible for the QF process. As a further verification of this result, absence of "shoulders" (hence, the QF component) in the decay of 192Pb* due to 48Ca+144Sm reaction is also shown to be given by the calculations, in agreement with experiments. The only parameter of the model is the neck-length ΔR which shows that the ER occurs first, having the largest values of ΔR, and the FF and QF processes occur almost simultaneously at lower incident energies but the FF takes over QF at higher incident

  1. 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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters...... using the hybrid model composed of Michaelis–Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large-scale networks where the exact rate laws are unknown.......The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters......, represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis–Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action...

  3. Mass asymmetry dependence of fusion time-scales in 11B+237Np and 12C, 16O, 19F+232Th reactions in a dynamical trajectory model

    International Nuclear Information System (INIS)

    Dynamical trajectory calculations were carried out for the reactions of 11B+237Np and 12C, 16O and 19F+232Th, having mass asymmetries on either side of the Businaro-Gallone critical mass asymmetry αBG, in order to examine the mass asymmetry dependence of fusion reactions in these systems. The compound nucleus formation times were calculated as a function of the partial wave of the reaction for all the systems. This study brings out that for systems with αBG, the formation times are significantly larger than for α>αBG, which is caused by the dynamical effects involved in the large scale shape changes taking place in the fusion process as well as due to the interplay between the thermal and the collective motion during the collision process. The calculated time scales are comparable to the experimental values derived from the pre-fission neutron multiplicity measurements. (author). 16 refs., 4 figs., 1 tab

  4. Dynamics of the reaction H2+(He,H)HeH+. Endoergic channels with H2+ in γ=0,1 vibrational states: beam experiment and trajectory calculations

    International Nuclear Information System (INIS)

    A vibrationally selected beam of H2+ was used to investigate experimentally the reaction dynamics of the lowest two (endoergic) channels of the process H2+(γ=0,1)+He=HeH++H at the relative collision energy 3.58 eV, and to provide data for comparison with quasi-classical trajectory calculations. The process proceeds via a direct mechanism. In comparison with the reaction dynamics observed for the non-selected beam, where various vibrationally excited reactant ions participated, the results show - in a good agreement between theory and experiment - a prominent decrease of the forward 'stripping' scattering, and apparently an increased peak value of the recoil translational energy. This is consistent with the simple idea that small impact-parameter collisions leading to large-angle scattering are required to achieve an effective translational energy transfer necessary to overcome the reaction barrier. (Auth.)

  5. Probing the dynamics of polyatomic multichannel elementary reactions by crossed molecular beam experiments with soft electron-ionization mass spectrometric detection.

    Science.gov (United States)

    Casavecchia, Piergiorgio; Leonori, Francesca; Balucani, Nadia; Petrucci, Raffaele; Capozza, Giovanni; Segoloni, Enrico

    2009-01-01

    In this Perspective we highlight developments in the field of chemical reaction dynamics. Focus is on the advances recently made in the investigation of the dynamics of elementary multichannel radical-molecule and radical-radical reactions, as they have become possible using an improved crossed molecular beam scattering apparatus with universal electron-ionization mass spectrometric detection and time-of-flight analysis. These improvements consist in the implementation of (a) soft ionization detection by tunable low-energy electrons which has permitted us to reduce interfering signals originating from dissociative ionization processes, usually representing a major complication, (b) different beam crossing-angle set-ups which have permitted us to extend the range of collision energies over which a reaction can be studied, from very low (a few kJ mol(-1), as of interest in astrochemistry or planetary atmospheric chemistry) to quite high energies (several tens of kJ mol(-1), as of interest in high temperature combustion systems), and (c) continuous supersonic sources for producing a wide variety of atomic and molecular radical reactant beams. Exploiting these new features it has become possible to tackle the dynamics of a variety of polyatomic multichannel reactions, such as those occurring in many environments ranging from combustion and plasmas to terrestrial/planetary atmospheres and interstellar clouds. By measuring product angular and velocity distributions, after having suppressed or mitigated, when needed, the problem of dissociative ionization of interfering species (reactants, products, background gases) by soft ionization detection, essentially all primary reaction products can be identified, the dynamics of each reaction channel characterized, and the branching ratios determined as a function of collision energy. In general this information, besides being of fundamental relevance, is required for a predictive description of the chemistry of these

  6. The smallest chemical reaction system with bistability

    Directory of Open Access Journals (Sweden)

    Wilhelm Thomas

    2009-09-01

    Full Text Available Abstract Background Bistability underlies basic biological phenomena, such as cell division, differentiation, cancer onset, and apoptosis. So far biologists identified two necessary conditions for bistability: positive feedback and ultrasensitivity. Results Biological systems are based upon elementary mono- and bimolecular chemical reactions. In order to definitely clarify all necessary conditions for bistability we here present the corresponding minimal system. According to our definition, it contains the minimal number of (i reactants, (ii reactions, and (iii terms in the corresponding ordinary differential equations (decreasing importance from i-iii. The minimal bistable system contains two reactants and four irreversible reactions (three bimolecular, one monomolecular. We discuss the roles of the reactions with respect to the necessary conditions for bistability: two reactions comprise the positive feedback loop, a third reaction filters out small stimuli thus enabling a stable 'off' state, and the fourth reaction prevents explosions. We argue that prevention of explosion is a third general necessary condition for bistability, which is so far lacking discussion in the literature. Moreover, in addition to proving that in two-component systems three steady states are necessary for bistability (five for tristability, etc., we also present a simple general method to design such systems: one just needs one production and three different degradation mechanisms (one production, five degradations for tristability, etc.. This helps modelling multistable systems and it is important for corresponding synthetic biology projects. Conclusion The presented minimal bistable system finally clarifies the often discussed question for the necessary conditions for bistability. The three necessary conditions are: positive feedback, a mechanism to filter out small stimuli and a mechanism to prevent explosions. This is important for modelling bistability with

  7. A Combined Experimental and Theoretical Study on the Formation of the 2-Methyl-1-silacycloprop-2-enylidene Molecule via the Crossed Beam Reactions of the Silylidyne Radical (SiH; X(2)Π) with Methylacetylene (CH3CCH; X(1)A1) and D4-Methylacetylene (CD3CCD; X(1)A1).

    Science.gov (United States)

    Yang, Tao; Dangi, Beni B; Kaiser, Ralf I; Bertels, Luke W; Head-Gordon, Martin

    2016-07-14

    The bimolecular gas-phase reactions of the ground-state silylidyne radical (SiH; X(2)Π) with methylacetylene (CH3CCH; X(1)A1) and D4-methylacetylene (CD3CCD; X(1)A1) were explored at collision energies of 30 kJ mol(-1) under single-collision conditions exploiting the crossed molecular beam technique and complemented by electronic structure calculations. These studies reveal that the reactions follow indirect scattering dynamics, have no entrance barriers, and are initiated by the addition of the silylidyne radical to the carbon-carbon triple bond of the methylacetylene molecule either to one carbon atom (C1; [i1]/[i2]) or to both carbon atoms concurrently (C1-C2; [i3]). The collision complexes [i1]/[i2] eventually isomerize via ring-closure to the c-SiC3H5 doublet radical intermediate [i3], which is identified as the decomposing reaction intermediate. The hydrogen atom is emitted almost perpendicularly to the rotational plane of the fragmenting complex resulting in a sideways scattering dynamics with the reaction being overall exoergic by -12 ± 11 kJ mol(-1) (experimental) and -1 ± 3 kJ mol(-1) (computational) to form the cyclic 2-methyl-1-silacycloprop-2-enylidene molecule (c-SiC3H4; p1). In line with computational data, experiments of silylidyne with D4-methylacetylene (CD3CCD; X(1)A1) depict that the hydrogen is emitted solely from the silylidyne moiety but not from methylacetylene. The dynamics are compared to those of the related D1-silylidyne (SiD; X(2)Π)-acetylene (HCCH; X(1)Σg(+)) reaction studied previously in our group, and from there, we discovered that the methyl group acts primarily as a spectator in the title reaction. The formation of 2-methyl-1-silacycloprop-2-enylidene under single-collision conditions via a bimolecular gas-phase reaction augments our knowledge of the hitherto poorly understood silylidyne (SiH; X(2)Π) radical reactions with small hydrocarbon molecules leading to the synthesis of organosilicon molecules in cold molecular

  8. 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.

  9. Decay studies of 59Cu* formed in the 35Cl + 24Mg reaction using the dynamical cluster-decay model

    Science.gov (United States)

    Karthikraj, C.; Balasubramaniam, M.

    2013-02-01

    The reformulated dynamical cluster-decay model (DCM) is applied to study the decay of odd-A and non-α structured 59Cu* formed in the 35Cl+24Mg reaction at Elab=275 MeV. Here, the temperature (T)-dependent binding energies due to Krappe are used. The roles of Wigner and pairing energies in the fragmentation potential are explicitly shown in this work. For the temperature T=4.1898 MeV corresponding to Elab=275 MeV, the contribution of pairing vanishes and the resulting structure of the fragmentation potential due to Wigner term is shown. In addition to this, we have studied the role of factor α appearing in the inertia part of the equation of motion dictating the mass-transfer process. It is shown that this factor has significant effect in the structure of preformation probability values and hence in turn we see significant changes in the cross sections. We compare the cross sections of the measured charge distributions of the fission fragments for two limiting values of the parameter α with the experimental data. In order to fit the total cross-section values, a linear relation is obtained between the free parameter of the model ▵R and the factor α appearing in the hydrodynamical mass.

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Chemical reaction dynamics of Rydberg atoms with neutral molecules: A comparison of molecular-beam and classical trajectory results for the H(n)+D2→HD+D(n') reaction

    International Nuclear Information System (INIS)

    Recent molecular-beam experiments have probed the dynamics of the Rydberg-atom reaction, H(n)+D2→HD+D(n) at low collision energies. It was discovered that the rotationally resolved product distribution was remarkably similar to a much more limited data set obtained at a single scattering angle for the ion-molecule reaction H++D2→D++HD. The equivalence of these two problems would be consistent with the Fermi-independent-collider model (electron acting as a spectator) and would provide an important new avenue for the study of ion-molecule reactions. In this work, we employ a classical trajectory calculation on the ion-molecule reaction to facilitate a more extensive comparison between the two systems. The trajectory simulations tend to confirm the equivalence of the ion+molecule dynamics to that for the Rydberg-atom+molecule system. The theory reproduces the close relationship of the two experimental observations made previously. However, some differences between the Rydberg-atom experiments and the trajectory simulations are seen when comparisons are made to a broader data set. In particular, the angular distribution of the differential cross section exhibits more asymmetry in the experiment than in the theory. The potential breakdown of the classical model is discussed. The role of the 'spectator' Rydberg electron is addressed and several crucial issues for future theoretical work are brought out

  16. 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.

  17. 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

  18. 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 ...

  19. 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.

  20. 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.

  1. Dinámica de reacciones unimoleculares en fase gas: Desviaciones del comportamiento estadístico Dynamics of unimolecular reactions in gas phase: deviations from statistical behavior

    Directory of Open Access Journals (Sweden)

    Emilio Martínez-Núñez

    2002-07-01

    Full Text Available The present review summarizes the most relevant results of our research group obtained recently in the field of unimolecular reaction dynamics. The following processes are specifically analyzed: the isomerization, dissociation and elimination in methyl nitrite, the fragmentation reactions of the mercaptomethyl cation, the C-CO dissociation in the acetyl and propionyl radicals, and the decomposition of vinyl fluoride. In all the cases, only state- or energy-selected systems are considered. Special emphasis is paid to the possibility of systems exhibiting non-statistical behavior.

  2. Neutral products from cation-molecule reactions in the gas phase

    International Nuclear Information System (INIS)

    The use of neutral product analysis for examining ionic reaction pathways from electron impact is described. This approach merges techniques of mass spectrometry with those of radiation chemistry. Comparisons are made between experimental results and predictions based on density-of-states arguments using RRKM microscopic rate coefficients. The importance of examining isomer distributions is stressed with special attention given to the question of the mechanism of bimolecular proton transfer in the gas phase. (author)

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Using high resolution and dynamic reaction cell for the improvement of the sensitivity of direct silicon determination in uranium materials by inductively coupled plasma mass spectrometry

    OpenAIRE

    Golik, V. M.; Kuz'mina, N. V.; Saprygin, A. V.; Trepachev, S. A.

    2013-01-01

    The paper describes solving the problem of direct silicon determination at low levels in uranium materials, caused by the spectral interferences of polyatomic ions and the high value of blank levels, using inductively coupled plasma mass spectrometry (ICP MS). To overcome the interference problem, two primary techniques have been applied: double focusing high-resolution ICP MS and dynamic reaction cell (DRC) filled with highly reactive ammonia gas. All measurements were performed at high reso...

  8. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    CERN Document Server

    Zobač, Vladmír; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2014-01-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code Fireball, suitable for the computational study of these problems. Our methodology enables simulating photo-induced reaction mechanisms over hundreds of trajectories; therefore, large statistically significant ensembles can be calculated to accurately represent a reaction profile. As an example of the application of this approach, we report results on the [2+2] cycloaddition of ethylene with maleic anhydride and on the [2+2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  9. 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.

  10. Elastic Vibrations in the Photosynthetic Bacterial Reaction Center Coupled to the Primary Charge Separation: Implications from Molecular Dynamics Simulations and Stochastic Langevin Approach.

    Science.gov (United States)

    Milanovsky, Georgy E; Shuvalov, Vladimir A; Semenov, Alexey Yu; Cherepanov, Dmitry A

    2015-10-29

    Primary electron transfer reactions in the bacterial reaction center are difficult for theoretical explication: the reaction kinetics, almost unalterable over a wide range of temperature and free energy changes, revealed oscillatory features observed initially by Shuvalov and coauthors (1997, 2002). Here the reaction mechanism was studied by molecular dynamics and analyzed within a phenomenological Langevin approach. The spectral function of polarization around the bacteriochlorophyll special pair PLPM and the dielectric response upon the formation of PL(+)PM(-) dipole within the special pair were calculated. The system response was approximated by Langevin oscillators; the respective frequencies, friction, and energy coupling coefficients were determined. The protein dynamics around PL and PM were distinctly asymmetric. The polarization around PL included slow modes with the frequency 30-80 cm(-1) and the total amplitude of 130 mV. Two main low-frequency modes of protein response around PM had frequencies of 95 and 155 cm(-1) and the total amplitude of 30 mV. In addition, a slowly damping mode with the frequency of 118 cm(-1) and the damping time >1.1 ps was coupled to the formation of PL(+)PM(-) dipole. It was attributed to elastic vibrations of α-helices in the vicinity of PLPM. The proposed trapping of P excitation energy in the form of the elastic vibrations can rationalize the observed properties of the primary electron transfer reactions, namely, the unusual temperature and ΔG dependences, the oscillating phenomena in kinetics, and the asymmetry of the charge separation reactions. PMID:26148224

  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. 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.

  13. Spatially Organized Enzymes Drive Cofactor-Coupled Cascade Reactions.

    Science.gov (United States)

    Ngo, Tien Anh; Nakata, Eiji; Saimura, Masayuki; Morii, Takashi

    2016-03-01

    We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes. PMID:26881296

  14. 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

  15. 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).

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

    OpenAIRE

    Doronin Fedor Leonidovich; Truchanova Lyudmila Nikolaevna; Fomina Marina Vasilyevna

    2014-01-01

    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 ...

  17. 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.

  18. Testing the Palma-Clary Reduced Dimensionality Model Using Classical Mechanics on the CH4 + H → CH3 + H2 Reaction.

    Science.gov (United States)

    Vikár, Anna; Nagy, Tibor; Lendvay, György

    2016-07-14

    Application of exact quantum scattering methods in theoretical reaction dynamics of bimolecular reactions is limited by the complexity of the equations of nuclear motion to be solved. Simplification is often achieved by reducing the number of degrees of freedom to be explicitly handled by freezing the less important spectator modes. The reaction cross sections obtained in reduced-dimensionality (RD) quantum scattering methods can be used in the calculation of rate coefficients, but their physical meaning is limited. The accurate test of the performance of a reduced-dimensionality method would be a comparison of the RD cross sections with those obtained in accurate full-dimensional (FD) calculations, which is not feasible because of the lack of complete full-dimensional results. However, classical mechanics allows one to perform reaction dynamics calculations using both the RD and the FD model. In this paper, an RD versus FD comparison is made for the 8-dimensional Palma-Clary model on the example of four isotopologs of the CH4 + H → CH3 + H2 reaction, which has 12 internal dimensions. In the Palma-Clary model, the only restriction is that the methyl group is confined to maintain C3v symmetry. Both RD and FD opacity and excitation functions as well as differential cross sections were calculated using the quasiclassical trajectory method. The initial reactant separation has been handled according to our one-period averaging method [ Nagy et al. J. Chem. Phys. 2016, 144, 014104 ]. The RD and FD excitation functions were found to be close to each other for some isotopologs, but in general, the RD reactivity parameters are lower than the FD reactivity parameters beyond statistical error, and for one of the isotopologs, the deviation is significant. This indicates that the goodness of RD cross sections cannot be taken for granted. PMID:26918703

  19. Reaction dynamics during pulsed light activation of ATX-S10 Na(II)-sensitized cell cultures: analysis based on fluorescence-oxygen diagram

    Science.gov (United States)

    Kawauchi, Satoko; Sato, Shunichi; Morimoto, Yuji; Kikuchi, Makoto

    2005-04-01

    To elucidate the mechanism of photosensitization with pulsed light excitation, we previously introduced fluorescence-oxygen diagram that shows the correlation between photochemical oxygen consumption and photobleaching during a treatment (Kawauchi et al., Photochem. Photobiol., 80, 216-223, 2004). In pulsed photodynamic treatment of A549 cells with ATX-S10"Na(II), the diagrams for treatments at relatively high repetition rates of 10 and 30 Hz showed the complex behaviors of photochemical reaction; photobleaching initially occurred with oxygen consumption but it was switched to oxygen-independent photobleaching, which was followed by a secondary oxygen-consuming regime. In this study, fluorescence microscopy revealed that for treatments at 10 and 30 Hz, subcellular fluorescence distribution of ATX-S10×Na(II) changed drastically from the high-intensity spotty patterns showing lysosomal accumulation to the diffusive patterns within the cytosol during certain ranges of total light dose. These ranges were found to coincide with those in which oxygen-independent reaction appeared. These findings suggest that the sensitizer started to be redistributed from lysosomes to the cytosol during the oxygen-independent reaction regime. On the other hand, at 5 Hz, such reaction switching was not clearly seen during whole irradiation period in the diagram; this was consistent with the observation that sensitizer redistribution efficiently occurred even in the early phase of irradiation. The appearance of oxygen-independent reaction at the higher repetition rates may be caused by high local concentration of the sensitizer and the resultant low concentration of oxygen in the reaction sites due to the shorter pulse-to-pulse time intervals. In pulsed photodynamic treatment, pulse frequency is an important parameter that affects the intracellular kinetics of the sensitizer and hence the photochemical reaction dynamics.

  20. 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

  1. A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait

    OpenAIRE

    Hamner, Samuel R.; Seth, Ajay; Steele, Katherine M.; Delp, Scott L.

    2013-01-01

    Recent advances in computational technology have dramatically increased the use of muscle-driven simulation to study accelerations produced by muscles during gait. Accelerations computed from muscle-driven simulations are sensitive to the model used to represent contact between the foot and ground. A foot-ground contact model must be able to calculate ground reaction forces and moments that are consistent with experimentally measured ground reaction forces and moments. We show here that a rol...

  2. Bimolecular Fluorescence Complementation (BiFC) Assay for Direct Visualization of Protein-Protein Interaction in vivo

    Science.gov (United States)

    Lai, Hsien-Tsung; Chiang, Cheng-Ming

    2016-01-01

    Bimolecular Fluorescence Complementation (BiFC) assay is a method used to directly visualize protein-protein interaction in vivo using live-cell imaging or fixed cells. This protocol described here is based on our recent paper describing the functional association of human chromatin adaptor and transcription cofactor Brd4 with p53 tumor suppressor protein (Wu et al., 2013). BiFC was first described by Hu et al. (2002) using two non-fluorescent protein fragments of enhanced yellow fluorescent protein (EYFP), which is an Aequorea victoria GFP variant protein, fused respectively to a Rel family protein and a bZIP family transcription factor to investigate interactions between these two family members in living cells. The YFP was later improved by introducing mutations to reduce its sensitivity to pH and chloride ions, thus generating a super-enhanced YFP, named Venus fluorescent protein, without showing diminished fluorescence at 37 °C as typically observed with EYFP (Nagai et al., 2006). The fluorescence signal is regenerated by complementation of two non-fluorescent fragments (e.g., the Venus N-terminal 1–158 amino acid residues, called Venus-N, and its C-terminal 159–239 amino acid residues, named Venus-C; see Figure 1A and Gully et al., 2012; Ding et al., 2006; Kerppola, 2006) that are brought together by interaction between their respective fusion partners (e.g., Venus-N to p53, and Venus-C to the PDID domain of human Brd4; see Figure 1B and 1C). The intensity and cellular location of the regenerated fluorescence signals can be detected by fluorescence microscope. The advantages of the proximity-based BiFC assay are: first, it allows a direct visualization of spatial and temporal interaction between two partner proteins in vivo; second, the fluorescence signal provides a sensitive readout for detecting protein-protein interaction even at a low expression level comparable to that of the endogenous proteins; third, the intensity of the fluorescence signal is

  3. 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.

  4. Non-adiabatic dynamics of reactions of O(1D) with Xe, CO, NO2, and CO2 from crossed atomic and molecular beam experiments

    Science.gov (United States)

    Boering, Kristie

    2015-03-01

    Reactions of the first excited state of atomic oxygen, O(1D), with small molecules such as CO, NO2, and CO2 continue to be of interest in aeronomy and atmospheric chemistry, thus providing additional motivation to understand the dynamics of these reactions and how well they are predicted by theory. In collaboration with Prof. Jim Lin of the Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan, we have studied the dynamics of quenching and non-quenching reactions between O(1D) and various small molecules using a universal crossed atomic and molecular beam apparatus. New experimental results for the dynamics of quenching of O(1D) by Xe and CO will be presented and compared with previous results for NO2 (K.A. Mar, A.L. Van Wyngarden, C.-W. Liang, Y.T. Lee, J.J. Lin, K.A. Boering, J. Chem. Phys., 137, 044302, doi: 10.1063/1.4736567, 2012) and CO2 (M.J. Perri, A.L. Van Wyngarden, K.A. Boering, J.J. Lin, and Y.T. Lee, J. Chem. Phys., 119(16), 8213-8216, 2003; M.J. Perri, A.L. Van Wyngarden, J.J. Lin, Y.T. Lee, and K.A. Boering, J. Phys. Chem. A, 108(39), 7995-8001, doi: 10.1021/jp0485845, 2004). Among the most intriguing of the new results are for quenching of O(1D) by Xe, for which marked oscillations in the differential cross sections were observed for the O(3P) and Xe products. The shape and relative phase of the oscillatory structure depended strongly on collision energy. This behavior is likely due to the quantum nature of the collision dynamics, caused by interferences among multiple curve crossing pathways accessible during electronic quenching, known as Stueckelberg oscillations.

  5. Modelling of gas-liquid reactors - stability and dynamic behaviour of gas-liquid mass transfer accompanied by irreversible reaction

    NARCIS (Netherlands)

    Elk, E.P. van; Borman, P.C.; Kuipers, J.A.M.; Versteeg, G.F.

    1999-01-01

    The dynamic behaviour and stability of single-phase reacting systems has been investigated thoroughly in the past and design rules for stable operation are available from literature. The dynamic behaviour of gas-liquid processes is considerably more complex and has received relatively little attenti

  6. Mode specific dynamics of the H{sub 2} + CH{sub 3} → H + CH{sub 4} reaction studied using quasi-classical trajectory and eight-dimensional quantum dynamics methods

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yan [Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); School of Chemical and Environmental Engineering, Hubei University for Nationalities, Enshi 445000 (China); Li, Jun; Guo, Hua, E-mail: yangmh@wipm.ac.cn, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Chen, Liuyang; Yang, Minghui, E-mail: yangmh@wipm.ac.cn, E-mail: hguo@unm.edu [Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Lu, Yunpeng [Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore)

    2015-10-21

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

  7. Experimental and theoretical studies of the O(3P) + C2H4 reaction dynamics: collision energy dependence of branching ratios and extent of intersystem crossing.

    Science.gov (United States)

    Fu, Bina; Han, Yong-Chang; Bowman, Joel M; Leonori, Francesca; Balucani, Nadia; Angelucci, Luca; Occhiogrosso, Angela; Petrucci, Raffaele; Casavecchia, Piergiorgio

    2012-12-14

    The reaction of O((3)P) with C(2)H(4), of importance in combustion and atmospheric chemistry, stands out as paradigm reaction involving not only the indicated triplet state potential energy surface (PES) but also an interleaved singlet PES that is coupled to the triplet surface. This reaction poses great challenges for theory and experiment, owing to the ruggedness and high dimensionality of these potentials, as well as the long lifetimes of the collision complexes. Crossed molecular beam (CMB) scattering experiments with soft electron ionization detection are used to disentangle the dynamics of this polyatomic multichannel reaction at a collision energy E(c) of 8.4 kcal∕mol. Five different primary products have been identified and characterized, which correspond to the five exothermic competing channels leading to H + CH(2)CHO, H + CH(3)CO, CH(3) + HCO, CH(2) + H(2)CO, and H(2) + CH(2)CO. These experiments extend our previous CMB work at higher collision energy (E(c) ∼ 13 kcal∕mol) and when the results are combined with the literature branching ratios from kinetics experiments at room temperature (E(c) ∼ 1 kcal∕mol), permit to explore the variation of the branching ratios over a wide range of collision energies. In a synergistic fashion, full-dimensional, QCT surface hopping calculations of the O((3)P) + C(2)H(4) reaction using ab initio PESs for the singlet and triplet states and their coupling, are reported at collision energies corresponding to the CMB and the kinetics ones. Both theory and experiment find almost an equal contribution from the triplet and singlet surfaces to the reaction, as seen from the collision energy dependence of branching ratios of product channels and extent of intersystem crossing (ISC). Further detailed comparisons at the level of angular distributions and translational energy distributions are made between theory and experiment for the three primary radical channel products, H + CH(2)CHO, CH(3) + HCO, and CH(2) + H(2)CO

  8. 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.

  9. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism

    International Nuclear Information System (INIS)

    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. (paper)

  10. 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.

  11. 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.

  12. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    International Nuclear Information System (INIS)

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures

  13. Experimental effects of dynamics and thermodynamics in nuclear reactions on the symmetry energy as seen by the CHIMERA 4 π detector

    Energy Technology Data Exchange (ETDEWEB)

    De Filippo, E.; Pagano, A. [INFN, Catania (Italy)

    2014-02-15

    Heavy-ion collisions have been widely used in the last decade to constrain the parameterizations of the symmetry energy term of the nuclear equation of state (EOS) for asymmetric nuclear matter as a function of baryonic density. In the Fermi energy domain one is faced with variations of the density within a narrow range of values around the saturation density ρ{sub 0}=0.16 fm{sup -3} down towards sub-saturation densities. The experimental observables which are sensitive to the symmetry energy are constructed starting from the detected light particles, clusters and heavy fragments that, in heavy-ion collisions, are generally produced by different emission mechanisms at different stages and time scales of the reaction. In this review the effects of dynamics and thermodynamics on the symmetry energy in nuclear reactions are discussed and characterized using an overview of the data taken so far with the CHIMERA multi detector array. (orig.)

  14. Experimental effects on dynamics and thermodynamics in nuclear reactions on the symmetry energy as seen by the CHIMERA 4$\\pi$ detector

    CERN Document Server

    De Filippo, E

    2013-01-01

    Heavy ion collisions have been widely used in the last decade to constraint the parameterizations of the symmetry energy term of nuclear equation of state (EOS) for asymmetric nuclear matter as a function of baryonic density. In the Fermi energy domain one is faced with variations of the density within a narrow range of values around the saturation density $\\rho_0$=0.16 fm$^{-3}$ down towards sub-saturation densities. The experimental observables which are sensitive to the symmetry energy are constructed starting from the detected light particles, clusters and heavy fragments that, in heavy ion collisions, are generally produced by different emission mechanisms at different stages and time scales of the reaction. In this review the effects of dynamics and thermodynamics on the symmetry energy in nuclear reactions are discussed and characterized using an overview of the data taken so far with the CHIMERA multi-detector array.

  15. Communication: Rate coefficients of the H + CH4 → H2 + CH3 reaction from ring polymer molecular dynamics on a highly accurate potential energy surface

    Science.gov (United States)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2015-09-01

    The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ≤ T ≤ 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.

  16. 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.

  17. On the dynamics of the H++D2(v=0,j=0)→HD+D+ reaction: A comparison between theory and experiment

    International Nuclear Information System (INIS)

    The H++D2(v=0,j=0)→HD+D+ reaction has been theoretically investigated by means of a time independent exact quantum mechanical approach, a quantum wave packet calculation within an adiabatic centrifugal sudden approximation, a statistical quantum model, and a quasiclassical trajectory calculation. Besides reaction probabilities as a function of collision energy at different values of the total angular momentum, J, special emphasis has been made at two specific collision energies, 0.1 and 0.524 eV. The occurrence of distinctive dynamical behavior at these two energies is analyzed in some detail. An extensive comparison with previous experimental measurements on the Rydberg H atom with D2 molecules has been carried out at the higher collision energy. In particular, the present theoretical results have been employed to perform simulations of the experimental kinetic energy spectra

  18. 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

  19. Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

    Science.gov (United States)

    Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

    2011-05-14

    We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

  20. 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.

  1. Trimolecular reactions of uranium hexafluoride with water.

    Science.gov (United States)

    Lind, Maria C; Garrison, Stephen L; Becnel, James M

    2010-04-01

    The hydrolysis reaction of uranium hexafluoride (UF(6)) is a key step in the synthesis of uranium dioxide (UO(2)) powder for nuclear fuels. Mechanisms for the hydrolysis reactions are studied here with density functional theory and the Stuttgart small-core scalar relativistic pseudopotential and associated basis set for uranium. The reaction of a single UF(6) molecule with a water molecule in the gas phase has been previously predicted to proceed over a relatively sizable barrier of 78.2 kJ x mol(-1), indicating this reaction is only feasible at elevated temperatures. Given the observed formation of a second morphology for the UO(2) product coupled with the observations of rapid, spontaneous hydrolysis at ambient conditions, an alternate reaction pathway must exist. In the present work, two trimolecular hydrolysis mechanisms are studied with density functional theory: (1) the reaction between two UF(6) molecules and one water molecule, and (2) the reaction of two water molecules with a single UF(6) molecule. The predicted reaction of two UF(6) molecules with one water molecule displays an interesting "fluorine-shuttle" mechanism, a significant energy barrier of 69.0 kJ x mol(-1) to the formation of UF(5)OH, and an enthalpy of reaction (DeltaH(298)) of +17.9 kJ x mol(-1). The reaction of a single UF(6) molecule with two water molecules displays a "proton-shuttle" mechanism, and is more favorable, having a slightly lower computed energy barrier of 58.9 kJ x mol(-1) and an exothermic enthalpy of reaction (DeltaH(298)) of -13.9 kJ x mol(-1). The exothermic nature of the overall UF(6) + 2H(2)O trimolecular reaction and the lowering of the barrier height with respect to the bimolecular reaction are encouraging. PMID:20210345

  2. A rolling constraint reproduces ground reaction forces and moments in dynamic simulations of walking, running, and crouch gait.

    Science.gov (United States)

    Hamner, Samuel R; Seth, Ajay; Steele, Katherine M; Delp, Scott L

    2013-06-21

    Recent advances in computational technology have dramatically increased the use of muscle-driven simulation to study accelerations produced by muscles during gait. Accelerations computed from muscle-driven simulations are sensitive to the model used to represent contact between the foot and ground. A foot-ground contact model must be able to calculate ground reaction forces and moments that are consistent with experimentally measured ground reaction forces and moments. We show here that a rolling constraint can model foot-ground contact and reproduce measured ground reaction forces and moments in an induced acceleration analysis of muscle-driven simulations of walking, running, and crouch gait. We also illustrate that a point constraint and a weld constraint used to model foot-ground contact in previous studies produce inaccurate reaction moments and lead to contradictory interpretations of muscle function. To enable others to use and test these different constraint types (i.e., rolling, point, and weld constraints) we have included them as part of an induced acceleration analysis in OpenSim, a freely-available biomechanics simulation package. PMID:23702045

  3. 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.

  4. A quasiclassical trajectory and quantum mechanical study of the O(D-1)+D-2 reaction dynamics. Comparison with high resolution molecular beam experiments

    OpenAIRE

    Aoiz, F. Javier; Bañares, Luis; Castillo, J. F.; Herrero, Víctor J.; Martínez-Haya, Bruno

    2002-01-01

    A theoretical study of the dynamics of the O(1D) + D2 reaction has been performed at the collision energies (Ec¼ 86.7 meV and 138.8 meV) of a recent high resolution molecular beam experiment using the D-atom Rydberg ‘‘ tagging’’ technique (X. Liu et al., Phys. Rev. Lett., 2001, 86, 408). The theoretical calculations havebeen carried out on the ab initio 11A0, 11A00 and 21A0potential energy surfaces (PES) by Dobbyn and Knowles.The quasiclassical trajectory (QCT) method was used for the investi...

  5. A Study of Primary Collision Dynamics in Inverse-Kinematics Reaction of 78Kr on 40Ca at a Bombarding Energy of 10 MeV per Nucleon

    Science.gov (United States)

    Henry, Eric M.

    The CHIMERA multi-detector array at LNS Catania has been used to study the inverse-kinematics reaction of 78Kr + 40Ca at a bombarding energy of 10 A MeV. The multi-detector is capable of detecting individual products of the collision essential for the reconstruction of the collision dynamics. This is the first time CHIMERA has been used at low-energy, which offered a unique challenge for the calibration and interpretation of experimental data. Initial interrogation of the calibrated data revealed a class of selected events characterized by two coincident heavy fragments (atomic number Z>3) that together account for the majority of the total mass of the colliding system. These events are consistent with the complete fusion and subsequent binary split (fission) of a composite nucleus. The observed fission fragments are characterized by a broad A, Z distribution and are centered about symmetric fission while exhibiting relative velocities significantly higher than given by Viola systematics. Additional analysis of the kinematic relationship between the fission fragments was performed. Of note, is that the center-of-mass angular distribution (dsigma/dtheta) of the fission fragments exhibits an unexpected anisotropy inconsistent with a compound-nucleus reaction. This anisotropy is indicative of a dynamic fusion/fission-like process. The observed angular distribution features a forward-backward anisotropy most prevalent for mass-asymmetric events. Furthermore, the more massive fragment of mass-asymmetric events appears to emerge preferentially in the forward direction, along the beam axis. Analysis of the angular distribution of alpha particles emitted from these fission fragments suggests the events are associated mostly with central collisions. The observations associated with this subset of events are similar to those reported for dynamic fragmentation of projectile-like fragments, but have not before been observed for a fusion/fission-like process. Comparisons to

  6. 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.

  7. Fusion dynamics of 2020Ne + 20882Pb reaction using static and energy dependent Woods-Saxon potential

    International Nuclear Information System (INIS)

    The present work compares the theoretical predictions based on static Woods-Saxon potential and the EDWSP model along with one dimensional Wong formula. For 2020Ne + 20882Pb reaction, the theoretical calculations obtained by using static Woods-Saxon potential are substantially smaller than that of experimental data at below barrier energies and explain the fusion data at above barrier energies only. On the other hand, the EDWSP model based calculations adequately describe the observed fusion enhancement of 2020Ne + 20882Pb reaction in whole range of energy spread across the Coulomb barrier. Furthermore, a wide range of the diffuseness parameter ranging from 0.96 fm to 0.85 fm is required to address the sub-barrier fusion data

  8. Crossed-beam reaction of carbon atoms with hydrocarbon molecules. V. Chemical dynamics of n-C4H3 formation from reaction of C(3Pj) with allene, H2CCCH2(X 1A1)

    Science.gov (United States)

    Kaiser, R. I.; Mebel, A. M.; Chang, A. H. H.; Lin, S. H.; Lee, Y. T.

    1999-06-01

    The crossed molecular beams technique was employed to investigate the reaction between ground state carbon atoms, C(3Pj), and allene, H2CCCH2(X 1A1), at two averaged collision energies of 19.6 and 38.8 kJ mol-1. Product angular distributions and time-of-flight spectra of C4H3 were recorded. Forward-convolution fitting of the data yields weakly polarized center-of-mass angular flux distributions isotropic at lower, but forward scattered with respect to the carbon beam at a higher collision energy. The maximum translational energy release and the angular distributions combined with ab initio and RRKM calculations are consistent with the formation of the n-C4H3 radical in its electronic ground state. The channel to the i-C4H3 isomer contributes less than 1.5%. Reaction dynamics inferred from the experimental data indicate that the carbon atom attacks the π-orbitals of the allenic carbon-carbon double bond barrierless via a loose, reactant-like transition state located at the centrifugal barrier. The initially formed cyclopropylidene derivative rotates in a plane almost perpendicular to the total angular momentum vector around its C-axis and undergoes ring opening to triplet butatriene. At higher collision energy, the butatriene complex decomposes within 0.6 ps via hydrogen emission to form the n-C4H3 isomer and atomic hydrogen through an exit transition state located 9.2 kJ mol-1 above the products. The explicit identification of the n-C4H3 radical under single collision represents a further example of a carbon-hydrogen exchange in reactions of ground state carbon atoms with unsaturated hydrocarbons. This channel opens a barrierless route to synthesize extremely reactive hydrocarbon radicals in combustion processes, interstellar chemistry, and hydrocarbon-rich atmospheres of Jupiter, Saturn, Titan, as well as Triton.

  9. Comparative Study of Cl-Atom Reactions in Solution Using Time-Resolved Vibrational Spectroscopy.

    Science.gov (United States)

    Shin, Jae Yoon; Case, Amanda S; Crim, F Fleming

    2016-04-28

    A Cl atom can react with 2,3-dimethylbutane (DMB), 2,3-dimethyl-2-butene (DMBE), and 2,5-dimethyl-2,4-hexadiene (DMHD) in solution via a hydrogen-abstraction reaction. The large exoergicity of the reaction between a Cl atom and alkenes (DMBE and DMHD) makes vibrational excitation of the HCl product possible, and we observe the formation of vibrationally excited HCl (v = 1) for both reactions. In CCl4, the branching fractions of HCl (v = 1), Γ (v = 1), for the Cl-atom reactions with DMBE and DMHD are 0.14 and 0.23, respectively, reflecting an increased amount of vibrational excitation in the products of the more exoergic reaction. In addition, Γ (v = 1) for both reactions is larger in the solvent CDCl3, being 0.23 and 0.40, as the less viscous solvent apparently dampens the vibrational excitation of the nascent HCl less effectively. The bimolecular reaction rates for the Cl reactions with DMB, DMBE, and DMHD in CCl4 are diffusion limited (having rate constants of 1.5 × 10(10), 3.6 × 10(10), and 17.5 × 10(10) M(-1) s(-1), respectively). In fact, the bimolecular reaction rate for Cl + DMHD exceeds a typical diffusion-limited reaction rate, implying that the attractive intermolecular forces between a Cl atom and a C═C bond increase the rate of favorable encounters. The 2-fold increase in the reaction rate of the Cl + DMBE reaction from that of the Cl + DMB reaction likely reflects the effect of the C═C bond, while both the number of C═C bonds and the molecular geometry likely play a role in the large reaction rate of the Cl + DMHD reaction.

  10. Coriolis coupling effects on the initial-state-resolved dynamics of the N(2D)+H2-->NH+H reaction.

    Science.gov (United States)

    Defazio, Paolo; Petrongolo, Carlo

    2007-11-28

    We present Coriolis coupling effects on the initial-state-resolved dynamics of the insertion reaction N((2)D)+H(2)(X (1)Sigma(g) (+))-->NH(X (3)Sigma(-) and a (1)Delta)+H((2)S), without and with nonadiabatic Renner-Teller (RT) interactions between the NH(2) X (2)B(1) and A (2)A(1) electronic states. We report coupled-channel (CC) Hamiltonian matrix elements, which take into account both Coriolis and RT couplings, use the real wave-packet and flux methods for calculating initial-state-resolved reaction probabilities, and contrast CC with centrifugal-sudden (CS) results. Without RT interactions, Coriolis effects are rather small up to J=40, and the CS approximation can be safely employed for calculating initial-state-resolved, integral cross sections. On the other hand, RT effects are associated with rather large Coriolis couplings, mainly near the linearity of NH(2), and the accuracy of the CS approximation thus breaks down at high collision energies, when the reaction starts on the excited A (2)A(1) surface. We also present the CC-RT distribution of the X (3)Sigma(-) and a (1)Delta electronic states of the NH products.

  11. Intracellular kinetics of ATX-S10·Na(II) and its correlation with photochemical reaction dynamics during a pulsed photosensitization process: effect of pulse repetition rate

    Science.gov (United States)

    Kawauchi, Satoko; Sato, Shunichi; Morimoto, Yuji; Kikuchi, Makoto

    2006-01-01

    Although photodynamic therapy with pulsed light excitation has interesting characteristics, its photosensitization mechanism has not been fully elucidated. In this study, we showed that the intracellular kinetics of ATX-S10.Na(II), a lysosomal sensitizer, was closely related to photochemical reaction dynamics during photodynamic treatment of A549 cells with nanosecond pulsed light. Fluorescence microscopy revealed that at high frequencies of 10 and 30 Hz the sensitizer initially localized mainly in lysosomes but that it started to be redistributed to the cytosol in certain ranges of radiant exposures. These ranges were found to coincide with a regime of fluorescence degradation with limited oxygen consumption. On the other hand, at 5 Hz, there was no such a discontinuous behavior in the sensitizer redistribution characteristics throughout the period of irradiation; this was consistent with the fact that no reaction switching was observed. Two possible reasons for the appearance of the regime with limited oxygen consumption are discussed: participation of an oxygen-independent reaction and change in the microenvironment for the sensitizer caused by lysosomal photodamage. The pulse frequency-dependent intracellular kinetics of the sensitizer also explains our previous results showing higher cytotoxicity at 5 Hz than at 10 and 30 Hz.

  12. Dynamic transformation of small Ni particles during methanation of CO2 under fluctuating reaction conditions monitored by operando X-ray absorption spectroscopy

    Science.gov (United States)

    Mutz, B.; Carvalho, H. W. P.; Kleist, W.; Grunwaldt, J.-D.

    2016-05-01

    A 10 wt.-% Ni/Al2O3 catalyst with Ni particles of about 4 nm was prepared and applied in the methanation of CO2 under dynamic reaction conditions. Fast phase transformations between metallic Ni, NiO and NiCO3 were observed under changing reaction atmospheres using operando X-ray absorption spectroscopy (XAS). Removing H2 from the feed gas and, thus, simulating a H2 dropout during the methanation reaction led to oxidation of the active sites. The initial reduced state of the Ni particles could not be recovered under methanation atmosphere (H2/CO2 = 4); this was only possible with an effective reactivation step applying H2 at increased temperatures. Furthermore, the cycling of the gas atmospheres resulted in a steady deactivation of the catalyst. Operando XAS is a powerful tool to monitor these changes and the behavior of the catalyst under working conditions to improve the understanding of the catalytic processes and deactivation phenomena.

  13. Proton transfer and unimolecular decay in the low-energy-reaction dynamics of H/sub 3/O/sup +/ with acetone

    Energy Technology Data Exchange (ETDEWEB)

    Creasy, W R; Farrar, J M

    1983-01-01

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

  14. Isobaric yield ratio difference between the 140 $A$ MeV $^{58, 64}$Ni + $^{9}$Be reactions studied by antisymmetric molecular dynamics model

    CERN Document Server

    Qiao, C Y; Ma, C W; Zhang, Y L; Wang, S S

    2015-01-01

    \\item[Background] The isobaric yield ratio difference (IBD) method is found to be sensitive to the density difference of neutron-rich nucleus induced reaction around the Fermi energy. \\item[Purpose] An investigation is performed to study the IBD results in the transport model. \\item[Methods] The antisymmetric molecular dynamics (AMD) model plus the sequential decay model GEMINI are adopted to simulate the 140$A$ MeV $^{58, 64}$Ni + $^{9}$Be reactions. A relative small coalescence radius R$_c =$ 2.5 fm is used for the phase space at $t =$ 500 fm/c to form the hot fragment. Two limitations on the impact parameter ($b1 = 0 - 2$ fm and $b2 = 0 - 9$ fm) are used to study the effect of central collisions in IBD. \\item[Results] The isobaric yield ratios (IYRs) for the large--$A$ fragments are found to be suppressed in the symmetric reaction. The IBD results for fragments with neutron-excess $I = $ 0 and 1 are obtained. A small difference is found in the IBDs with the $b1$ and $b2$ limitations in the AMD simulated re...

  15. Influence of van der Waals wells on the quantum scattering dynamics of the Cl(2P) + HCl → ClH + Cl(2P) reaction

    International Nuclear Information System (INIS)

    We investigate the influence of van der Waals wells on the quantum scattering dynamics of the Cl + HCl → ClH + Cl reaction in which the three electronic states that correlate asymptotically to the ground state of Cl(2P) + HCl(1Σ+) are included in the dynamical calculations. The short range region of the potential energy surfaces is taken from recent restricted open-shell coupled-cluster singles doubles with perturbative triples and multireference configuration-interaction ab initio computations of Dobbyn et al. [Phys. Chem. Chem. Phys. 1 (1999) 957], as refined by Whiteley et al. [Phys. Chem. Chem. Phys. 2 (2000) 549]. The long range van der Waals region of the potential surfaces is derived from multisurface empirical potentials due to Dubernet and Hutson [J. Phys. Chem. 98 (1994) 5844]. We manipulate the van der Waals portions of the global potential surfaces by scaling the interaction of the Cl quadrupole with the HCl multipoles. This results in van der Waals wells that are either deeper or shallower than the unscaled reference case. Spin-orbit coupling is included using a spin-orbit parameter that is assumed to be independent of nuclear geometry, and Coriolis interactions are calculated accurately. Reactive scattering calculations have been performed for total angular momentum quantum number, J=1/2, using a hyperspherical-coordinate coupled-channel method in full dimensionality. We investigate how the cumulative reaction probability and the fine-structure-resolved cumulative reaction probabilities are influenced by variations in the van der Waals wells

  16. Study of the dynamics of the MoO2-Mo2C system for catalytic partial oxidation reactions

    Science.gov (United States)

    Cuba Torres, Christian Martin

    On a global scale, the energy demand is largely supplied by the combustion of non-renewable fossil fuels. However, their rapid depletion coupled with environmental and sustainability concerns are the main drivers to seek for alternative energetic strategies. To this end, the sustainable generation of hydrogen from renewable resources such as biodiesel would represent an attractive alternative solution to fossil fuels. Furthermore, hydrogen's lower environmental impact and greater independence from foreign control make it a strong contender for solving this global problem. Among a wide variety of methods for hydrogen production, the catalytic partial oxidation offers numerous advantages for compact and mobile fuel processing systems. For this reaction, the present work explores the versatility of the Mo--O--C catalytic system under different synthesis methods and reforming conditions using methyl oleate as a surrogate biodiesel. MoO2 exhibits good catalytic activity and exhibits high coke-resistance even under reforming conditions where long-chain oxygenated compounds are prone to form coke. Moreover, the lattice oxygen present in MoO2 promotes the Mars-Van Krevelen mechanism. Also, it is introduced a novel beta-Mo2C synthesis by the in-situ formation method that does not utilize external H2 inputs. Herein, the MoO 2/Mo2C system maintains high catalytic activity for partial oxidation while the lattice oxygen serves as a carbon buffer for preventing coke formation. This unique feature allows for longer operation reforming times despite slightly lower catalytic activity compared to the catalysts prepared by the traditional temperature-programmed reaction method. Moreover, it is demonstrated by a pulse reaction technique that during the phase transformation of MoO2 to beta-Mo2C, the formation of Mo metal as an intermediate is not responsible for the sintering of the material wrongly assumed by the temperature-programmed method.

  17. Adsorption effect on the dynamic response of a biochemical reaction in a biofilm reactor for wastewater treatment

    Energy Technology Data Exchange (ETDEWEB)

    Tsuneda, S.; Inoue, Y.; Auresenia, J.; Hirata, A. [Department of Chemical Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555 (Japan)

    2003-09-01

    The dynamic behavior of a completely mixed, three-phase, fluidized bed biofilm reactor treating simulated domestic wastewater was studied with step changes in inlet concentration. It was found that the response curves showed second order characteristics, i.e., as the inlet concentration was increased, the outlet concentration also increased, reached a peak value and then decreased until it leveled to a new steady-state value corresponding to the new inlet concentration level. Nonlinear regression analysis was performed using Monod-type rate equations with and without an adsorption term. As a result, the theoretical curve of the kinetic model that incorporates the adsorption term has best fit to the actual response in most cases. Thus, it was concluded that the adsorption of a substrate onto the biofilm and carrier particles has a significant effect on the dynamic response in biofilm processes. (Abstract Copyright [2003], Wiley Periodicals, Inc.)

  18. Dynamic of bioelectric activity back hypothalamus changes in conditions of pyroxan application on the background of stress-reaction developmen

    Directory of Open Access Journals (Sweden)

    T. G. Chaus

    2005-04-01

    Full Text Available The dynamic of changes of capacity of electroencephalogram’s rhythms back hypothalamus at animals of control group and group in stress conditions in parallel with rats who on a background of stress development accepted pyroxan is analyzed. The submitted results have shown influence of a pharmacological preparation pyroxan on bioelectric activity of back hypothalamus in stress conditions that restoration of electric activity under action of this preparation was more shown at 3 weeks of its application.

  19. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    International Nuclear Information System (INIS)

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H2 reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H2 reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H2 reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables

  20. Theoretical study of quantum molecular reaction dynamics and of the effects of intense laser radiation on a diatomic molecule

    Energy Technology Data Exchange (ETDEWEB)

    Dardi, P.S.

    1984-11-01

    Within the very broad field of molecular dynamics, we have concentrated on two simple yet important systems. The systems are simple enough so that they are adequately described with a single Born-Oppenheimer potential energy surface and that the dynamics can be calculated accurately. They are important because they give insight into solving more complicated systems. First we discuss H + H/sub 2/ reactive scattering. We present an exact formalism for atom-diatom reactive scattering which avoids the problem of finding a coordinate system appropriate for both reactants and products. We present computational results for collinear H + H/sub 2/ reactive scattering which agree very well with previous calculations. We also present a coupled channel distorted wave Born approximation for atom-diatom reactive scattering which we show is a first order approximation to our exact formalism. We present coupled channel DWBA results for three dimensional H + H/sub 2/ reactive scattering. The second system is an isolated HF molecule in an intense laser field. Using classical trajectories and quantum dynamics, we look at energy absorbed and transition probabilities as a function of the laser pulse time and also averaged over the pulse time. Calculations are performed for both rotating and nonrotating HF. We examine one and two photon absorption about the fundamental frequency, multiphoton absorption, and overtone absorption. 127 references, 31 figures, 12 tables.