RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Allen, Joshua W.; Green, William H; Suleimanov, Yu. V.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett–Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any ...
Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
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.
Recent Advances in Quantum Dynamics of Bimolecular Reactions.
Zhang, Dong H; Guo, Hua
2016-05-27
In this review, we survey the latest advances in theoretical understanding of bimolecular reaction dynamics in the past decade. The remarkable recent progress in this field has been driven by more accurate and efficient ab initio electronic structure theory, effective potential-energy surface fitting techniques, and novel quantum scattering algorithms. Quantum mechanical characterization of bimolecular reactions continues to uncover interesting dynamical phenomena in atom-diatom reactions and beyond, reaching an unprecedented level of sophistication. In tandem with experimental explorations, these theoretical developments have greatly advanced our understanding of key issues in reaction dynamics, such as microscopic reaction mechanisms, mode specificity, product energy disposal, influence of reactive resonances, and nonadiabatic effects. PMID:26980305
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
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.
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
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
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
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.
Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions
The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound → bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN-, NCO- and NCS-. Transition state photoelectron spectra are presented for the following systems Br + HI, Cl + HI, F + HI, F + CH30H,F + C2H5OH,F + OH and F + H2. A time dependent framework for the simulation and interpretation of the bound → free transition state photoelectron spectra is subsequently developed and applied to the hydrogen transfer reactions Br + HI, F + OH → O(3P, 1D) + HF and F + H2. The theoretical approach for the simulations is a fully quantum-mechanical wave packet propagation on a collinear model reaction potential surface. The connection between the wavepacket time evolution and the photoelectron spectrum is given by the time autocorrelation function. For the benchmark F + H2 system, comparisons with three-dimensional quantum calculations are made
Generation of radicals by bimolecular reactions
Denisov, Evgenii T; Denisova, Taisa G [Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)
2002-05-31
The published data on bimolecular processes of radical generation in chain degradation, polymerisation, oxidation and halogenation reactions of organic compounds are systematised and analysed within the framework of the parabolic model of homolytic bimolecular reactions. The specific features of these highly endothermic reactions are discussed with a special emphasis on their striking similarity to radical abstraction processes with identical reaction centres in the transition state. The feasibility of theoretical evaluation of the activation energies and the rate constants of bimolecular reactions in radical generation is demonstrated. The bibliography includes 86 references.
An exact solution to Brownian dynamics of a reversible bimolecular reaction in one dimension
Smith, Stephen; Grima, Ramon
2016-01-01
Brownian dynamics is a popular fine-grained method for simulating systems of interacting particles, such as chemical reactions. Though the method is simple to simulate, it is generally assumed that the dynamics is impossible to solve exactly and analytically, aside from some trivial systems. We here give the first exact analytical solution to a non-trivial Brownian dynamics system: the reaction $A+B\\xrightleftharpoons[]{}C$ in equilibrium in one-dimensional periodic space. The solution is a f...
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.
Resonance Reaction in Diffusion-Influenced Bimolecular Reactions
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.
Communication: Resonance reaction in diffusion-influenced bimolecular reactions
Kolb, Jakob J.; Angioletti-Uberti, Stefano; Dzubiella, Joachim
2016-02-01
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new "resonant reaction" behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance, the standard reciprocal additivity law for diffusion and surface reaction rates is violated due to the dynamical coupling of multiple kinetic processes. Together, these findings may have important repercussions on the correct interpretation of various kinetic reaction problems in complex systems, as, e.g., in biomolecular association or catalysis.
Resonance Reaction in Diffusion-Influenced Bimolecular Reactions
Kolb, Jakob J.; Angioletti-Uberti, Stefano; Dzubiella, Joachim
2016-01-01
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance the standard reciprocal additivity law for diffusion and surface reaction rates is viola...
Theory of Crowding Effects on Bimolecular Reaction Rates.
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
Morse bifurcations of transition states in bimolecular reactions
MacKay, R. S.; Strub, D. C.
2015-12-01
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo Morse bifurcations, in which they change diffeomorphism class, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces.
Morse bifurcations of transition states in bimolecular reactions
MacKay, Robert S
2015-01-01
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces. The reduction of the $n$-body systems representing the reactions is discussed and reviewed with comments on the difficulties associated with choosing appropriate charts and the global geometry of the reduced spaces.
The power-law reaction rate coefficient for an elementary bimolecular reaction
Yin, Cangtao; Du, Jiulin
2013-01-01
The power-law TST reaction rate coefficient for an elementary bimolecular reaction is studied when the reaction takes place in a nonequilibrium system with power-law distributions. We derive a generalized TST rate coefficient, which not only depends on a power-law parameter but also on the reaction coordinate frequency of transition state. The numerical analyses show a very strong dependence of TST rate coefficient on the power-law parameter, and clearly indicate that a tiny deviation from un...
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.
Photoinduced electron transfer (ET) reactions between anthraquinone derivatives and aromatic amines have been investigated in sodium dodecyl sulphate (SDS) micellar solutions. Significant static quenching of the quinone fluorescence due to high amine concentration in the micellar phase has been observed in steady-state measurements. The bimolecular rate constants for the dynamic quenching in the present systems kqTR, as estimated from the time-resolved measurements, have been correlated with the free energy changes ΔG0 for the ET reactions. Interestingly it is seen that the kqTR vs ΔG0 plot displays an inversion behavior with maximum kqTR at around 0.7 eV, a trend similar to that predicted in Marcus ET theory. Like the present results, Marcus inversion in the kqTR values was also observed earlier in coumarin-amine systems in SDS and TX-100 micellar solutions, with maximum kqTR at around the same exergonicity. These results thus suggest that Marcus inversion in bimolecular ET reaction is a general phenomenon in micellar media. Present observations have been rationalized on the basis of the two-dimensional ET (2DET) theory, which seems to be more suitable for micellar ET reactions than the conventional ET theory. For the quinone-amine systems, it is interestingly seen that kqTR vs ΔG0 plot is somewhat wider in comparison to that of the coumarin-amine systems, even though the maxima in the kqTR vs ΔG0 plots appear at almost similar exergonicity for both the acceptor-donor systems. These observations have been rationalized on the basis of the differences in the reaction windows along the solvation axis, as envisaged within the framework of the 2DET theory, and arise due to the differences in the locations of the quinones and coumarin dyes in the micellar phase
A transition in the spatially integrated reaction rate of bimolecular reaction-diffusion systems
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.
Kochhar, Gurpaul S.; Mosey, Nicholas J.
2016-03-01
Mechanochemistry, i.e. the application of forces, F, at the molecular level, has attracted significant interest as a means of controlling chemical reactions. The present study uses quantum chemical calculations to explore the abilities to mechanically eliminate activation energies, ΔE‡, for unimolecular and bimolecular reactions. The results demonstrate that ΔE‡ can be eliminated for unimolecular reactions by applying sufficiently large F along directions that move the reactant and/or transition state (TS) structures parallel to the zero-F reaction coordinate, S0. In contrast, eliminating ΔE‡ for bimolecular reactions requires the reactant to undergo a force-induced shift parallel to S0 irrespective of changes in the TS. Meeting this requirement depends upon the coupling between F and S0 in the reactant. The insights regarding the differences in eliminating ΔE‡ for unimolecular and bimolecular reactions, and the requirements for eliminating ΔE‡, may be useful in practical efforts to control reactions mechanochemically.
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...
Photochemical reaction dynamics
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.
Piazza, Francesco; Foffi, Giuseppe; De Michele, Cristiano
2013-06-19
We investigate numerically pseudo-first-order irreversible bimolecular reactions of the type A + B → B between hard spheres undergoing event-driven Brownian dynamics. We study the encounter rate and the survival probability of A particles as functions of the packing fraction ϕ in the trapping (a single particle diffusing among static non-overlapping traps) and target (many traps diffusing in the presence of a single static target particle) settings, as well as in the case of diffusing traps and particles (full mobility). We show that, since inertial effects are accounted for in our simulation protocol, the standard Smoluchowski theory of coagulation of non-interacting colloids is recovered only at times greater than a characteristic time Δt, marking the transition from the under-damped to the over-damped regime. We show that the survival probability S(t) decays exponentially during this first stage, with a rate 1/τ0 is proportional to φ. Furthermore, we work out a simple analytical expression that is able to capture to an excellent extent the numerical results for t < Δt at low and intermediate densities. Moreover, we demonstrate that the time constant of the asymptotic exponential decay of S(t) for diffusing traps and particles is k(S)(-1), where kS = 4π(DA + DB)Rρ is the Smoluchowski rate. Detailed analyses of the effective decay exponent β = d [log(-logS(t))]/d (logt) and of the steady-state encounter rate reveal that the full mobility and trapping problem are characterized by very similar kinetics, rather different from the target problem. Our results do not allow one to ascertain whether the prediction S(t) is proportional to exp(-at(3/2)) (a = const.) as t → ∞ for the trapping problem in 3D is indeed recovered. In fact, at high density, S(t) is dominated by short encounter times, which makes it exceedingly hard to record the events corresponding to the exploration of large, trap-free regions. As a consequence, at high densities the steady
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 (eaq. 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 eaq 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.
Modeling Bimolecular Reactions and Transport in Porous Media Via Particle Tracking
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
It has been demonstrated that a mixture of reactant molecules can be induced by pulsed infrared laser radiation to react via a route which is totally different from the pathway resulting from heating the mixture at 3000C. The high-energy unimolecular elimination of H2O from ethanol in the presence of 2-propanol and HBr can be selectively induced with a pulsed CO2 laser in preference to either a lower energy bimolecular HBr-catalyzed dehydration or the more facile dehydration of 2-propanol. Heating the mixture resulted in the almost exclusive reaction of 2-propanol to produce propylene. It was demonstrated that the bimolecular ethanol + HBr reaction cannot be effectively induced by the infrared laser radiation as evidenced by the detrimental effect on the yield of ethylene as the HBr pressure was increased. The selective, nonthermal inducement of H2O elimination from vibrationally excited ethanol in the presence of 2-propanol required relatively low reactant pressures. At higher pressures intermolecular V--V energy transfer allowed the thermally more facile dehydration from 2-propanol to become the predominant reaction channel
Manifestations of the “cage effect” at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a “cage complex.” Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the “cage effect” leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants
Photoinduced electron transfer (ET) between coumarin dyes and aromatic amine has been investigated in two cationic micelles, namely, cetyltrimethyl ammonium bromide (CTAB) and dodecyltrimethyl ammonium bromide (DTAB), and the results have been compared with those observed earlier in sodium dodecyl sulphate (SDS) and triton-X-100 (TX-100) micelles for similar donor-acceptor pairs. Due to a reasonably high effective concentration of the amines in the micellar Stern layer, the steady-state fluorescence results show significant static quenching. In the time-resolved (TR) measurements with subnanosecond time resolution, contribution from static quenching is avoided. Correlations of the dynamic quenching constants (kqTR), as estimated from the TR measurements, show the typical bell-shaped curves with the free-energy changes (ΔG0) of the ET reactions, as predicted by the Marcus outersphere ET theory. Comparing present results with those obtained earlier for similar coumarin-amine systems in SDS and TX-100 micelles, it is seen that the inversion in the present micelles occurs at an exergonicity (-ΔG0>∼1.2-1.3 eV) much higher than that observed in SDS and TX-100 micelles (-ΔG0>∼0.7 eV), which has been rationalized based on the relative propensities of the ET and solvation rates in different micelles. In CTAB and DTAB micelles, the kqTR values are lower than the solvation rates, which result in the full contribution of the solvent reorganization energy (λs) towards the activation barrier for the ET reaction. Contrary to this, in SDS and TX-100 micelles, kqTR values are either higher or comparable with the solvation rates, causing only a partial contribution of λs in these cases. Thus, Marcus inversion in present cationic micelles is inferred to be the true inversion, whereas that in the anionic SDS and neutral TX-100 micelles are understood to be the apparent inversion, as envisaged from two-dimensional ET theory
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
Luminescence Spectroscopy and Bimolecular Quenching
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…
Berndt, Torsten; Kaethner, Ralf; Voigtländer, Jens; Stratmann, Frank; Pfeifle, Mark; Reichle, Patrick; Sipilä, Mikko; Kulmala, Markku; Olzmann, Matthias
2015-08-14
Stabilized Criegee Intermediates (sCIs) have been identified as oxidants of atmospheric trace gases such as SO2, NO2, carboxylic acids or carbonyls. The atmospheric sCI concentrations, and accordingly their importance for trace gas oxidation, are controlled by the rate of the most important loss processes, very likely the unimolecular reactions and the reaction with water vapour (monomer and dimer) ubiquitously present at high concentrations in the troposphere. In this study, the rate coefficients of the unimolecular reaction of the simplest sCI, formaldehyde oxide, CH2OO, and its bimolecular reaction with the water monomer have been experimentally determined at T = (297 ± 1) K and at atmospheric pressure by using a free-jet flow system. CH2OO was produced by the reaction of ozone with C2H4, and CH2OO concentrations were probed indirectly by detecting H2SO4 after titration with SO2. Time-resolved experiments yield a rate coefficient of the unimolecular reaction of k(uni) = (0.19 ± 0.07) s(-1), a value that is supported by quantum-chemical and statistical rate theory calculations as well as by additional measurements performed under CH2OO steady-state conditions. A rate coefficient of k(CH2OO+H2O) = (3.2 ± 1.2) × 10(-16) cm(3) molecule(-1) s(-1) has been determined for sufficiently low H2O concentrations (<10(15) molecule cm(-3)) that allow separation from the CH2OO reaction with the water dimer. In order to evaluate the accuracy of the experimental approach, the rate coefficients of the reactions with acetaldehyde and acetone were reinvestigated. The obtained rate coefficients k(CH2OO+acetald) = (1.7 ± 0.5) × 10(-12) and k(CH2OO+acetone) = (3.4 ± 0.9) × 10(-13) cm(3) molecule(-1) s(-1) are in good agreement with literature data. PMID:26159709
Roaming dynamics in radical addition-elimination reactions
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.
The kinetics of bimolecular pseudo-self-exchange reactions such as that between pentaammine(pyridine)ruthenium(II) and pentaammine(3-fluoropyridine)ruthenium(III) shown below,(NH3)5RuII(py)2++(NH3)5RuIII(3-Fpy)3+-bar kex(NH3)5RuIII(py)3++(NH3)5RuII(3-Fpy)2+reveal a novel form of non-covalently mediated electron transfer over distance when salts of non-innocent electrolytes such as the conjugated dicarboxylic acid anions trans,trans-muconate2- or terephthalate2- are added to the solution. The kinetic accelerations are distinct from those seen with simple electrolytes such as KCl or CaCl2, and are thus outside the realm of classical electrolyte effects described by the Debye-Huckel theory of ion atmospheres. Kinetic simulations are presented, and the rate acceleration is interpreted in the context of possible superexchange-type interactions taking place in hydrogen-bonded ternary (or higher) association complexes which create new kinetic pathways for electron transfer over distance in aqueous solution
New methods for quantum mechanical reaction dynamics
Quantum mechanical methods are developed to describe the dynamics of bimolecular chemical reactions. We focus on developing approaches for directly calculating the desired quantity of interest. Methods for the calculation of single matrix elements of the scattering matrix (S-matrix) and initial state-selected reaction probabilities are presented. This is accomplished by the use of absorbing boundary conditions (ABC) to obtain a localized (L2) representation of the outgoing wave scattering Green's function. This approach enables the efficient calculation of only a single column of the S-matrix with a proportionate savings in effort over the calculation of the entire S-matrix. Applying this method to the calculation of the initial (or final) state-selected reaction probability, a more averaged quantity, requires even less effort than the state-to-state S-matrix elements. It is shown how the same representation of the Green's function can be effectively applied to the calculation of negative ion photodetachment intensities. Photodetachment spectroscopy of the anion ABC- can be a very useful method for obtaining detailed information about the neutral ABC potential energy surface, particularly if the ABC- geometry is similar to the transition state of the neutral ABC. Total and arrangement-selected photodetachment spectra are calculated for the H3O- system, providing information about the potential energy surface for the OH + H2 reaction when compared with experimental results. Finally, we present methods for the direct calculation of the thermal rate constant from the flux-position and flux-flux correlation functions. The spirit of transition state theory is invoked by concentrating on the short time dynamics in the area around the transition state that determine reactivity. These methods are made efficient by evaluating the required quantum mechanical trace in the basis of eigenstates of the Boltzmannized flux operator
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.
Reaction dynamics and photochemistry of divalent systems
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.
Dynamics of anion-molecule reactions at low energy
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.)
Dynamics of anion-molecule reactions at low energy
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.)
Semiclassical methods in chemical reaction dynamics
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
Semiclassical methods in chemical reaction dynamics
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.
Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions
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…
Some Concepts in Reaction Dynamics
Polannyi, John C.
1972-01-01
In 1929 London 1 published a very approximate solution of the Schroedinger equation for a system of chemical interest: H3. To the extent that chemistry can be regarded as existing separately from physics, this was a landmark in the history of chemistry, comparable in importance to the landmark in the history of physics marked by the appearance of the Heitler-London equation for H2. The expression for H3, was, of necessity, even less accurate than that for H2, but chemists, like the habitual poor, were accustomed to this sort of misfortune. Together with the physicists they enjoyed the sensation of living in a renaissance. The physicists still could not calculate a great deal that was of interest to them, and the chemists could calculate less, but both could now dream. It would be too easy to say that their dreams were dreams of unlimited computer time. Their dreams were a lot more productive than that. Two years after London published his equation, H. Eyring and M. Polanyi obtained the first numerical energy surface for H3. They infused the London equation with a measure of empiricism to produce an energy surface which, whether or not it was correct in its details, provided a basis for further speculations of an important sort. The existence of a tangible energy surface in 1931 stimulated speculation along two different lines. The following year Pelzer and Wigner used this London-Eyring-Polanyi (LEP) energy surface for a thermodynamic treatment of the reaction rate in H + H2. This important development reached its full flowering a few years later. In these remarks I shall be concerned with another line of development. A second more-or-less distinct category of speculation that began with (and, indeed, in) the 1931 paper has to do with the dynamics of individual reactive encounters under the influence of specified interaction potentials.
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
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
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 O_{2}. 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 NaO_{2} + Na and NaO + NaO. NaO_{2} 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 O_{2}, which is likely a result of a charge transfer from Na_{2} to the excited state orbital of O_{2-}. The scattering of sodium dimers from ammonium and methanol produced novel molecules, NaNH_{3} and Na(CH_{3}OH), 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.
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....
Molecular dynamics simulation of a chemical reaction
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Markovian Dynamics on Complex Reaction Networks
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...
Chemical Reaction Dynamics in Nanoscle Environments
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.
Markovian dynamics on complex reaction networks
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.
Markovian dynamics on complex reaction networks
Goutsias, J.; Jenkinson, G.
2013-08-01
Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.
Reaction dynamics in polyatomic molecular systems
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.
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...
A dynamical model of surrogate reactions
Aritomo, Y; Nishio, K
2010-01-01
A new dynamical model is developed to describe the whole process of surrogate reactions; transfer of several nucleons at an initial stage, thermal equilibration of residues leading to washing out of shell effects and decay of populated compound nuclei are treated in a unified framework. Multi-dimensional Langevin equations are employed to describe time-evolution of collective coordinates with a time-dependent potential energy surface corresponding to different stages of surrogate reactions. The new model is capable of calculating spin distributions of the compound nuclei, one of the most important quantity in the surrogate technique. Furthermore, various observables of surrogate reactions can be calculated, e.g., energy and angular distribution of ejectile, and mass distributions of fission fragments. These features are important to assess validity of the proposed model itself, to understand mechanisms of the surrogate reactions and to determine unknown parameters of the model. It is found that spin distribut...
Quantum effects in unimolecular reaction dynamics
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.
Theoretical studies of chemical reaction dynamics
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.
Molecular beam studies of reaction dynamics
Lee, Y.T.
1987-03-01
Purpose of this research project is two-fold: (1) to elucidate detailed dynamics of simple elementary reactions which are theoretically important and to unravel the mechanism of complex chemical reactions or photo chemical processes which play an important role in many macroscopic processes and (2) to determine the energetics of polyatomic free radicals using microscopic experimental methods. Most of the information is derived from measurement of the product fragment translational energy and angular distributions using unique molecular beam apparati designed for these purposes.
Neural Networks in Chemical Reaction Dynamics
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
Molecular beam studies of reaction dynamics
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.
Catalytic reaction dynamics in inhomogeneous networks.
Watanabe, Akitomo; Yakubo, Kousuke
2014-05-01
Biochemical reactions in a cell can be modeled by a catalytic reaction network (CRN). It has been reported that catalytic chain reactions occur intermittently in the CRN with a homogeneous random-graph topology and its avalanche-size distribution obeys a power law with the exponent 4/3 [A. Awazu and K. Kaneko, Phys. Rev. E 80, 010902(R) (2009)]. This fact indicates that the catalytic reaction dynamics in homogeneous CRNs exhibits self-organized criticality (SOC). Structures of actual CRNs are, however, known to be highly inhomogeneous. We study the influence of various types of inhomogeneities found in real-world metabolic networks on the universality class of SOC. Our numerical results clarify that SOC keeps its universality class even for networks possessing structural inhomogeneities such as the scale-free property, community structures, and degree correlations. In contrast, if the CRN has inhomogeneous catalytic functionality, the universality class of SOC depends on how widely distributed the number of reaction paths catalyzed by a single chemical species is. PMID:25353843
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
Dynamics of the F(-) + CH3I → HF + CH2I(-) Proton Transfer Reaction.
Zhang, Jiaxu; Xie, Jing; Hase, William L
2015-12-17
Direct chemical dynamics simulations, at collision energies Erel of 0.32 and 1.53 eV, were performed to obtain an atomistic understanding of the F(-) + CH3I reaction dynamics. There is only the F(-) + CH3I → CH3F + I(-) bimolecular nucleophilic substitution SN2 product channel at 0.32 eV. Increasing Erel to 1.53 eV opens the endothermic F(-) + CH3I → HF + CH2I(-) proton transfer reaction, which is less competitive than the SN2 reaction. The simulations reveal proton transfer occurs by two direct atomic-level mechanisms, rebound and stripping, and indirect mechanisms, involving formation of the F(-)···HCH2I complex and the roundabout. For the indirect trajectories all of the CH2I(-) is formed with zero-point energy (ZPE), while for the direct trajectories 50% form CH2I(-) without ZPE. Without a ZPE constraint for CH2I(-), the reaction cross sections for the rebound, stripping, and indirect mechanisms are 0.2 ± 0.1, 1.2 ± 0.4, and 0.7 ± 0.2 Å(2), respectively. Discarding trajectories that do not form CH2I(-) with ZPE reduces the rebound and stripping cross sections to 0.1 ± 0.1 and 0.7 ± 0.5 Å(2). The HF product is formed rotationally and vibrationally unexcited. The average value of J is 2.6 and with histogram binning n = 0. CH2I(-) is formed rotationally excited. The partitioning between CH2I(-) vibration and HF + CH2I(-) relative translation energy depends on the treatment of CH2I(-) ZPE. Without a CH2I(-) ZPE constraint the energy partitioning is primarily to relative translation with little CH2I(-) vibration. With a ZPE constraint, energy partitioning to CH2I(-) rotation, CH2I(-) vibration, and relative translation are statistically the same. The overall F(-) + CH3I rate constant at Erel of both 0.32 and 1.53 eV is in good agreement with experiment and negligibly affected by the treatment of CH2I(-) ZPE, since the SN2 reaction is the major contributor to the total reaction rate constant. The potential energy surface and reaction dynamics for F
Quantum dynamics of fast chemical reactions
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.
Mode specificity in unimolecular reaction dynamics
Theoretical studies on mode specificity in unimolecular reaction dynamics are presented, based on essentially exact quantum mechanical methods, a semi-classical multichannel branching model, and classical trajectory methods. The principal aim is to discover the relevant factors governing whether a unimolecular system exhibits mode specificity in its individual state rate constants, i.e., whether quasi-degenerate metastable states decay with significantly different rates. Model studies of two nonlinearly coupled oscillators (one of which can dissociate) demonstrate the effects of various features of potential energy surfaces on the character of the rates (e.g., degeneracy of modes, reaction path curvature, frequency modulation, etc.). These results and those obtained for the Henon-Heiles potential energy surface indicate and apparent absence of correlation between the quasi-periodic/ergodic motion of classical mechanics and the mode specific/statistical behavior of the unimolecular rate constants
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
A network dynamics approach to chemical reaction networks
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
The molecular dynamics of atmospheric reaction
Polanyi, J. C.
1971-01-01
Detailed information about the chemistry of the upper atmosphere took the form of quantitative data concerning the rate of reaction into specified states of product vibration, rotation and translation for exothermic reaction, as well as concerning the rate of reaction from specified states of reagent vibration, rotation and translation for endothermic reaction. The techniques used were variants on the infrared chemiluminescence method. Emphasis was placed on reactions that formed, and that removed, vibrationally-excited hydroxyl radicals. Fundamental studies were also performed on exothermic reactions involving hydrogen halides.
Mode-coupling theory for reaction dynamics in liquids
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...
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}.
Electromagnetic Reactions and Few-Nucleon Dynamics
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.
Electromagnetic reactions and few-nucleon dynamics
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)
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.
Dynamics of fission and heavy ion reactions
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
Testing string dynamics in lepton nucleus reactions
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
Yu Angyang; Zhonghua Yang
2015-01-01
The theoretical background and basic definition of the resonances in chemical reaction dynamics have been introduced in this article. The historical breakthrough in the experimental search for the reaction resonances has been reviewed in this report, with an emphasis on the crossed molecular beam apparatus. The research of the chemical reaction resonances has attracted many scientists’ attention from 80s of last century. The chemical reaction resonances in the F+H2 reaction were firstly obser...
NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics
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...
Transverse flow reactor studies of the dynamics of radical reactions
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.
Skeletal Isomerization and Inter-molecular Hydrogen Transfer Reactions in Catalytic Cracking
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.
A network dynamics approach to chemical reaction networks
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.
Crossed molecular beam studies of unimolecular reaction dynamics
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
Roaming dynamics in the MgH + H→Mg + H 2 reaction: Quantum dynamics calculations
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.
Many-body quantum reaction dynamics near the fusion barrier
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)
Many-body Quantum Reaction Dynamics near the Fusion Barrier
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.
Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions.
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
Dynamical dipole mode in heavy-ion fusion reactions
The dynamical dipole mode, excited in charge asymmetric heavy-ion collisions, was investigated in the mass region of the 192Pb compound nucleus, formed by using the 40,48Ca + 152,144Sm reactions at ∼11 MeV/nucleon. Preliminary results of this measurement, concerning both fusion-evaporation and fission events are presented. As a fast cooling mechanism on the fusion path, the dynamical dipole mode could be useful for the synthesis of super heavy elements through 'hot' fusion reactions.
Simulation of chemical reaction dynamics on an NMR quantum computer
Lu, Dawei; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng
2011-01-01
Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.
Dynamics of synchrotron VUV-induced intracluster reactions
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.
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 ...
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.
Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
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.
Finite temperature amplitudes and reaction rates in Thermofield dynamics
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.
Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics.
Marchand, Adrien; Ferreira, Rubén; Tateishi-Karimata, Hisae; Miyoshi, Daisuke; Sugimoto, Naoki; Gabelica, Valérie
2013-10-17
Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely sensitive to the sequence and to the chemical environment, for example, solvation. Dehydrating conditions are known to stabilize G-quadruplex structures, but information on how solvation influences the individual rates of folding and unfolding of G-quadruplexes remains scarce. Here, we used electrospray mass spectrometry for the first time to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands, in the presence of common organic cosolvents (methanol, ethanol, isopropanol, and acetonitrile). Based on the ammonium ion distribution, the total dimer signal was decomposed into contributions from the parallel and antiparallel structures to obtain individual reaction rates, and the antiparallel G-quadruplex structure was found to form faster than the parallel one. A dimeric reaction intermediate, in rapid equilibrium with the single strands, was also identified. Organic cosolvents increase the stability of the final structures mainly by increasing the folding rates. Our quantitative analysis of reaction rate dependence on cosolvent percentage shows that organic cosolvent molecules can be captured or released upon G-quadruplex formation, highlighting that they are not inert with DNA. In contrast to the folding rates, the G-quadruplex unfolding rates are almost insensitive to solvation effects, but are instead governed by the sequence and by the final structure: parallel dimers dissociate slower than antiparallel dimers only when thymine bases are present at the 5'-end. These results contribute unraveling the folding pathways of telomeric G-quadruplexes. The solvent effects revealed here enlighten that G-quadruplex structure in dehydrated, and molecularly crowded environments are modulated by the nature of cosolvent (e.g., methanol favors antiparallel structures) due to direct interactions, and by the time scale of the reaction, with >200-fold acceleration of
A dynamical theory of incomplete fusion reactions: The breakup-fusion reaction approach
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
Quantum Dynamics of Radical-Ion-Pair Reactions
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.
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
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...
Understanding bimolecular machines: Theoretical and experimental approaches
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
Structure, dynamics, and surface reactions of bioactive glasses
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
Crossed molecular beam studies of atmospheric chemical reaction dynamics
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.
The photodissociation and reaction dynamics of vibrationally excited molecules
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.
Untangling knots via reaction-diffusion dynamics of vortex strings
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.
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.
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
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
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.
Simulation of chemical reaction dynamics on an NMR quantum computer
Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng
2011-01-01
Quantum simulation can beat current classical computers with minimally a few tens of qubits and will likely become the first practical use of a quantum computer. One promising application of quantum simulation is to attack challenging quantum chemistry problems. Here we report an experimental demonstration that a small nuclear-magnetic-resonance (NMR) quantum computer is already able to simulate the dynamics of a prototype chemical reaction. The experimental results agree well with classical ...
Fluid dynamic modeling of nano-thermite reactions
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.
Fluid dynamic modeling of nano-thermite reactions
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.
Fluid dynamic modeling of nano-thermite reactions
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
Reaction dynamics studies for the system 7Be+58Ni
Torresi, D.; Mazzocco, M.; Acosta, L.; Boiano, A.; Boiano, C.; Diaz-Torres, A.; Fierro, N.; Glodariu, T.; Grilj, L.; Guglielmetti, A.; Keeley, N.; La Commara, M.; Martel, I.; Mazzocchi, C.; Molini, P.; Pakou, A.; Parascandolo, C.; Parkar, V. V.; Patronis, N.; Pierroutsakou, D.; Romoli, M.; Rusek, K.; Sanchez-Benitez, A. M.; Sandoli, M.; Signorini, C.; Silvestri, R.; Soramel, F.; Stiliaris, E.; Strano, E.; Stroe, L.; Zerva, K.
2015-04-01
The study of reactions induced by exotic weakly bound nuclei at energies around the Coulomb barrier had attracted a large interest in the last decade, since the features of these nuclei can deeply affect the reaction dynamics. The discrimination between different reaction mechanisms is, in general, a rather difficult task. It can be achieved by using detector arrays covering high solid angle and with high granularity that allow to measure the reaction products and, possibly, coincidences between them, as, for example, recently done for stable weakly bound nuclei [1, 2]. We investigated the collision of the weakly bound nucleus 7Be on a 58Ni target at the beam energy of 1.1 times the Coulomb barrier, measuring the elastic scattering angular distribution and the energy and angular distributions of 3He and 4He. The 7Be radioactive ion beam was produced by the facility EXOTIC at INFN-LNL with an energy of 22 MeV and an intensity of ~3×105 pps. Results showed that the 4He yeld is about 4 times larger than 3He yield, suggesting that reaction mechanisms other than the break-up mostly produce the He isotopes. Theoretical calculations for transfer channels and compound nucleus reactions suggest that complete fusion accounts for (41±5%) of the total reaction cross section extracted from optical model analysis of the elastic scattering data, and that 3He and 4He stripping are the most populated reaction channels among direct processes. Eventually estimation of incomplete fusion contributions to the 3,4He production cross sections was performed through semi-classical calculations with the code PLATYPUS [3].
[2+2] Photocycloaddition reaction dynamics of triplet pyrimidines.
Yang, Chunfan; Yu, Youqing; Liu, Kunhui; Song, Di; Wu, Lidan; Su, Hongmei
2011-06-01
Taking the 266 nm excited pyrimidine (uracil or thymine) with cyclopentene as model reaction systems, we have examined the photoproduct formation dynamics from the [2 + 2] photocycloaddition reactions of triplet pyrimidines in solution and provided mechanistic insights into this important DNA photodamage reaction. By combining two compliment methods of nanosecond time-resolved transient IR and UV-vis laser flash-photolysis spectroscopy, the photoproduct formation dynamics as well as the triplet quenching kinetics are measured. Characteristic IR absorption bands due to photoproduct formation have been observed and product quantum yields are determined to be ∼0.91% for uracil and ∼0.41% for thymine. Compared to the measured large quenching rate constants of triplet uracil (1.5 × 10(9) M(-1)s(-1)) or thymine (0.6 × 10(9) M(-1)s(-1)) by cyclopentene, the inefficiency in formation of photoproducts indicates competitive physical quenching processes may exist on the route leading to photoproducts, resulting in very small product yields eventually. Such an energy wasting process is found to be resulted from T(1)/S(0) surface crossings by the hybrid density functional calculations, which compliments the experiments and reveals the reaction mechanism. PMID:21557584
Switching dynamics in reaction networks induced by molecular discreteness
To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however, the discreteness in the number of molecules cannot be neglected since the number of molecules must be an integer. This discreteness can be important in biochemical reactions, where the total number of molecules is not significantly larger than the number of chemical species. To elucidate the effects of such discreteness, we study autocatalytic reaction systems comprising several chemical species through stochastic particle simulations. The generation of novel states is observed; it is caused by the extinction of some molecular species due to the discreteness in their number. We demonstrate that the reaction dynamics are switched by a single molecule, which leads to the reconstruction of the acting network structure. We also show the strong dependence of the chemical concentrations on the system size, which is caused by transitions to discreteness-induced novel states
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.
Two recent developments in the theory of chemical reaction dynamics are reviewed. First, it has recently been discovered that the S- matrix version of the Kohn variational principle is free of the ''Kohn anomalies'' that have plagued other versions and prevented its general use. This has considerably simplified quantum mechanical reactive scattering calculations, which provide the rigorous characterizations of bimolecular reactions. Second, a new kind of reaction path Hamiltonian has been developed, one based on the ''least motion'' path that interpolates linearly between the reactant and product geometry of the molecule (rather than the previously used minimum energy, or ''intrinsic'' reaction path). The form of Hamiltonian which results is much simpler than the original reaction path Hamiltonian, but more important is the fact that it provides a more physically correct description of hydrogen atom transfer reactions. 44 refs., 4 figs
Use of bimolecular fluorescence complementation in yeast Saccharomyces cerevisiae.
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
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.
Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics
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.
Recycling probability and dynamical properties of germinal center reactions
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 ...
Crossed-beam studies of the dynamics of radical reactions
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.
The quantum dynamics of electronically nonadiabatic chemical reactions
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
The quantum dynamics of electronically nonadiabatic chemical reactions
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
Dynamics of GeV light-ion-induced reactions
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.)
Dynamics of GeV light-ion-induced reactions
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.
Dynamics of helix-coil transition and isotope exchange reaction
A dynamical theory is presented for the helix-coil transition and the isotope exchange reaction in a short polypeptide chain. In this theory it is assumed that there is always one and only one helical sequence. The boundaries of the helix are assumed to move randomly along the chain. If we assume slow movement of the boundaries, our model theory explains the experimental results, i.e., the very low rate of the isotope exchange in the central portion of the chain and the site dependence of the rate. (author)
Adsorption Isotherms and Surface Reaction Kinetics
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)
Reaction mechanisms in medium energy collisions: influence of dynamical fluctuations
Dynamical fluctuations in heavy ion collisions at beam energies 20 - 200 MeV are discussed. The main topics are: fragment formation from dynamical instabilities; neck fragmentation and variances; dynamics of fluctuations. A detailed study between the fragment formation time and the freeze-out time has been performed. Different theoretical models are proposed. For more peripheral collisions a novel reaction mechanism is revealed, due to the onset of new neck instabilities coupled to an increasing amount of dynamical fluctuations. Expected consequences are: possibility of intermediate mass fragment emission from the neck region and larger variances in projectile-like and target-like observables. A great variety of sources for dynamically emitted particles are predicted. Isospin effects and possibilities of producing of highly exotic nuclear systems from neck ruptures are also expected. A fully consistent treatment of fluctuation dynamics is presented, including short range (Langevin type) and long range (mean field) correlations. A stochastic transport model is constructed with the presence of the random force related to consistent density fluctuations. The Boltzmann-Nordheim-Vlasov equation for a mean phase space trajectory is modified by a correlation term with the structure of a diffusion in momentum space. Effects for collective motions and for regions of mean field instabilities are discussed. Relevant contributions from fluctuations are predicted for the production of high energy photons with a coherent mechanism. In particular a soft component in the Bremsstrahlung gamma spectrum is strongly enhanced, with important consequences on the properties of hot giant resonances that can be extracted from experiments. 5 refs
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
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
Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations
Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)
2015-12-07
In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.
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.
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...
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
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.
Dynamical calculations of nuclear fission and heavy-ion reactions
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
Dynamical Monte Carlo methods for plasma-surface reactions
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.
Femtosecond stimulated Raman spectroscopy of ultrafast biophysical reaction dynamics
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.
The power-law reaction rate coefficient for barrierless reactions
Yin, Cangtao; Du, Jiulin
2014-01-01
The power-law reaction rate coefficient for the barrierless reactions is studied if the reactions take place in systems with power-law distributions, and a generalized rate formula for the barrierless reactions in Gorin model is derived. We show that due to barrierless, different from those for bimolecular and unimolcular reactions, the power-law rate coefficient for the barrierless reactions does not have the factor of power-law distribution function and thus it is not very strongly dependen...
Chemical kinetics of gas reactions
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
Bimolecular recombination and complete photocurrent decay in metallophthalocyanine thin films
Noah, Ramsey S.
Metallophthalocyanines (MPc) are a class of planar small molecule semiconductors that are of great interest due to their applications in organic solar cells. However, a thorough understanding of many of their charge transport properties, especially those related to trap states, is lacking. In previous works the increase of grain size in MPc thin films with higher substrate temperature during the thermal evaporation process was quantified. Here, we investigate the charge transport properties of phthalocyanine with varying grain sizes in five ways: 1) intensity-varied photocurrent measurements are used to study the order of recombination in zinc phthalocyanine (ZnPc) thin films; 2) the conduction dependence on oxygen doping in copper phthalocyanine (CuPc) and ZnPc is investigated through oxygen deprivation in a closed-cycle refrigerator; 3) the complete photocurrent decay in CuPc and ZnPc is explored; 4) the bandgap of CuPc and ZnPc is derived from wide temperature range (˜ 80K - 351K) resistance measurements; 5) thermally stimulated currents (TSC) in CuPc and ZnPc are induced using a modified Reber methodology. An explanation for oxygen doping in these type of thin films is presented and in addition to bimolecular recombination a second model is also applied to measurements of intensity-varied photocurrent. Our data suggest several interesting aspects of the charge transport properties in these organic semiconductors. Recombination may not be dominated by monomolecular processes but instead bimolecular. More amorphous (low deposition temperature) samples show a greater change in conductivity due to oxygen doping. The photocurrent of more crystalline samples decays more rapidly compared to amorphous samples, suggesting that deeper trap states are present in lower deposition temperature samples. The bandgap derived from temperature-varied resistance measurements is systematically low due to slow detrapping. Unlike TSC measurements in micrometer-thick organic films
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)
Zhang, Fan; Chen, Nanhao; Wu, Ruibo
2016-05-23
The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery. PMID:27082764
Isospin dynamics on neck fragmentation in isotopic nuclear reactions
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...
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
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.
Can post-error dynamics explain sequential reaction time patterns?
StephanieGoldfarb
2012-07-01
Full Text Available We investigate human error dynamics in sequential two-alternative choice tasks. When subjects repeatedly discriminate between two stimuli, their error rates and mean reaction times (RTs systematically depend on prior sequences of stimuli. We analyze these sequential effects on RTs, separating error and correct responses, and identify a sequential RT tradeoff: a sequence of stimuli which yields a relatively fast RT on error trials will produce a relatively slow RT on correct trials and vice versa. We reanalyze previous data and acquire and analyze new data in a choice task with stimulus sequences generated by a first-order Markov process having unequal probabilities of repetitions and alternations. We then show that relationships among these stimulus sequences and the corresponding RTs for correct trials, error trials, and averaged over all trials are significantly influenced by the probability of alternations; these relationships have not been captured by previous models. Finally, we show that simple, sequential updates to the initial condition and thresholds of a pure drift diffusion model can account for the trends in RT for correct and error trials. Our results suggest that error-based parameter adjustments are critical to modeling sequential effects.
Molecular Dynamics Simulations of Chemical Reactions for Use in Education
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…
Benet, L.; Chadderton, L. T.; Kun, S. Yu.; Qi, Wang
2006-01-01
We study coherent superpositions of clockwise and anti-clockwise rotating intermediate complexes with overlapping resonances formed in bimolecular chemical reactions. Disintegration of such complexes represents an analog of famous double-slit experiment. The time for disappearance of the interference fringes is estimated from heuristic arguments related to fingerprints of chaotic dynamics of a classical counterpart of the coherently rotating complex. Validity of this estimate is confirmed num...
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.
Dynamical resonance in F+H2 chemical reaction and rotational excitation effect
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.
Langevin dynamics of A+A reactions in one dimension
We propose a set of Langevin equations of motion together with a reaction rule for the study of binary reactions. Our scheme is designed to address this problem for arbitrary friction γ and temperature T. It easily accommodates the inclusion of a substrate potential, and it lends itself to straightforward numerical integration. We test this approach on diffusion-limited (γ → ∞) as well as ballistic (γ = 0) A+A → P reactions for which there are extensive exact and approximate theoretical results as well as extensive Monte Carlo results. We reproduce the known results using our integration scheme, and also present new results for the ballistic reactions
Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach
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
Dynamic order reduction of thin-film deposition kinetics models: A reaction factorization approach
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.
Direct Dynamics Study on CH2O + CH·3 → CHO + CH4 Reaction
无
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.
An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction
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.
Fission as a probe to understand heavy ion reaction mechanism and dynamics
The study of nucleus-nucleus collisions provides a way to learn about the nuclear equilibration process in several collective degrees of freedom of much physical significance and their characteristics relaxation times. The reactions resulting from nucleus-nucleus collisions at intermediate energies can be broadly classified in four types: elastic (and quasi elastic) reaction, dinucleus reactions involving deep inelastic collisions, non-compound nucleus fusion reactions like fast-fission, quasi-fission and pre-equilibrium fission and true compound nucleus reactions. Experimentally, it is not always possible to identify uniquely the reaction products as belonging to the pre or post compound nucleus phase. This often leads to apparent anomaly in the interpretation of some of the experimental results in heavy ion reaction studies. Measurements of various observables in fission-like reactions provides information about the reaction mechanism and dynamics. Fission fragment angular distributions, which depend on the spin distributions and the shape parameters of the fissioning nucleus, give information about the fusion dynamics. Pre and post scission neutron multiplicities in fusion-fission reactions are used to determine pre-scission life times. Fragment-fragment angular correlation acts as a probe for linear momentum transfer characterising the reaction mechanism. The experimental results on the different aspects of the heavy ion fission studies and the information obtained on the dynamical features of the heavy ion collisions are summarised. (author). 36 refs., 12 figs
Mass Action Dynamics of Coupled Reactions using Fluctuation Theory
Cannon, William R.; Baker, Scott E.
2015-01-01
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary state...
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...
Analysis of the nucleon-nucleus reactions by the quantum molecular dynamics
The quantum molecular dynamics + statistical decay model has been applied to analyze the nucleon-induced nuclear reactions in the energy range from 50 to 3 GeV in order to verify its applicability to light-ion induced nuclear reactions. It was found that the present approach could give a quantitative description of various cross sections such as (p,p'), (p,n), (n,p) reactions from a wide range of targets and also target-like isotope production cross sections from p+Fe reaction, showing its basic ability as a tool for the study of intermediate energy nuclear reactions and nuclear data evaluation. (author)
Dynamics of ion–molecule reactions from beam experiments: A historical survey
Herman, Zdeněk; Futrell, J. H.
2015-01-01
Roč. 377, FEB 2015 (2015), s. 84-92. ISSN 1387-3806 Institutional support: RVO:61388955 Keywords : Ion–molecule reactions * Dynamics * Beam scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.972, year: 2014
HYTAR : a Hybrid Telescope Array for Reaction dynamics
HYTAR is an array of Hybrid detector telescopes developed at IUAC for the study of reaction mechanisms around coulomb barrier. The hybrid detector module is a combination of gas (ΔE) and silicon detector (stopping). They have been developed for heavy ion detection and particle identification in nuclear physics experiments in GPSC/NAND facility at IUAC. Currently the array has 13 such telescopes. The detector telescopes have been earlier used for studying the angular distribution of fission fragments. The detector system can also be used to identify projectile like fragments and thus can be used for studying quasi-elastic scattering, transfer and breakup reactions
Isotope yield ratios as a probe of the reaction dynamics
Isotopically resolved yields of particles and complex fragments from 12C and 18O induced reactions on 53Ni, 54Ni, Ag, and 197Au in the intermediate range of bombarding energies 30 MeV ≤ E/A ≤ 84 MeV were measured. The systematic variation of the deduced isotope yield ratios with projectile and target is used to determine the degree of N/Z equilibration achieved and to establish time scales for the reaction process. A quantum statistical model is employed in order to derive entropies of the emitting systems from the measured isotope yield ratios. (orig.)
Theoretical studies of the dynamics of chemical reactions
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.
Static and dynamic fusion barriers in heavy-ion reactions
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.)
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.
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)
Resonances and reactions from mean-field dynamics
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.
Reaction dynamics for fusion of weakly-bound nuclei
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...
Space station structural dynamics/reaction control system interaction study
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.
On the Compensation of Dynamic Reaction Forces in Stationary Machinery
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 ...
Ultrafast reaction dynamics and vibrational spectroscopy at surfaces
Hess, Christian
2001-01-01
A mechanistic understanding of the surface femtochemistry leading to the formation of hydrogen and the desorption and oxidation of CO from a Ru(001) single crystal surface is obtained by application of a variety of experimental methods. Among these are measurements of the translational energy distributions, two-pulse-correlations, isotope effects, and vibrational spectra of the reaction products after excitation with near-infrared (800 nm) femtosecond laser pulses. It is demonstrated t...
Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.
Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E
2016-05-10
Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks. PMID:26990904
Low-energy heavy-ion reactions: a link between nuclear structure and reaction dynamics
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.
Global dynamics of a reaction-diffusion system
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.
Structural parameter identifiability analysis for dynamic reaction networks
Davidescu, Florin Paul; Jørgensen, Sten Bay
2008-01-01
A fundamental problem in model identification is to investigate whether unknown parameters in a given model structure potentially can be uniquely recovered from experimental data. This issue of global or structural identifiability is essential during nonlinear first principles model development...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models. The...
Reaction dynamics of molecular hydrogen on silicon surfaces
Bratu, P.; Brenig, W.; Gross, A.; Hartmann, M.; Höfer, U.; Kratzer, Peter; Russ, R.
1996-01-01
Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective...... five-dimensional model is presented taking lattice distortion, corrugation, and molecular vibrations into account within the framework of coupled-channel calculations. While the temperature dependence of the sticking is dominated by lattice distortion, the main effect of corrugation is a reduction of...
Competitive Pressure: Competitive Dynamics as Reactions to Multiple Rivals
Zucchini, Leon; Kretschmer, Tobias
2011-01-01
Competitive dynamics research has focused primarily on interactions between dyads of firms. Drawing on the awareness-motivation-capability framework and strategic group theory we extend this by proposing that firms? actions are influenced by perceived competitive pressure resulting from actions by several rivals. We predict that firms? action magnitude is influenced by the total number of rival actions accumulating in the market, and that this effect is moderated by strategic group membership...
Electron-Wavepacket Reaction Dynamics in Proton Transfer of Formamide
Nagashima, Kengo; Takatsuka, Kazuo
2009-10-01
We apply the semiclassical Ehrenfest theory, which provides electron wavepacket dynamics coupled to nuclear motion, to a study of water-assisted proton relay in formamide compared with a forced proton transfer in gas phase, both of which are associated with the tautomerization. We start with the enol (imidic acid) form HO-CH═NH and track its proton transfer process to the keto (amide) form O═CH-NH2. Identifying the fact that this is indeed a "proton transfer process" rather than hydrogen-atom migration in terms of radical character on the proton, we show a collective quantum flux of electrons, which flows backward against the proton motion. This backward flux compensates the electrons tightly covering the proton, as represented in the Mulliken charge. The enol form formamide is one of the simplest species in the group O═CR1-NHR2, which is a unit of polypeptide. In the gas phase, the nitrogen atom may have a pyramidal structure as in the ammonium molecule; therefore, the C-N bond may allow low barrier rotation along it. This rotation is strongly prohibited by the formation of the double bond C═N induced by the proton transfer. Not only the dynamical process of proton transfer itself but also the electronic structures left behind are greatly affected by the presence of water molecule(s) and polar solvents. In discussing the relative stability of the formamide after the proton transfer, the following resonance structures are frequently mentioned, O--CH═N+H2 ↔ O═CH-NH2. Here we address the dynamical manifestation of the resonance structures in terms of our dynamical electron theory.
Reduction of dynamical biochemical reactions networks in computational biology
Radulescu, O.; Gorban, A.N.; Zinovyev, A.; Noel, V.
2012-01-01
Biochemical networks are used in computational biology, to model mechanistic details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as combinatorial explosion are strong obstacles against analyzing the dynamics of large models of this type. Multiscaleness, an important property of these networks, can be used to get past some of these obstacles. Networks with many well separated time scales, can be reduced to...
Optimal Sampling of a Reaction Coordinate in Molecular Dynamics
Pohorille, Andrew
2005-01-01
Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.
Dynamics of fluctuations in a reactive system of low spatial dimension
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.
Quasi-elastic reactions: an interplay of reaction dynamics and nuclear structure
Recchia F.
2011-10-01
Full Text Available Multinucleon transfer reactions have been investigated in 40Ar+208Pb with the Prisma+Clara set-up. The experimental differential cross sections of different neutron transfer channels have been obtained at three different angular settings taking into account the transmission through the spectrometer. The experimental yields of the excited states have been determined via particle-γ coincidences. In odd Ar isotopes, we reported a signif cant population of 11/2− states, reached via neutron transfer. Their structure matches a stretched conf guration of the valence neutron coupled to vibration quanta.
The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak
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.
The Dynamic Mutation Characteristics of Thermonuclear Reaction in Tokamak
Li, Jing; Quan, Tingting; Zhang, Wei; Deng, Wei
2014-01-01
The stability and bifurcations of multiple limit cycles for the physical model of thermonuclear reaction in Tokamak are investigated in this paper. The one-dimensional Ginzburg-Landau type perturbed diffusion equations for the density of the plasma and the radial electric field near the plasma edge in Tokamak are established. First, the equations are transformed to the average equations with the method of multiple scales and the average equations turn to be a Z2-symmetric perturbed polynomial Hamiltonian system of degree 5. Then, with the bifurcations theory and method of detection function, the qualitative behavior of the unperturbed system and the number of the limit cycles of the perturbed system for certain groups of parameter are analyzed. At last, the stability of the limit cycles is studied and the physical meaning of Tokamak equations under these parameter groups is given. PMID:24892099
Three-dimensional wave packet dynamics of H2 + D2 reaction
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.
A general expression for bimolecular association rates with orientational constraints
Schlosshauer, M; Schlosshauer, Maximilian; Baker, David
2002-01-01
We present a general expression for the association rate for partially diffusion-controlled reactions between spherical molecules with an asymmetric reactive patch on each surface. Reaction can occur only if the two patches are in contact and properly aligned to within specified angular tolerances. This extends and generalizes previous approaches that considered only axially symmetric patches; the earlier solutions are shown to be limiting cases of our general expression. Previous numerical results on the rate of protein-protein association with high steric specificity are in very good agreement with the value computed from our analytic expression. Using the new expression, we investigate the influence of orientational constraints on the rate constant. We find that for angular constraints of ~5-15 degrees, a typical range for example in the case of protein-protein interactions, the reaction rate is about 2 to 3 orders of magnitude higher than expected from a simple geometric model.
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.
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.
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
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.
Pico-second laser spectroscopy and reaction dynamics in liquids
The dynamic relaxation of excited singlet states of molecules and ions in liquid solution is investigated using picosecond laser spectroscopy. The more efficient process for the deactivation of the first excited singlet state of pinacyanol is internal conversion S1 → S0 between iso-energetic states. At low viscosity, the rate constant is inversely proportional to the macroscopic viscosity and depends on the relaxation of the angle between the quinoline end groups around the polymethinic chain. Electron photodetachment by 265 nm excitation of the ferrocyanide and phenolate anions and photoionisation of neutral molecules, phenol, indole and tryptophan in polar solvents give rise to the solvated electron formation. The mono-or bi-photonic nature of the ejection process and the solvent relaxation around the excess electron are analyzed. (author)
Spectroscopy and reaction dynamics of collision complexes containing hydroxyl radicals
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.
Benjamin, Ilan; Pohorille, Andrew
1993-01-01
The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.
Plyasunov, S
2005-01-01
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and elimination of degrees of freedom via the renormalization of transition rates of slow reactions. The method suggested in this work is more general than other approaches presented previously: it is not limited to a particular type of stochastic processes and can be applied to different types of processes describing fast dynamics, and also provides crossover to the case when separation of time scales is not well pronounced. We derive a family of exact fluctuation-dissipation relations which establish the connection between effective rates and the statistics of the reaction events in fast reaction channels. An illustration of the technique is provided. Examples show that renormalized transition rates exhibit in general non-exponential relaxation behavior with a broad range of pos...
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
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.
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
Structural dynamics effects on the ultrafast chemical bond cleavage of a photodissociation reaction
Corrales, Maria E.; Loriot, Vincent; Balerdi, Garikoitz; González-Vázquez, Jesús; de Nalda, Rebeca; Bañares, Luis; Zewail, Ahmed H.
2014-01-01
The correlation between chemical structure and dynamics has been explored in a series of molecules with increasing structural complexity in order to investigate its influence on bond cleavage reaction times in a photodissociation event. Femtosecond time-resolved velocity map imaging spectroscopy reveals specificity of the ultrafast carbon–iodine (C–I) bond breakage for a series of linear (unbranched) and branched alkyl iodides, due to the interplay between the pure reaction coordinate and the...
Dynamical Coupled-Channel Model of Meson Production Reactions in the Nucleon Resonance Region
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.
Study of reaction dynamics in 16O+115In system using recoil range distribution
The study of reaction dynamics of heavy ion (HI) induced reactions has been a topic of interest at incident energies from Coulomb barrier to 7 MeV/ nucleon. The Incomplete Fusion (ICF) reactions had been observed for the first time by H.C. Britt and A.R. Quinton at 10.5 MeV/nucleon energy. But recent studies show that the ICF competes with Complete Fusion (CF) even at energies just above the Coulomb barrier. It has been observed that ICF reaction dynamics depends on various entrance channel effects such as projectile energy, mass asymmetry of interacting ions and input angular momentum. To study the comparison between CF and ICF, Forward Recoil Range Distribution (FRRD) is used as a probe. Moreover, CF and ICF products can be disentangled on the basis of recoil velocity of reaction products, depending upon the degree of linear momentum transfer. Hence, the present work is carried out to study the interplay between CF and ICF reaction dynamics, using recoil range distribution in 16O+115In system at about 102 MeV energy
End-to-surface reaction dynamics of a single surface-attached DNA or polypeptide.
Cheng, Ryan R; Makarov, Dmitrii E
2010-03-11
The dynamics of surface-attached polymers play a key role in the operation of a number of biological sensors, yet its current understanding is rather limited. Here we use computer simulations to study the dynamics of a reaction between the free end of a polymer chain and a surface, to which its other end has been attached. We consider two limiting cases, the diffusion-controlled limit, where the reaction is accomplished whenever the free chain end diffuses to within a specified distance from the surface, and the reaction-controlled limit, where slow, intrinsic reaction kinetics rather than diffusion of the chain is rate limiting. In the diffusion-controlled limit, we find that the overall rate scales as N(-b), where N is the number of monomers in the chain and b approximately = 2.2 for excluded volume chains. This value of the scaling exponent b is close to that derived from a simple approximate theory treating the dynamics of the chain end relative to the surface as one-dimensional diffusion in an effective potential. In the reaction-controlled limit, the value of the scaling exponent b is close to 1. We compare our findings with those for the related (and better studied) problem of end-to-end reactions within an unconstrained polymer chain and discuss their implications for electrochemical DNA sensors. PMID:20151703
Yamakov, V.; Wolf, D.; Phillpot, S. R.; Gleiter, H.; Materials Science Division; Forschungszentrum Karlsruhe
2003-08-15
We use massively parallel molecular dynamics simulations of polycrystal plasticity to elucidate the intricate dislocation dynamics that evolves during the process of deformation of columnar nanocrystalline Al microstructures of grain size between 30 and 100 nm. We analyze in detail the mechanisms of dislocation-dislocation and dislocation-twin boundary reactions that take place under sufficiently high stress. These reactions are shown to lead to the formation of complex twin networks, i.e. structures of coherent twin boundaries connected by stair-rod dislocations. Consistent with recent experimental observations, these twin networks may cause dislocation pile-ups and thus give rise to strain hardening.
Modification of an amplification reaction in recursively dynamic compartments driven by stirring.
Ichii, Tetsuo; Tanahashi, Genya; Suzuki, Hiroaki; Yomo, Tetsuya
2013-12-17
In living systems, biochemical reactions are confined to cellular or subcellular compartments, such as the plasma membrane and the organelles within a cell. These biological compartments are usually subjected to recursive changes, such as combinations of growth, fusion, and division, to constitute repeating cell cycles. In such recursively dynamic compartments, the encapsulated biochemical reaction may exhibit dynamics that differ from those of the static compartment (i.e., test tubes) used in conventional biochemistry experiments. To test this hypothesis in a simplified model, we mechanically stirred femtoliter-sized water-in-oil emulsion droplets so that individual droplets were subjected to repeated coalescence and breakage. We show that recursive dynamics appeared in the emulsion, which were measured by the exponential propagation of a water-soluble dye. The rate of the propagation, μ, was controlled by modulating the pulse-width of stirring in an electromagnetic stirrer. Within this system, we studied the dynamics of an RNA-amplification reaction in recursively increasing reaction compartments at various values of μ. We showed that there was an optimal value of μ that maximized RNA amplification. This effect was explained by the balance between the opposing effects of supply of substrate and the dilution of amplified RNA both resulting from coalescence. Moreover, when we mixed two RNA species with different kinetic properties, we found a preferential amplification for one of the species only in the recursively dynamic emulsion. This effect was partly explained by a separation effect which preferentially amplifies the number of compartments for the molecular specie that can better follow the breakage dynamics of the compartments. The present work demonstrated how the recursive dynamics of compartments modifies the internal biochemical reaction. PMID:24219119
Molecular dynamic simulation of thermite reaction of Al nanosphere/Fe2O3 nanotube
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.
Proceedings of the Workshop on open problems in heavy ion reaction dynamics at VIVITRON energies
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.)
Denzler, Daniel N.
2003-01-01
The goal of this work is to acquire detailed insight into the fundamental interaction mechanisms in surface chemistry and physics. Therefore the dynamic and static-structural properties of two prototypical adsorbate systems have been investigated: The ultrafast reaction dynamics of hydrogen on the Ru(001)-surface, and the interfacial structure of water on Ru(001). The investigation of the recombinative hydrogen formation according to Had+Had -> H2,gas was performed by irradiation...
Ramsey, S. A.; Hu, B. L.
1997-01-01
We present a detailed and systematic analysis of the nonperturbative, nonequilibrium dynamics of a quantum field in the reheating phase of inflatonary cosmology, including full back reactions of the quantum field on the curved spacetime, as well as the fluctuations on the mean field. We use the O(N) field theory with unbroken symmetry in a spatially flat FRW universe to study the dynamics of the inflaton in the post-inflaton, preheating stage. Oscillations of the inflaton's zero mode induce p...
Bimolecular fluorescence complementation analysis of eukaryotic fusion products
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 ...
The time-resolved electron spin echo (ESE) method has been employed to measure the bimolecular contribution to electron spin relaxation in the acetate radical xCH2CO-2, formed by pulse radiolysis. Time-resolved ESE signals from solutions containing up to 4 x 10-4 M initial radical concentrations were analyzed using Bloch equations modified to include the effects of strong Heisenberg exchange, chemical reaction, and CIDEP. It is found that the electron exchange rate is approx.3 times faster than the chemical reaction rate, contrary to a simple model involving only statistical factors which predicts equal rates for the two processes. It is also found that the CIDEP enhancement factor is independent of initial radical concentration over the ten fold range of concentrations studied
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.
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)
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...
Herman, Zdeněk
2015-01-01
Roč. 378, FEB 2015 (2015), s. 113-126. ISSN 1387-3806 Institutional support: RVO:61388955 Keywords : Multiply-charged ions * Dynamics of chemical reactions * Beam scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.972, year: 2014
Dynamics of the Spiral Tip in a Closed Belousov-Zhabotinsky Reaction
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.
Fusion and quasi-fission dynamics in nearly-symmetric reactions
Wang, Ning; Zhao, Kai; Li, ZhuXia
2015-11-01
Some nearly-symmetric fusion reactions are systematically investigated with the improved quantum molecular dynamics (ImQMD) model. By introducing two-body inelastic scattering in the Fermi constraint procedure, the stability of an individual nucleus and the description of fusion cross sections at energies near the Coulomb barrier can be further improved. Simultaneously, the quasifission process in 154Sm+160Gd is also investigated with the microscopic dynamics model for the first time. We find that at energies above the Bass barrier, the fusion probability is smaller than 10-5 for this reaction, and the nuclear contact time is generally smaller than 1500 fm/ c. From the central collisions of Sm+Gd, the neutron-rich fragments such as 164,165Gd, 192W can be produced in the ImQMD simulations, which implies that the quasi-fission reaction could be an alternative way to synthesize new neutron-rich heavy nuclei.
Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field
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.
Fusion and quasi-fission dynamics in nearly-symmetric reactions
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.
Dynamical Dipole mode in heavy-ion fusion reactions by using stable and radioactive beams
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)
Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki
2016-05-01
The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.
We study coherent superpositions of clockwise and anticlockwise rotating intermediate complexes with overlapping resonances formed in bimolecular chemical reactions. Disintegration of such complexes represents an analog of a famous double-slit experiment. The time for disappearance of the interference fringes is estimated from heuristic arguments related to fingerprints of chaotic dynamics of a classical counterpart of the coherently rotating complex. Validity of this estimate is confirmed numerically for the H+D2 chemical reaction. Thus we demonstrate the quantum-classical transition in temporal behavior of highly excited quantum many-body systems in the absence of external noise and coupling to an environment
Chiral Dynamics and Dubna-Mainz-Taipei Dynamical Model for Pion-Photoproduction Reaction
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.
A Convergent Reaction-Diffusion Master Equation
Isaacson, Samuel A
2012-01-01
The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME has been shown to have the drawback of losing bimolecular reactions in the continuum limit that the lattice spacing approaches zero (in two or more dimensions). In this work we derive a new convergent RDME (CRDME) that eliminates this problem. The CRDME is obtained by finite volume discretization of a spatially-continuous stochastic reaction-diffusion model. We demonstrate the empirical numerical convergence of reaction time statistics associated with the CRDME. Although the reaction time statistics of the RDME diverge as the lattice spacing approaches zero, we show they approach those of the CRDME for sufficiently large lattice spacings or slow bimolecular reaction rates. As such, the RDME may be interpreted as an approximation to the CRDME in several asymptotic limits.
On the study of nonlinear dynamics of complex chemical reaction systems
XIN; Houwen; HOU; Zhonghuai
2006-01-01
With ever-increasing attentions being paid to complex systems such as the life system, soft matter, and nano-systems, theoretical studies of non-equilibrium nonlinear problems involved in chemical dynamics are now of general interest. In this mini-review, we mainly give a brief introduction to some frontier topics in this field, namely, nonlinear state-state dynamics, nonlinear chemical dynamics on complex networks, and nonlinear dynamics in mesoscopic chemical reaction systems. Deep study of these topics will make great contribution to discovering new laws of chemical dynamics, to exploring new control methods of complex chemical processes, to figuring out the very roles of chemical processes in the life system, and to crosslinking the scientific study of chemistry, physics and biology.
Molecular dynamics study of phase separation in fluids with chemical reactions
Krishnan, Raishma; Puri, Sanjay
2015-11-01
We present results from the first d =3 molecular dynamics (MD) study of phase-separating fluid mixtures (AB) with simple chemical reactions (A ⇌B ). We focus on the case where the rates of forward and backward reactions are equal. The chemical reactions compete with segregation, and the coarsening system settles into a steady-state mesoscale morphology. However, hydrodynamic effects destroy the lamellar morphology which characterizes the diffusive case. This has important consequences for the phase-separating structure, which we study in detail. In particular, the equilibrium length scale (ℓeq) in the steady state suggests a power-law dependence on the reaction rate ɛ :ℓeq˜ɛ-θ with θ ≃1.0 .
Molecular dynamics simulations of the reaction mechanism in Ni/Al reactive intermetallics
We present an atomistic level description of the reaction mechanisms in thermally ignited samples of reactive core/shell Ni/Al wires. The combination of very long simulation times (up to 0.1 μs) and very reactive core/shell nanostructures enables ignition at unprecedentedly low temperatures for molecular dynamics simulations. Samples ignited at low temperatures (900 K or less) follow a multi-stage reaction process involving solid-phase diffusion and the formation of the B2 NiAl phase, while samples ignited at higher temperatures, follow a direct reaction path with accelerated diffusion of Ni into molten Al, leading to a completely molten final state. Interestingly, NiAl nucleates and grows under a significant concentration gradient, which may explain the absence of other phases like AlNi3. The formation of the B2 intermetallic slows atomic diffusion and consequently the reaction rates
7Be- and 8B-reaction dynamics at Coulomb barrier energies
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.
Spin distribution as a probe to investigate the dynamical effects in fusion reactions
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.
7Be- and 8B-reaction dynamics at Coulomb barrier energies
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.
Dynamics of Surface Exchange Reactions Between Au and Pt for HER and HOR
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...
Dynamic Modelling and Identification of Precipitation Reactions in Full-Scale WWTP
Mbamba, Christian Kazadi; Tait, Stephan; Flores-Alsina, Xavier;
, this paper evaluates plant-wide modelling of precipitation reactions using a generic approach integrated within activated sludge and anaerobic models. Preliminary results of anaerobic digester sludge in batch system suggest that the model is able to simulate the dynamics of precipitation reactions. Kinetic...... rate coefficients, identified by mathematical optimization, were 4.65(±0.74) hrs- and 2.98(± 0.48) hrs- for struvite and amorphous calcium phosphate (ACP), respectively. The joint parameter confidence regions found were highly nonlinear and asymmetric, indicating that the model was more tolerant...
The research program at Rochester is devoted to an understanding of the dynamics of elementary gas phase ionic reactions by using the molecular beam methods. We seek to elucidate pathways for energy disposal in elementary reactions, with the goal of using this information to understand the topology of the potential surfaces which govern the reaction, applying the results to ionic channels in combustion systems. We have made significant accomplishments in several distinct areas of research in crossed beam studies of ion-neutral reaction dynamics in the past three years. Our research has focused on the following topics and has resulted in 15 publications and submissions to major journals, with several additional manuscripts in preparation: dynamics of gas phase proton transfer reactions, gas phase carbon and methyl cation chemistry, reactive scattering from double minimum potentials, reactions of highly vibrationally excited ions: NH3+ + D2, and electron and proton transfer reactions of anions. 9 refs
Takayoshi Kobayashi; Atsushi Yabushita; Shigehiko Hayashi; Izumi Iwakura; Yu Kaneko
2013-01-01
Chemical bond breaking and formation during chemical reactions can be observed using “transition state spectroscopy”. Comparing the measurement result of the transition state spectroscopy with the simulation result of single direct-dynamics trajectory, we have elucidated the reaction dynamics of Claisen rearrangement of allyl vinyl ether. Observed the reaction of the neat sample liquid, we have estimated the time constants of transformation from straight-chain structure to aromatic-like six-m...
Plane wave density functional molecular dynamics study of exothermic reactions of Al/CuO thermites
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.
Introduction to dynamic spin chemistry magnetic field effects on chemical and biochemical reactions
Hayashi, Hisaharu
2004-01-01
This book presents a detailed account of one of the most mysterious problems in science - whether ordinary magnetic fields can exert an appreciable influence on chemical and biochemical reactions. The first aim of the book is to introduce this research, through theoretical and dynamic spin chemistry, to graduate students and researchers, by means of detailed theoretical and experimental descriptions. The second aim is to review typical recent investigations, which will stimulate new interest and applications in the 21st century. Because dynamic spin chemistry is based on established science, i
Nonadiabatic dynamics in the CH3+HCl→CH4+Cl(2PJ) reaction
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
Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.
Raff, L. M.; Thompson, D. L.; Sims, L. B.; Porter, R. N.
1972-01-01
The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.
Nonadiabatic quantum wave packet dynamics of the H + H2 reaction including the coriolis coupling
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.
Phase-space geometry and reaction dynamics near index 2 saddles
We study the phase-space geometry associated with index 2 saddles of a potential energy surface and its influence on reaction dynamics for n degree-of-freedom (DoF) Hamiltonian systems. In recent years, similar studies have been carried out for index 1 saddles of potential energy surfaces, and the phase-space geometry associated with classical transition state theory has been elucidated. In this case, the existence of a normally hyperbolic invariant manifold (NHIM) of saddle stability type has been shown, where the NHIM serves as the 'anchor' for the construction of dividing surfaces having the no-recrossing property and minimal flux. For the index 1 saddle case, the stable and unstable manifolds of the NHIM are co-dimension 1 in the energy surface and have the structure of spherical cylinders, and thus act as the conduits for reacting trajectories in phase space. The situation for index 2 saddles is quite different, and their relevance for reaction dynamics has not previously been fully recognized. We show that NHIMs with their stable and unstable manifolds still exist, but that these manifolds by themselves lack sufficient dimension to act as barriers in the energy surface in order to constrain reactions. Rather, in the index 2 case there are different types of invariant manifolds, containing the NHIM and its stable and unstable manifolds, that act as co-dimension 1 barriers in the energy surface. These barriers divide the energy surface in the vicinity of the index 2 saddle into regions of qualitatively different trajectories exhibiting a wider variety of dynamical behavior than for the case of index 1 saddles. In particular, we can identify a class of trajectories, which we refer to as 'roaming trajectories', which are not associated with reaction along the classical minimum energy path (MEP). We illustrate the significance of our analysis of the index 2 saddle for reaction dynamics with two examples. The first involves isomerization on a potential energy
Neutron evaporation as a probe for dynamical effects in heavy ion fusion reactions
The compound nucleus 76Kr* was populated at the excitation energy of 75 MeV and angular momentum of 39 (ℎ/2π) in fusion reactions with two complementary, mass-symmetric (31P+45Sc) and mass asymmetric (12C+64Zn) entrance channels. The neutron evaporation spectra were measured and compared with the predictions of the statistical model calculations. The results for the mass-asymmetric reaction are found to be consistent with the predictions of the statistical model calculations. However, for the mass-symmetric reaction (31P+45Sc), the experimental spectra are found to be harder than the theoretical neutron spectra. The dynamical model calculations of Feldmeier show that the formation time for the compound nucleus for the symmetric system is relatively larger as compared to the asymmetric system
Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions
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.
Pion-photon reactions and chiral dynamics in Primakoff processes at COMPASS
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.
Back reaction effects on the dynamics of heavy probes in heavy quark cloud
Chakrabortty, Shankhadeep
2016-01-01
We holographically study the effect of back reaction on the hydrodynamical properties of $\\mathcal{N} = 4$ strongly coupled super Yang-Mills (SYM) thermal plasma. The back reaction we consider arises from the presence of static heavy quarks uniformly distributed over $\\mathcal{N} = 4$ SYM plasma. In order to study the hydrodynamical properties, we use heavy quark as well as heavy quark-antiquark bound state as probes and compute the jet quenching parameter, screening length and binding energy. We also consider the rotational dynamics of heavy probe quark in the back-reacted plasma and analyse associated energy loss. We observe that the presence of back reaction enhances the energy-loss in the thermal plasma. Finally, we show that there is no effect of angular drag on the rotational motion of quark-antiquark bound state probing the back reacted thermal plasma.
Pion-photon reactions and chiral dynamics in Primakoff processes at COMPASS
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
Theoretical and Experimental Study of Proton Transfer Reaction Dynamics in Pyrrole 2-Caboxyldehyde
Chowdhury, Papia; Pathak, Anirban
2009-01-01
Photophysical and photochemical dynamics of ground state and excited state proton transfer reaction is reported for Pyrrole 2-Caboxyldehyde (PCL). Steady state absorption and emission measurements are conducted in this five member heterocyclic system (PCL). The theoretical investigation is done by using different quantum mechanical methods (e.g. Hartree Fock, DFT, MP2, CCSD etc.). The reaction pathway and two dimensional potential energy surfaces are computed in various level of theory. A transition state is also reported in gas phase and reaction filed calculation. It is established that PCL forms different emitting species in different media. A large Stokes shifted emission band, which is attributed to species undergoing excited state intramolecular proton transfer, is observed in hydrocarbon solvent. Intermolecular proton transfer is observed in hydroxylic polar solvent. Experimental observations yield all possible signatures of intramolecular and intermolecular proton transfer in excited state of PCL. The...
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 $\\theta$.
Chemical Reaction Rates from Ring Polymer Molecular Dynamics: Theory and Practical Applications
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.
Microscopic dynamics simulations of heavy-ion fusion reactions induced by neutron-rich nuclei
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 ...
Heavy ion collision dynamics of 10,11B+10,11B reactions
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.
Hu, Lin; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu [Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003-9303 (United States); Hammond, Karl D. [Department of Chemical Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Wirth, Brian D. [Department of Nuclear Engineering, University of Tennessee, Knoxville, Tennessee 37996 (United States)
2015-10-28
We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (He{sub n}, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He{sub 4} and He{sub 5} clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.
Theory of the reaction dynamics of small molecules on metal surfaces
Jackson, Bret
2016-09-09
The objective of this project has been to develop realistic theoretical models for gas-surface interactions, with a focus on processes important in heterogeneous catalysis. The dissociative chemisorption of a molecule on a metal is a key step in many catalyzed reactions, and is often the rate-limiting step. We have explored the dissociative chemisorption of H2, H2O and CH4 on a variety of metal surfaces. Most recently, our extensive studies of methane dissociation on Ni and Pt surfaces have fully elucidated its dependence on translational energy, vibrational state and surface temperature, providing the first accurate comparisons with experimental data. We have explored Eley-Rideal and hot atom reactions of H atoms with H- and C- covered metal surfaces. H atom interactions with graphite have also been explored, including both sticking and Eley-Rideal recombination processes. Again, our methods made it possible to explain several experiments studying these reactions. The sticking of atoms on metal surfaces has also been studied. To help elucidate the experiments that study these processes, we examine how the reaction dynamics depend upon the nature of the molecule-metal interaction, as well as experimental variables such as substrate temperature, beam energy, angle of impact, and the internal states of the molecules. Electronic structure methods based on Density Functional Theory are used to compute each molecule-metal potential energy surface. Both time-dependent quantum scattering techniques and quasi-classical methods are used to examine the reaction or scattering dynamics. Much of our effort has been directed towards developing improved quantum methods that can accurately describe reactions, as well as include the effects of substrate temperature (lattice vibration).
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
Hu, Lin; Hammond, Karl D.; Wirth, Brian D.; Maroudas, Dimitrios
2015-10-01
We report the results of a systematic atomic-scale analysis of the reactions of small mobile helium clusters (Hen, 4 ≤ n ≤ 7) near low-Miller-index tungsten (W) surfaces, aiming at a fundamental understanding of the near-surface dynamics of helium-carrying species in plasma-exposed tungsten. These small mobile helium clusters are attracted to the surface and migrate to the surface by Fickian diffusion and drift due to the thermodynamic driving force for surface segregation. As the clusters migrate toward the surface, trap mutation (TM) and cluster dissociation reactions are activated at rates higher than in the bulk. TM produces W adatoms and immobile complexes of helium clusters surrounding W vacancies located within the lattice planes at a short distance from the surface. These reactions are identified and characterized in detail based on the analysis of a large number of molecular-dynamics trajectories for each such mobile cluster near W(100), W(110), and W(111) surfaces. TM is found to be the dominant cluster reaction for all cluster and surface combinations, except for the He4 and He5 clusters near W(100) where cluster partial dissociation following TM dominates. We find that there exists a critical cluster size, n = 4 near W(100) and W(111) and n = 5 near W(110), beyond which the formation of multiple W adatoms and vacancies in the TM reactions is observed. The identified cluster reactions are responsible for important structural, morphological, and compositional features in the plasma-exposed tungsten, including surface adatom populations, near-surface immobile helium-vacancy complexes, and retained helium content, which are expected to influence the amount of hydrogen re-cycling and tritium retention in fusion tokamaks.
Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.
2004-01-01
Roč. 70, č. 6 (2004), 0611031-0611034. ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant ostatní: NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004
In this study either cluster fragmentation, using a time-dependent Hartree-Fock formulation, or cluster deposition, based on classical molecular dynamics, have been studied. An exhaustive analysis has been performed on the many parameters acting on the two processes. Fragmentation calculations show a primary dependence on the input energy whereas the interatomic forces play a primary role in deposition. However the central result of this study is the essential agreement between the classical and quantum mechanical calculation
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
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
Role of Long-Range Protein Dynamics in Different Thymidylate Synthase Catalyzed Reactions
Thelma Abeysinghe
2015-04-01
Full Text Available Recent studies of Escherichia coli thymidylate synthase (ecTSase showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-monophosphate (dUMP, its altered dynamics is more pronounced on the binding of the remote cofactor, (6R-N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4folate, revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function.
Dynamical Dipole and Equation of State in N/Z Asymmetric Fusion Reactions
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.