Science.gov

Sample records for oscillating chemical reaction

  1. Oscillating Chemical Reactions

    ERIC Educational Resources Information Center

    Hawkins, M. D.; And Others

    1975-01-01

    Describes several oscillating chemical reactions which can be used in undergraduate chemistry laboratories. In one such reaction, ferroin oscillates from red (reducing solution) to blue (oxidizing solution) for about an hour at a frequency which can readily be shown to depend on such factors as the temperature, type of solvent, and concentration…

  2. Mechanism and nonlinear dynamics of an oscillating chemical reaction

    SciTech Connect

    Zhabotinsky, A.M.; Rovinsky, A.B.

    1987-09-01

    A mechanism and a model of a ferroin-catalyzed oscillating chemical system are described. This reaction presents an excellent example of a far-from-equilibrium system that forms spatial and temporal dissipative structures. The model shows that while the well-stirred system has a unique and stable stationary state, the same reagent spread in a thin layer may form complex spatiotemporal patterns. Stationary periodic patterns of both small and large amplitude, standing waves, and inhomogeneous chaotic oscillations are found in the model.

  3. Mechanism and nonlinear dynamics of an oscillating chemical reaction

    NASA Astrophysics Data System (ADS)

    Zhabotinsky, A. M.; Rovinsky, A. B.

    1987-09-01

    A mechanism and a model of a ferroin-catalyzed oscillating chemical system are descrined. This reaction presents an excellent example of a far-from-equilibrium system that forms spatial and temporal dissipative structures. The model shows that while the well-stirred system has a unique and stable stationary state, the same reagent spread in a thin layer may form complex spatiotemporal paterns. Stationary periodic patterns of both small and large amplitude, standing waves, and inhomogeneous chaotic oscillations are found in the model.

  4. Determination of caffeine using oscillating chemical reaction in a CSTR.

    PubMed

    Gao, Jinzhang; Ren, Jie; Yang, Wu; Liu, XiuHui; Yang, Hua

    2003-07-14

    A new analytical method for the determination of caffeine by the sequential perturbation caused by different amounts of caffeine on the oscillating chemical system involving the manganese(II)-catalyzed reaction between potassium bromate and tyrosine in acidic medium in a CSTR was proposed. The method exposed for the first time in this work. It relies on the relationship between the changes in the oscillation amplitude of the chemical system and the concentration of caffeine. The calibration curve fits a second-order polynomial equation very well when the concentration of caffeine over the range 4.0 x 10(-6) - 1.2 x 10(-4) M (r = 0.9968). The effect of influential variables, such as the concentration of reaction components, injection point, temperature, flow rate and stirring rate were studied. Some aspects of the potential mechanism of action of caffeine on the chemical oscillating system were also discussed. A real sample was determined and the result was satisfactory.

  5. Oscillating Reactions: Two Analogies

    ERIC Educational Resources Information Center

    Petruševski, Vladimir M.; Stojanovska, Marina I.; Šoptrajanov, Bojan T.

    2007-01-01

    Oscillating chemical reactions are truly spectacular phenomena, and demonstrations are always appreciated by the class. However, explaining such reactions to high school or first-year university students is problematic, because it may seem that no acceptable explanation is possible unless the students have profound knowledge of both physical…

  6. The effect of oxygen on time-dependent bifurcations in the Belousov-Zhabotinsky oscillating chemical reaction in a batch.

    PubMed

    Kalishyn, Yevhen Yu; Rachwalska, Małgorzata; Khavrus, Vyacheslav O; Strizhak, Peter E

    2005-04-21

    We have studied the effect of oxygen on the time-dependent bifurcations of transient oscillations in the Belousov-Zhabotinsky oscillating chemical reaction in a closed system. Experiments show that oscillations disappear through different bifurcations depending on the oxygen concentration in gas phase above the reaction solution. Oscillations disappear through the time-delayed Hopf bifurcation at low oxygen concentrations, whereas at high oxygen concentrations they disappear through the time-dependent SNIPER (saddle-node infinite period) bifurcation. We propose a kinetic scheme that describes the effects observed in experiments. Good agreement between the experimental data and simulations is obtained.

  7. Chemical oscillations and waves in the catalyzed bromate-pyrocatechol reaction.

    PubMed

    Harati, Mohammad; Wang, Jichang

    2008-05-08

    Long time series of temporal oscillations and wave formation are observed in the catalyzed bromate-pyrocatechol reaction conducted in a batch reactor, in which the induction time is insensitive to the presence of ferroin but is greatly shortened by Ce(III) or Mn(II). On the other hand, the number of oscillations is significantly increased by ferroin, while it is less sensitive to Ce(III) and Mn(II). The ferroin-catalyzed system also exhibits strong photosensitivity, in which illumination could quench the oscillatory behavior. A phase diagram illustrates that the oscillatory behavior of the studied system is more sensitive to the ratio of [pyrocatechol]/[bromate] than their absolute concentrations. Reactions conducted in a spatially extended medium show that the ferroin-catalyzed system supports a two-stage pattern formation with the wave activity surviving for up to 10 h.

  8. Effect of gravity field on the nonequilibrium/nonlinear chemical oscillation reactions.

    PubMed

    Fujieda, S; Mori, Y; Nakazawa, A; Mogami, Y

    2001-01-01

    Biological systems have evolved for a long time under the normal gravity. The Belousov-Zhabotinsky (BZ) reaction is a nonlinear chemical system far from the equilibrium that may be considered as a simplified chemical model of the biological systems so as to study the effect of gravity. The reaction solution is comprised of bromate in sulfuric acid as an oxidizing agent, 1,4-cyclohexanedione as an organic substrate, and ferroin as a metal catalyst. Chemical waves in the BZ reaction-diffusion system are visualized as blue and red patterns of ferriin and ferroin, respectively. After an improvement to the tubular reaction vessels in the experimental setup, the traveling velocity of chemical waves in aqueous solutions was measured in time series under normal gravity, microgravity, hyper-gravity, and normal gravity using the free-fall facility of JAMIC (Japan Microgravity Center), Hokkaido, Japan. Chemical patterns were collected as image data via CCD camera and analyzed by the software of NIH image after digitization. The estimated traveling velocity increased with increasing gravity as expected. It was clear experimentally that the traveling velocity of target patterns in reaction diffusion system was influenced by the effect of convection and correlated closely with the gravity field. c2001 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

  9. Effect of gravity field on the nonequilibrium/nonlinear chemical oscillation reactions

    NASA Astrophysics Data System (ADS)

    Fujieda, S.; Mori, Y.; Nakazawa, A.; Mogami, Y.

    2001-01-01

    Biological systems have evolved for a long time under the normal gravity. The Belousov-Zhabotinsky (BZ) reaction is a nonlinear chemical system far from the equilibrium that may be considered as a simplified chemical model of the biological systems so as to study the effect of gravity. The reaction solution is comprised of bromate in sulfuric acid as an oxidizing agent, 1,4-cyclohexanedione as an organic substrate, and ferroin as a metal catalyst. Chemical waves in the BZ reaction-diffusion system are visualized as blue and red patterns of ferriin and ferroin, respectively. After an improvement to the tubular reaction vessels in the experimental setup, the traveling velocity of chemical waves in aqueous solutions was measured in time series under normal gravity, microgravity, hyper-gravity, and normal gravity using the free-fall facility of JAMIC (Japan Microgravity Center), Hokkaido, Japan. Chemical patterns were collected as image data via CCD camera and analyzed by the software of NIH image after digitization. The estimated traveling velocity increased with increasing gravity as expected. It was clear experimentally that the traveling velocity of target patterns in reaction diffusion system was influenced by the effect of convection and correlated closely with the gravity field.

  10. Oscillations and multiscale dynamics in a closed chemical reaction system: second law of thermodynamics and temporal complexity.

    PubMed

    Li, Yongfeng; Qian, Hong; Yi, Yingfei

    2008-10-21

    We investigate the oscillatory reaction dynamics in a closed isothermal chemical system: the reversible Lotka-Volterra model. The second law of thermodynamics dictates that the system ultimately reaches an equilibrium. Quasistationary oscillations are analyzed while the free energy of the system serves as a global Lyapunov function of the dissipative dynamics. A natural distinction between regions near and far from equilibrium in terms of the free energy can be established. The dynamics is analogous to a nonlinear mechanical system with time-dependent increasing damping. Near equilibrium, no oscillation is possible as dictated by Onsager's reciprocal symmetry relation. We observe that while the free energy decreases in the closed system's dynamics, it does not follow the steepest descending path.

  11. Influence of thallium(I) and thallium(III) on parameters of oscillating chemical reaction in a bromate-cerium(III,IV)-malonic acid-sulfuric acid system

    SciTech Connect

    Yatsimirskii, K.B.; Matyushov, D.V.; Tikhonova, L.P.

    1987-06-01

    The influence of thallium(I) and thallium(III) on the parameters of the Belousov-Zhabotinskii oscillating chemical reaction in the bromate-cerium-(III, IV)-malonic acid-sulfuric acid system was studied. As a result of the addition of thallium(I) and thallium(III), the oscillation parameters change in the same way, which cannot be explained by the complexation of these ions with the bromide only. It was found that during the oscillating reaction, thallium(I) can be oxidized by bromine-containing compounds and thallium(III) reduced by the transformation products of malonic and bromomalonic acids. A scheme of action of a thallium(III)/thallium(I) two-electron redox pair in the oscillating chemical reaction studied has been proposed.

  12. Chemical oscillator as a generalized Rayleigh oscillator

    NASA Astrophysics Data System (ADS)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2013-10-01

    We derive the conditions under which a set of arbitrary two dimensional autonomous kinetic equations can be reduced to the form of a generalized Rayleigh oscillator which admits of limit cycle solution. This is based on a linear transformation of field variables which can be found by inspection of the kinetic equations. We illustrate the scheme with the help of several chemical and bio-chemical oscillator models to show how they can be cast as a generalized Rayleigh oscillator.

  13. Effects of magnetic, radiation and chemical reaction on unsteady heat and mass transfer flow of an oscillating cylinder

    NASA Astrophysics Data System (ADS)

    Ahmed, Rubel; Rana, B. M. Jewel; Ahmmed, S. F.

    2017-06-01

    The effects of magnetic, radiation and chemical reaction parameters on the unsteady heat and mass transfer boundary layer flow past an oscillating cylinder is considered. The dimensionless momentum, energy and concentration equations are solved numerically by using explicit finite difference method with the help of a computer programming language Compaq visual FORTRAN 6.6a. The obtained results of this study have been discussed for different values of well-known parameters with different time steps. The effect of these parameters on the velocity field, temperature field and concentration field, skin-friction, Nusselt number, streamlines and isotherms has been studied and results are presented by graphically represented by the tabular form quantitatively. The stability and convergence analysis of the solution parameters that have been used in the mathematical model have been tested.

  14. Communication: Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields.

    PubMed

    Craven, Galen T; Bartsch, Thomas; Hernandez, Rigoberto

    2014-07-28

    When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product--for example, an energy barrier--becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G. T. Craven, T. Bartsch, and R. Hernandez, "Persistence of transition state structure in chemical reactions driven by fields oscillating in time," Phys. Rev. E 89, 040801(R) (2014)], and the rates calculated by simulation of ensembles of trajectories. This result opens the possibility to extract rates directly from the intrinsic stability of the transition state, even when it is time-dependent, without requiring a numerically expensive simulation of the long-time dynamics of a large ensemble of trajectories.

  15. Arrays of coupled chemical oscillators

    PubMed Central

    Forrester, Derek Michael

    2015-01-01

    Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a “worship”. Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning. PMID:26582365

  16. Arrays of coupled chemical oscillators

    NASA Astrophysics Data System (ADS)

    Forrester, Derek Michael

    2015-11-01

    Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a “worship”. Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning.

  17. Arrays of coupled chemical oscillators.

    PubMed

    Forrester, Derek Michael

    2015-11-19

    Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a "worship". Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning.

  18. MHD Convective rotating flow past an oscillating porous plate with chemical reaction and Hall effects

    NASA Astrophysics Data System (ADS)

    Veera Krishna, M.; Gangadhar Reddy, M.

    2016-09-01

    In this paper, we have considered Hall effects on the unsteady MHD free convective rotating flow of visco-elastic fluid with heat and mass transfer near oscillating porous plate. The equations of the flow are solved by perturbation method for small elastic parameter. The analytical expressions for the velocity, temperature, concentration have been derived and also its behaviour is computationally discussed with the help of graphs. The skin friction, Nusselt number, and Sherwood number are also obtained analytically and their behaviour discussed.

  19. Effect of temperature oscillation on chemical reaction rates in the atmosphere

    NASA Technical Reports Server (NTRS)

    Eberstein, I. J.

    1974-01-01

    The effect of temperature fluctuations on atmospheric ozone chemistry is examined by considering the Chapman photochemical theory of ozone transport to calculate globally averaged ozone production rates from mean reaction rates, activation energies, and recombination processes.

  20. Enhancing chemical reactions

    DOEpatents

    Morrey, John R.

    1978-01-01

    Methods of enhancing selected chemical reactions. The population of a selected high vibrational energy state of a reactant molecule is increased substantially above its population at thermal equilibrium by directing onto the molecule a beam of radiant energy from a laser having a combination of frequency and intensity selected to pump the selected energy state, and the reaction is carried out with the temperature, pressure, and concentrations of reactants maintained at a combination of values selected to optimize the reaction in preference to thermal degradation by transforming the absorbed energy into translational motion. The reaction temperature is selected to optimize the reaction. Typically a laser and a frequency doubler emit radiant energy at frequencies of .nu. and 2.nu. into an optical dye within an optical cavity capable of being tuned to a wanted frequency .delta. or a parametric oscillator comprising a non-centrosymmetric crystal having two indices of refraction, to emit radiant energy at the frequencies of .nu., 2.nu., and .delta. (and, with a parametric oscillator, also at 2.nu.-.delta.). Each unwanted frequency is filtered out, and each desired frequency is focused to the desired radiation flux within a reaction chamber and is reflected repeatedly through the chamber while reactants are fed into the chamber and reaction products are removed therefrom.

  1. Rayleigh-type parametric chemical oscillation.

    PubMed

    Ghosh, Shyamolina; Ray, Deb Shankar

    2015-09-28

    We consider a nonlinear chemical dynamical system of two phase space variables in a stable steady state. When the system is driven by a time-dependent sinusoidal forcing of a suitable scaling parameter at a frequency twice the output frequency and the strength of perturbation exceeds a threshold, the system undergoes sustained Rayleigh-type periodic oscillation, wellknown for parametric oscillation in pipe organs and distinct from the usual forced quasiperiodic oscillation of a damped nonlinear system where the system is oscillatory even in absence of any external forcing. Our theoretical analysis of the parametric chemical oscillation is corroborated by full numerical simulation of two well known models of chemical dynamics, chlorite-iodine-malonic acid and iodine-clock reactions.

  2. Rayleigh-type parametric chemical oscillation

    SciTech Connect

    Ghosh, Shyamolina; Ray, Deb Shankar

    2015-09-28

    We consider a nonlinear chemical dynamical system of two phase space variables in a stable steady state. When the system is driven by a time-dependent sinusoidal forcing of a suitable scaling parameter at a frequency twice the output frequency and the strength of perturbation exceeds a threshold, the system undergoes sustained Rayleigh-type periodic oscillation, wellknown for parametric oscillation in pipe organs and distinct from the usual forced quasiperiodic oscillation of a damped nonlinear system where the system is oscillatory even in absence of any external forcing. Our theoretical analysis of the parametric chemical oscillation is corroborated by full numerical simulation of two well known models of chemical dynamics, chlorite-iodine-malonic acid and iodine-clock reactions.

  3. Rayleigh-type parametric chemical oscillation

    NASA Astrophysics Data System (ADS)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2015-09-01

    We consider a nonlinear chemical dynamical system of two phase space variables in a stable steady state. When the system is driven by a time-dependent sinusoidal forcing of a suitable scaling parameter at a frequency twice the output frequency and the strength of perturbation exceeds a threshold, the system undergoes sustained Rayleigh-type periodic oscillation, wellknown for parametric oscillation in pipe organs and distinct from the usual forced quasiperiodic oscillation of a damped nonlinear system where the system is oscillatory even in absence of any external forcing. Our theoretical analysis of the parametric chemical oscillation is corroborated by full numerical simulation of two well known models of chemical dynamics, chlorite-iodine-malonic acid and iodine-clock reactions.

  4. Synchronization in the discrete chemical oscillation system

    NASA Astrophysics Data System (ADS)

    Miyakawa, Kenji; Okabe, Tadao; Mizoguchi, Michiko; Sakamoto, Fumitaka

    1995-12-01

    The properties of the coupling between chemical oscillators were studied in the discrete chemical oscillation system which was realized by immersing cation exchange beads loaded with ferroin in the Belousov-Zabotinskii reaction solution. A phase diagram of coupling states was obtained as a function of natural frequencies of oscillators and the distance d between oscillators. The synchronization was found not to be attributed to a simple entrainment of the slower oscillator by the faster one. Various entrainments between oscillators occurred depending on ratios of natural frequencies in the uncoupled state. A chaotic behavior was found at the boundary between stably coupled regions with frequency ratios of n/1 where n is an integer. Furthermore, effects of external perturbation on the coupling were investigated. Irregular oscillations were induced by illumination with a He-Ne laser light, which strongly depended on the phase of oscillator at the beginning of illumination. Such irregular behaviors were localized within the illuminated bead. This indicates that two oscillators are decoupled by illumination.

  5. The Strange World of Chemical Oscillations.

    ERIC Educational Resources Information Center

    MOSAIC, 1978

    1978-01-01

    Describes an oscillating chemical reaction, and discusses numerous parallels to it in research, such as in fibrillation of the heart, body-clock rhythms of animals and plants, the self-assembly of multicellular organisms, and certain stripes in volcanic rock. (GA)

  6. The Strange World of Chemical Oscillations.

    ERIC Educational Resources Information Center

    MOSAIC, 1978

    1978-01-01

    Describes an oscillating chemical reaction, and discusses numerous parallels to it in research, such as in fibrillation of the heart, body-clock rhythms of animals and plants, the self-assembly of multicellular organisms, and certain stripes in volcanic rock. (GA)

  7. Microfluidic chemical reaction circuits

    SciTech Connect

    Lee, Chung-cheng; Sui, Guodong; Elizarov, Arkadij; Kolb, Hartmuth C; Huang, Jiang; Heath, James R; Phelps, Michael E; Quake, Stephen R; Tseng, Hsian-rong; Wyatt, Paul; Daridon, Antoine

    2012-06-26

    New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

  8. Nonlinear thermal radiation and cubic autocatalysis chemical reaction effects on the flow of stretched nanofluid under rotational oscillations.

    PubMed

    Kumar, Rakesh; Sood, Shilpa; Sheikholeslami, Mohsen; Shehzad, Sabir Ali

    2017-11-01

    Combined effects of nonlinear thermal radiation and cubic autocatalysis chemical reaction on the three dimensional flow of stretched nanofluid along a rotating sheet have been investigated in this paper. The flow field is assumed to be suspended with magnetic iron oxide nanoparticles (IONPs). Hamilton-Crosser model is applied to measure effective thermal conductivity of nanofluid. Rosseland approximation is employed to obtain the nonlinear radiative heat flux. For novelty and practical point of view, influence of fluctuating surface velocity and periodic surface temperature constraints are incorporated into the governing equations which in turn are made dimension free by employing suitable transformations. For numerical solutions, an explicit finite difference scheme has been proposed under the restrictions of derived stability conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Experimental study on three chemical oscillators coupled with time delay

    NASA Astrophysics Data System (ADS)

    Nishiyama, Nobuaki; Eto, Kaori

    1994-05-01

    A new experimental system of coupled chemical oscillators is presented. Three cation-exchange beads loaded with ferroin are spatially distributed in triangular forms and immersed in the Belousov-Zabotinsky reaction mixture. The cation-exchange beads were in no contact with each other. The cation-exchange bead was used as a chemical oscillator. Spontaneous switching between two out-of-phase oscillation was observed.

  10. Nanomotor dynamics in a chemically oscillating medium

    SciTech Connect

    Robertson, Bryan Kapral, Raymond

    2015-04-21

    Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.

  11. Chemical burn or reaction

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/000059.htm Chemical burn or reaction To use the sharing features on this page, please enable JavaScript. Chemicals that touch skin can lead to a reaction on the skin, throughout the body, or both. ...

  12. Chemical Reaction Problem Solving.

    ERIC Educational Resources Information Center

    Veal, William

    1999-01-01

    Discusses the role of chemical-equation problem solving in helping students predict reaction products. Methods for helping students learn this process must be taught to students and future teachers by using pedagogical skills within the content of chemistry. Emphasizes that solving chemical reactions should involve creative cognition where…

  13. Cyanohydrin reactions enhance glycolytic oscillations in yeast.

    PubMed

    Hald, Bjørn Olav; Nielsen, Astrid Gram; Tortzen, Christian; Sørensen, Preben Graae

    2015-01-01

    Synchronous metabolic oscillations can be induced in yeast by addition of glucose and removal of extracellular acetaldehyde (ACAx). Compared to other means of ACAx removal, cyanide robustly induces oscillations, indicating additional cyanide reactions besides ACA to lactonitrile conversion. Here, (13)C NMR is used to confirm our previous hypothesis, that cyanide directly affects glycolytic fluxes through reaction with carbonyl-containing compounds. Intracellularly, at least 3 cyanohydrins were identified. Extracellularly, all signals could be identified and lactonitrile was found to account for ~66% of total cyanide removal. Simulations of our updated computational model show that intracellular cyanide reactions increase the amplitude of oscillations and that cyanide addition lowers [ACA] instantaneously. We conclude that cyanide provides the following means of inducing global oscillations: a) by reducing [ACAx] relative to oscillation amplitude, b) by targeting multiple intracellular carbonyl compounds during fermentation, and c) by acting as a phase resetting stimulus.

  14. Superconductivity in nonclassical superconductors as a periodical (oscillating) redox reaction

    SciTech Connect

    Kostikova, G.P.; Korol`kov, D.V.; Kostikov, Yu.P.

    1995-10-20

    Comparison of the properties of high-temperature superconductors with those of chemical systems where a periodical (oscillating) redox reaction is realized suggests that the high-temperature superconducting of nonclassical superconductors (in particular, ternary oxides) results from activation of a periodical redox reaction within a single compounds containing heterovalent forms of each of two dissimilar elements. In this redox reaction, reversible converison of the corresponding heterovalent forms occur. 37 refs., 1 fig., 1 tab.

  15. Translated chemical reaction networks.

    PubMed

    Johnston, Matthew D

    2014-05-01

    Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems of polynomial ordinary differential equations. The steady states of these mass action systems have been analyzed via a variety of techniques, including stoichiometric network analysis, deficiency theory, and algebraic techniques (e.g., Gröbner bases). In this paper, we present a novel method for characterizing the steady states of mass action systems. Our method explicitly links a network's capacity to permit a particular class of steady states, called toric steady states, to topological properties of a generalized network called a translated chemical reaction network. These networks share their reaction vectors with their source network but are permitted to have different complex stoichiometries and different network topologies. We apply the results to examples drawn from the biochemical literature.

  16. Synchronization Dynamics of Coupled Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Tompkins, Nathan

    The synchronization dynamics of complex networks have been extensively studied over the past few decades due to their ubiquity in the natural world. Prominent examples include cardiac rhythms, circadian rhythms, the flashing of fireflies, predator/prey population dynamics, mammalian gait, human applause, pendulum clocks, the electrical grid, and of the course the brain. Detailed experiments have been done to map the topology of many of these systems and significant advances have been made to describe the mathematics of these networks. Compared to these bodies of work relatively little has been done to directly test the role of topology in the synchronization dynamics of coupled oscillators. This Dissertation develops technology to examine the dynamics due to topology within networks of discrete oscillatory components. The oscillatory system used here consists of the photo-inhibitable Belousov-Zhabotinsky (BZ) reaction water-in-oil emulsion where the oscillatory drops are diffusively coupled to one another and the topology is defined by the geometry of the diffusive connections. Ring networks are created from a close-packed 2D array of drops using the Programmable Illumination Microscope (PIM) in order to test Turing's theory of morphogenesis directly. Further technology is developed to create custom planar networks of BZ drops in more complicated topologies which can be individually perturbed using illumination from the PIM. The work presented here establishes the validity of using the BZ emulsion system with a PIM to study the topology induced effects on the synchronization dynamics of coupled chemical oscillators, tests the successes and limitations of Turing's theory of morphogenesis, and develops new technology to further probe the effects of network topology on a system of coupled oscillators. Finally, this Dissertation concludes by describing ongoing experiments which utilize this new technology to examine topology induced transitions of synchronization

  17. Chemical sensor with oscillating cantilevered probe

    DOEpatents

    Adams, Jesse D

    2013-02-05

    The invention provides a method of detecting a chemical species with an oscillating cantilevered probe. A cantilevered beam is driven into oscillation with a drive mechanism coupled to the cantilevered beam. A free end of the oscillating cantilevered beam is tapped against a mechanical stop coupled to a base end of the cantilevered beam. An amplitude of the oscillating cantilevered beam is measured with a sense mechanism coupled to the cantilevered beam. A treated portion of the cantilevered beam is exposed to the chemical species, wherein the cantilevered beam bends when exposed to the chemical species. A second amplitude of the oscillating cantilevered beam is measured, and the chemical species is determined based on the measured amplitudes.

  18. Noise induced oscillations and coherence resonance in a generic model of the nonisothermal chemical oscillator

    PubMed Central

    Simakov, David S. A.; Pérez-Mercader, Juan

    2013-01-01

    Oscillating chemical reactions are common in biological systems and they also occur in artificial non-biological systems. Generally, these reactions are subject to random fluctuations in environmental conditions which translate into fluctuations in the values of physical variables, for example, temperature. We formulate a mathematical model for a nonisothermal minimal chemical oscillator containing a single negative feedback loop and study numerically the effects of stochastic fluctuations in temperature in the absence of any deterministic limit cycle or periodic forcing. We show that noise in temperature can induce sustained limit cycle oscillations with a relatively narrow frequency distribution and some characteristic frequency. These properties differ significantly depending on the noise correlation. Here, we have explored white and colored (correlated) noise. A plot of the characteristic frequency of the noise induced oscillations as a function of the correlation exponent shows a maximum, therefore indicating the existence of autonomous stochastic resonance, i.e. coherence resonance. PMID:23929212

  19. Chemical Reactions at Surfaces

    SciTech Connect

    Michael Henderson and Nancy Ryan Gray

    2010-04-14

    Chemical reactions at surfaces underlie some of the most important processes of today, including catalysis, energy conversion, microelectronics, human health and the environment. Understanding surface chemical reactions at a fundamental level is at the core of the field of surface science. The Gordon Research Conference on Chemical Reactions at Surfaces is one of the premiere meetings in the field. The program this year will cover a broad range of topics, including heterogeneous catalysis and surface chemistry, surfaces in environmental chemistry and energy conversion, reactions at the liquid-solid and liquid-gas interface, electronic materials growth and surface modification, biological interfaces, and electrons and photons at surfaces. An exciting program is planned, with contributions from outstanding speakers and discussion leaders from the international scientific community. The conference provides a dynamic environment with ample time for discussion and interaction. Attendees are encouraged to present posters; the poster sessions are historically well attended and stimulate additional discussions. The conference provides an excellent opportunity for junior researchers (e.g. graduate students or postdocs) to present their work and interact with established leaders in the field.

  20. Desynchronization of stochastically synchronized chemical oscillators

    SciTech Connect

    Snari, Razan; Tinsley, Mark R. E-mail: kshowalt@wvu.edu; Faramarzi, Sadegh; Showalter, Kenneth E-mail: kshowalt@wvu.edu; Wilson, Dan; Moehlis, Jeff; Netoff, Theoden Ivan

    2015-12-15

    Experimental and theoretical studies are presented on the design of perturbations that enhance desynchronization in populations of oscillators that are synchronized by periodic entrainment. A phase reduction approach is used to determine optimal perturbation timing based upon experimentally measured phase response curves. The effectiveness of the perturbation waveforms is tested experimentally in populations of periodically and stochastically synchronized chemical oscillators. The relevance of the approach to therapeutic methods for disrupting phase coherence in groups of stochastically synchronized neuronal oscillators is discussed.

  1. Chemical Reactions in Clusters

    DTIC Science & Technology

    1992-11-04

    NH 3)n, n _> 4, clusters has been attributed to the (solvated) naphtholate anion.3a A single picosecond decay measurement has been reported which...vibrational energy in the cluster Sl state. The data are summarized in Table I. A model to explain these decay results can be constructed based on a proton...11 TITLE (Include Security Classification) Chemical Reactions in Clusters 12 PERSONAL AUTHOR(S) Elliot R. Bernstein 13a TYPE OF REPORT 13b TIME COVERED

  2. High-frequency oscillations in the Belousov-Zhabotinsky reaction.

    PubMed

    Bánsági, Tamás; Leda, Marcin; Toiya, Masahiro; Zhabotinsky, Anatol M; Epstein, Irving R

    2009-05-14

    Chemical oscillations in the classic Belousov-Zhabotinsky (BZ) system typically have a period of a few minutes, which can be increased significantly by changing the organic substrate. Here we show that by changing the temperature and concentrations, an increase of 3-4 orders of magnitude in the frequency of BZ oscillations can be obtained. At elevated temperatures, in high concentration mixtures, the cerium-catalyzed reaction exhibits sinusoidal oscillations with frequencies of 10 Hz or greater. We report the effect of temperature on the frequency and shape of oscillations in experiments under batch conditions and in a four-variable model. We show that our simple model accurately captures the complex temporal behavior of the system and suggests paths toward even higher frequencies.

  3. A Lattice Boltzmann Model for Oscillating Reaction-Diffusion

    NASA Astrophysics Data System (ADS)

    Rodríguez-Romo, Suemi; Ibañez-Orozco, Oscar; Sosa-Herrera, Antonio

    2016-07-01

    A computational algorithm based on the lattice Boltzmann method (LBM) is proposed to model reaction-diffusion systems. In this paper, we focus on how nonlinear chemical oscillators like Belousov-Zhabotinsky (BZ) and the chlorite-iodide-malonic acid (CIMA) reactions can be modeled by LBM and provide with new insight into the nature and applications of oscillating reactions. We use Gaussian pulse initial concentrations of sulfuric acid in different places of a bidimensional reactor and nondiffusive boundary walls. We clearly show how these systems evolve to a chaotic attractor and produce specific pattern images that are portrayed in the reactions trajectory to the corresponding chaotic attractor and can be used in robotic control.

  4. Chemical Reactions in DSMC

    NASA Astrophysics Data System (ADS)

    Bird, G. A.

    2011-05-01

    DSMC simulations of chemically reacting gas flows have generally employed procedures that convert the macroscopic chemical rate equations to reaction cross-sections at the microscopic level. They therefore depend on the availability of experimental data that has been fitted to equations of the Arrhenius form. This paper presents a physical model for dissociation and recombination reactions and a phenomenological model for exchange and chain reactions. These are based on the vibrational states of the colliding molecules and do not require any experimentally-based data. The simplicity of the models allows the corresponding rate equations to be written down and, while these are not required for the implementation of the models, they facilitate their validation. The model is applied to a typical hypersonic atmospheric entry problem and the results are compared with the corresponding results from the traditional method. It is also used to investigate both spontaneous and forced ignition as well as the structure of a deflagration wave in an oxygen-hydrogen mixture.

  5. Chemical Reactions in DSMC

    SciTech Connect

    Bird, G. A.

    2011-05-20

    DSMC simulations of chemically reacting gas flows have generally employed procedures that convert the macroscopic chemical rate equations to reaction cross-sections at the microscopic level. They therefore depend on the availability of experimental data that has been fitted to equations of the Arrhenius form. This paper presents a physical model for dissociation and recombination reactions and a phenomenological model for exchange and chain reactions. These are based on the vibrational states of the colliding molecules and do not require any experimentally-based data. The simplicity of the models allows the corresponding rate equations to be written down and, while these are not required for the implementation of the models, they facilitate their validation. The model is applied to a typical hypersonic atmospheric entry problem and the results are compared with the corresponding results from the traditional method. It is also used to investigate both spontaneous and forced ignition as well as the structure of a deflagration wave in an oxygen-hydrogen mixture.

  6. Concordant Chemical Reaction Networks

    PubMed Central

    Shinar, Guy; Feinberg, Martin

    2015-01-01

    We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with any weakly monotonic kinetics, invariably give rise to kinetic systems that are injective — a quality that, among other things, precludes the possibility of switch-like transitions between distinct positive steady states. We also provide persistence characteristics of concordant networks, instability implications of discordance, and consequences of stronger variants of concordance. Some of our results are in the spirit of recent ones by Banaji and Craciun, but here we do not require that every species suffer a degradation reaction. This is especially important in studying biochemical networks, for which it is rare to have all species degrade. PMID:22659063

  7. Creation and perturbation of planar networks of chemical oscillators

    NASA Astrophysics Data System (ADS)

    Tompkins, Nathan; Cambria, Matthew Carl; Wang, Adam L.; Heymann, Michael; Fraden, Seth

    2015-06-01

    Methods for creating custom planar networks of diffusively coupled chemical oscillators and perturbing individual oscillators within the network are presented. The oscillators consist of the Belousov-Zhabotinsky (BZ) reaction contained in an emulsion. Networks of drops of the BZ reaction are created with either Dirichlet (constant-concentration) or Neumann (no-flux) boundary conditions in a custom planar configuration using programmable illumination for the perturbations. The differences between the observed network dynamics for each boundary condition are described. Using light, we demonstrate the ability to control the initial conditions of the network and to cause individual oscillators within the network to undergo sustained period elongation or a one-time phase delay.

  8. Creation and perturbation of planar networks of chemical oscillators

    PubMed Central

    Tompkins, Nathan; Cambria, Matthew Carl; Wang, Adam L.; Heymann, Michael; Fraden, Seth

    2015-01-01

    Methods for creating custom planar networks of diffusively coupled chemical oscillators and perturbing individual oscillators within the network are presented. The oscillators consist of the Belousov-Zhabotinsky (BZ) reaction contained in an emulsion. Networks of drops of the BZ reaction are created with either Dirichlet (constant-concentration) or Neumann (no-flux) boundary conditions in a custom planar configuration using programmable illumination for the perturbations. The differences between the observed network dynamics for each boundary condition are described. Using light, we demonstrate the ability to control the initial conditions of the network and to cause individual oscillators within the network to undergo sustained period elongation or a one-time phase delay. PMID:26117136

  9. Irregular behaviors of two chemical oscillators with a diffusion coupling

    NASA Astrophysics Data System (ADS)

    Miyakawa, Kenji; Okabe, Tadao; Sakamoto, Fumitaka

    1997-02-01

    Dynamic behaviors of two chemical oscillators coupled with a time delay were investigated at the border between regions of 1:1 and 2:1 entrainment. Chemical oscillators were realized by immersing cation exchange beads loaded with the ferroin catalyst in the Belousov-Zabotinskii reaction solution. On decreasing the distance d between two oscillators, subharmonic entrainment at commensurate frequency ratios such as 2:1, 3:2, and 4:3 occurred in that order. When d was further decreased, an irregular behavior was observed in the slower oscillator near the coupling region of 1:1. The time series for these states were characterized in terms of their power spectra, reconstructed attractors, and the largest Lyapunov exponent to confirm the feature of chaos.

  10. Mass Transfer with Chemical Reaction.

    ERIC Educational Resources Information Center

    DeCoursey, W. J.

    1987-01-01

    Describes the organization of a graduate course dealing with mass transfer, particularly as it relates to chemical reactions. Discusses the course outline, including mathematics models of mass transfer, enhancement of mass transfer rates by homogeneous chemical reaction, and gas-liquid systems with chemical reaction. (TW)

  11. Mass Transfer with Chemical Reaction.

    ERIC Educational Resources Information Center

    DeCoursey, W. J.

    1987-01-01

    Describes the organization of a graduate course dealing with mass transfer, particularly as it relates to chemical reactions. Discusses the course outline, including mathematics models of mass transfer, enhancement of mass transfer rates by homogeneous chemical reaction, and gas-liquid systems with chemical reaction. (TW)

  12. Parametric spatiotemporal oscillation in reaction-diffusion systems.

    PubMed

    Ghosh, Shyamolina; Ray, Deb Shankar

    2016-03-01

    We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

  13. Parametric spatiotemporal oscillation in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2016-03-01

    We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

  14. Chemical reactions at aqueous interfaces

    NASA Astrophysics Data System (ADS)

    Vecitis, Chad David

    2009-12-01

    ) Adsorption of dilute PFOS(aq) and PFOA(aq) to acoustically cavitating bubble interfaces was greater than equilibrium expectations due to high-velocity bubble radial oscillations; 2) Relative ozone oxidation kinetics of aqueous iodide, sulfite, and thiosulfate were at variance with previously reported bulk aqueous kinetics; 3) Organics that directly chelated with the anode surface were oxidized by direct electron transfer, resulting in immediate carbon dioxide production but slower overall oxidation kinetics. Chemical reactions at aqueous interfaces can be the rate-limiting step of a reaction network and often display novel mechanisms and kinetics as compared to homogeneous chemistry.

  15. Echo Behavior in Large Populations of Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Chen, Tianran; Tinsley, Mark R.; Ott, Edward; Showalter, Kenneth

    2016-10-01

    Experimental and theoretical studies are reported, for the first time, on the observation and characterization of echo phenomena in oscillatory chemical reactions. Populations of uncoupled and coupled oscillators are globally perturbed. The macroscopic response to this perturbation dies out with time: At some time τ after the perturbation (where τ is long enough that the response has died out), the system is again perturbed, and the initial response to this second perturbation again dies out. Echoes can potentially appear as responses that arise at 2 τ ,3 τ ,... after the first perturbation. The phase-resetting character of the chemical oscillators allows a detailed analysis, offering insights into the origin of the echo in terms of an intricate structure of phase relationships. Groups of oscillators experiencing different perturbations are analyzed with a geometric approach and in an analytical theory. The characterization of echo phenomena in populations of chemical oscillators reinforces recent theoretical studies of the behavior in populations of phase oscillators [E. Ott et al., Chaos 18, 037115 (2008)]. This indicates the generality of the behavior, including its likely occurrence in biological systems.

  16. Noise-enhanced phase locking in a chemical oscillator system

    NASA Astrophysics Data System (ADS)

    Miyakawa, Kenji; Isikawa, Hironobu

    2002-05-01

    Dynamical responses of a chemical oscillator to an external electric field were investigated in the Belousov-Zabotinsky reaction system with the catalyst Ru(bpy)2+3 [tris-(2,2'-bipyridine) ruthenium (II)] immobilized in cation exchange beads. Periodic forcing above the threshold induced phase locking, whose synchronization region has a shape similar to the Arnold tongue. When a certain amount of noise together with a subthreshold periodic signal was imposed on the chemical oscillator, 1:1 phase locking to the periodic signal occurred. Its degree passed through a maximum with increase in the noise intensity, a manifestation of stochastic resonance in the form of noise-enhanced phase locking. The experimentally observed features were reproduced in a numerical simulation with a forced Oregonator reaction-diffusion model.

  17. Grip on complexity in chemical reaction networks

    PubMed Central

    2017-01-01

    A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior. PMID:28845192

  18. Grip on complexity in chemical reaction networks.

    PubMed

    Wong, Albert S Y; Huck, Wilhelm T S

    2017-01-01

    A new discipline of "systems chemistry" is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

  19. Transition from an unstable synchronization state with transient oscillation cessations to spiral rotation in a coupled chemical oscillator system

    NASA Astrophysics Data System (ADS)

    Nishiyama, Nobuaki; Matsuyama, Tomoko

    1997-02-01

    Spatiotemporal patterns of chemical wave propagation in the assemblies of nine cation-exchange beads loaded with the catalyst ferroin of Belousov-Zhabotinsky reaction are reported. The beads are immersed in the reaction mixture, on which periodic chemical waves are emerged. In the bead assemblies, abrupt changes of initiation site and direction of the periodic chemical waves were observed. In some cases, it was observed that transient oscillation cessations and the following rotating spiral wave occur.

  20. More on Chemical Reaction Balancing.

    ERIC Educational Resources Information Center

    Swinehart, D. F.

    1985-01-01

    A previous article stated that only the matrix method was powerful enough to balance a particular chemical equation. Shows how this equation can be balanced without using the matrix method. The approach taken involves writing partial mathematical reactions and redox half-reactions, and combining them to yield the final balanced reaction. (JN)

  1. Speeding chemical reactions by focusing.

    PubMed

    Lacasta, A M; Ramírez-Piscina, L; Sancho, J M; Lindenberg, K

    2013-04-14

    We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate ∼t(-1/2) to very close to the perfect mixing rate, ∼t(-1).

  2. Speeding chemical reactions by focusing

    NASA Astrophysics Data System (ADS)

    Lacasta, A. M.; Ramírez-Piscina, L.; Sancho, J. M.; Lindenberg, K.

    2013-04-01

    We present numerical results for a chemical reaction of colloidal particles which are transported by a laminar fluid and are focused by periodic obstacles in such a way that the two components are well mixed and consequently the chemical reaction is speeded up. The roles of the various system parameters (diffusion coefficients, reaction rate, and obstacles sizes) are studied. We show that focusing speeds up the reaction from the diffusion limited rate ˜t-1/2 to very close to the perfect mixing rate, ˜t-1.

  3. Synchronization in Networks of Coupled Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Showalter, Kenneth; Tinsley, Mark; Nkomo, Simbarashe; Ke, Hua

    2014-03-01

    We have studied networks of coupled photosensitive chemical oscillators. Experiments and simulations are carried out on networks with different topologies and modes of coupling. We describe experimental and modeling studies of chimera and phase-cluster states and their relation to other synchronization states. Networks of integrate-and-fire oscillators are also studied in which sustained coordinated activity is exhibited. Individual nodes display incoherent firing events; however, a dominant frequency within the collective signal is exhibited. The introduction of spike-timing-dependent plasticity allows the network to evolve and leads to a stable unimodal link-weight distribution. M. R. Tinsley et al., Nature Physics 8, 662 (2012); S. Nkomo et al., Phys. Rev. Lett. 110, 244102 (2013); H. Ke et al., in preparation.

  4. Chemiluminescent Oscillating Demonstrations: The Chemical Buoy, the Lighting Wave, and the Ghostly Cylinder

    ERIC Educational Resources Information Center

    Prypsztejn, Hernan E.; Mulford, Douglas R.; Stratton, Doug

    2005-01-01

    Oscillating reactions have been extensively used in chemical demonstrations. They involve several chemical concepts about kinetics, catalysts, and thermodynamics. The spontaneous cyclic color change of a solution is an attraction in any educational-level course. Chemiluminescent reactions are also among the most fascinating demonstrations and have…

  5. Chemiluminescent Oscillating Demonstrations: The Chemical Buoy, the Lighting Wave, and the Ghostly Cylinder

    ERIC Educational Resources Information Center

    Prypsztejn, Hernan E.; Mulford, Douglas R.; Stratton, Doug

    2005-01-01

    Oscillating reactions have been extensively used in chemical demonstrations. They involve several chemical concepts about kinetics, catalysts, and thermodynamics. The spontaneous cyclic color change of a solution is an attraction in any educational-level course. Chemiluminescent reactions are also among the most fascinating demonstrations and have…

  6. Reduction of chemical reaction models

    NASA Technical Reports Server (NTRS)

    Frenklach, Michael

    1991-01-01

    An attempt is made to reconcile the different terminologies pertaining to reduction of chemical reaction models. The approaches considered include global modeling, response modeling, detailed reduction, chemical lumping, and statistical lumping. The advantages and drawbacks of each of these methods are pointed out.

  7. Properties of a photonic crystal formed in a solution featuring the Briggs-Rauscher oscillating reaction

    NASA Astrophysics Data System (ADS)

    Usanov, D. A.; Rytik, A. P.

    2016-06-01

    It is shown that a solution featuring the Briggs-Rauscher (BR) oscillating chemical reaction can exhibit the properties of a photonic crystal with alternating bandgap width. Thicknesses and dielectric permittivities of structural elements in the BR reaction solution have been determined by measuring the reflection and transmission spectra of microwave radiation in the range of 5-8 GHz.

  8. Kinematically complete chemical reaction dynamics

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  9. Effects of additives on the oscillations of the Briggs-Rauscher reaction

    NASA Astrophysics Data System (ADS)

    Cervellati, R.; Furrow, S. D.

    2013-12-01

    Perturbations with chemical species that have dissimilar physico-chemical properties, such as bromide ions, polyphenols or iron complexes, are often used to investigate the detailed molecular mechanism of the Briggs-Rauscher (BR) oscillating reaction. We describe in this review the effects caused by some of these species and present their mechanistic interpretations. Some new original results are also reported.

  10. Quorum Sensing and Synchronization in Populations of Coupled Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Taylor, Annette F.; Tinsley, Mark R.; Showalter, Kenneth

    2013-12-01

    Experiments and simulations of populations of coupled chemical oscillators, consisting of catalytic particles suspended in solution, provide insights into density-dependent dynamics displayed by many cellular organisms. Gradual synchronization transitions, the "switching on" of activity above a threshold number of oscillators (quorum sensing) and the formation of synchronized groups (clusters) of oscillators have been characterized. Collective behavior is driven by the response of the oscillators to chemicals emitted into the surrounding solution.

  11. Nonequilibrium / nonlinear chemical oscillation in the virtual absence of gravity.

    PubMed

    Fujieda, S; Mogami, Y; Moriyasu, K; Mori, Y

    1999-01-01

    The Belousov-Zhabotinsky (BZ) reactions were used as typical examples of a nonlinear system far from equilibrium in connection with biological evolution. The virtual absence of gravity in the present work was given from the free-fall facility of Japan Microgravity Center (JAMIC) in Hokkaido. The reaction solution of BZ reaction was composed of bromate in sulfuric acid, 1,4-cyclohexanedione and ferroin to visualize the time development of patterns of chemical oscillations in the reaction-diffusion system. It is a bubble-free constitution in the aging of the reaction. Therefore, the setup constructed to collect image data via CCD cameras was simplified. The operation sequences of necessary devices were comprised of simple solid state relays which were started by a command from the operation room of JAMIC. The propagation profile of chemical patterns under microgravity of 10(-5) g was collected as image data for 9.8 s, and processed by a software of STM-STS2. In the aqueous solutions, propagation velocity of chemical patterns under microgravity was decreased to 80.9 % of that under normal gravity, owing to suppression of convection. On the other hand, in gel matrix, gravity did not influence the propagation velocity. c1999 COSPAR. Published by Elsevier Science Ltd.

  12. Nonequilibrium / nonlinear chemical oscillation in the virtual absence of gravity

    NASA Astrophysics Data System (ADS)

    Fujieda, S.; Mogami, Y.; Moriyasu, K.; Mori, Y.

    1999-01-01

    The Belousov-Zhabotinsky (BZ) reactions were used as typical examples of a nonlinear system far from equilibrium in connection with biological evolution. The virtual absence of gravity in the present work was given from the free-fall facility of Japan Microgravity Center (JAMIC) in Hokkaido. The reaction solution of BZ reaction was composed of bromate in sulfuric acid, 1,4-cyclohexanedione and ferroin to visualize the time development of patterns of chemical oscillations in the reaction-diffusion system. It is a bubble-free constitution in the aging of the reaction. Therefore, the setup constructed to collect image data via CCD cameras was simplified. The operation sequences of necessary devices were comprised of simple solid state relays which were started by a command from the operation room of JAMIC. The propagation profile of chemical patterns under microgravity of 10-5 g was collected as image data for 9.8 s, and processed by a software of STM-STS2. In the aqueous solutions, propagation velocity of chemical patterns under microgravity was decreased to 80.9 % of that under normal gravity, owing to suppression of convection. On the other hand, in gel matrix, gravity did not influence the propagation velocity.

  13. Slow manifolds and mixed-mode oscillations in the Belousov--Zhabotinskii reaction

    SciTech Connect

    Barkley, D.

    1988-11-01

    The mixed-mode oscillations observed at high flow rates in the Belousov--Zhabotinskii (BZ) reaction are considered and comparison is made between these oscillations and the dynamics of three different mathematical models based on slow manifolds. It is shown that the model proposed by Roessler for the generation of complex behavior in nonequilibrium chemical reactions is in conflict with the behavior of the BZ reaction. It is also shown that a slow-manifold model based on the hysteresis-Hopf normal form fails to accurately reproduce the oscillations found at high flow rates in the BZ system. A model of the type first proposed by Boissonade is presented; the model consists of the coupling of two simple systems. It is shown that this model naturally generates mixed-mode oscillations like those observed in the BZ reaction.

  14. Experimental investigation of a unidirectional network of four chemical oscillators pulse-coupled through an inhibitor

    NASA Astrophysics Data System (ADS)

    Smelov, P. S.; Vanag, V. K.

    2017-06-01

    Dynamical synchronous modes in a network of four nearly identical chemical oscillators unidirectionally coupled via inhibitory pulse coupling with time delay τ (when a spike in one oscillator inhibits the next oscillator in the circle after time delay τ), are obtained experimentally. The Belousov-Zhabotinsky reaction is used as a chemical oscillator. The existence of four main modes is confirmed experimentally: in-phase (IP) oscillations; an anti-phase (AP) mode, in which any two neighboring oscillators have a phase shift equal to half of global period T; a walk mode (W), in which oscillators produce consecutive spikes in the direction of the connection with a phase shift between neighboring oscillators equal to T/4; and a walk-reverse mode (WR), when the oscillators produce consecutive spikes (with phase shift T/4), but in the direction opposite the connections (the mode opposite to the W mode). In addition to the main modes, OS modes in which at least one of the four oscillators is suppressed, and "2+1+1" modes in which two neighboring oscillators produce spikes simultaneously and the phases of the third and the fourth oscillators are shifted by T/3 and 2 T/3, respectively, are found. It is shown that the modes found experimentally correspond to those found in simulations.

  15. Coupling among three chemical oscillators: Synchronization, phase death, and frustration

    NASA Astrophysics Data System (ADS)

    Yoshimoto, Minoru; Yoshikawa, Kenichi; Mori, Yoshihito

    1993-02-01

    Various modes in three coupled chemical oscillators in a triangular arrangement were observed. As a well-defined nonlinear oscillator, the Belousov-Zhabotinsky reaction was studied in a continuous-flow stirred tank reactor (CSTR). Coupling among CSTR's was performed by mass exchange. The coupling strength was quantitatively controlled by changing the flow rate of reacting solutions among the three CSTR's using peristaltic pumps between each pair of the reactors. As a key parameter to control the model of coupling, we changed the symmetry of the interaction between the oscillators. In the case of the symmetric coupling, a quasiperiodic state or a biperiodic mode, an all-death mode and two kinds of synchronized modes appeared, depending on the coupling strength. On the other hand, under the asymmetric coupling, a quasiperiodic state or a biperiodic mode, an all death mode and four kinds of synchronized modes appeared. Those modes have been discussed in relation to the idea of ``frustration'' in the Ising spin system, where the three-phase mode appears as a transition from the Ising spin system to the XY spin system.

  16. Experimental Demonstrations in Teaching Chemical Reactions.

    ERIC Educational Resources Information Center

    Hugerat, Muhamad; Basheer, Sobhi

    2001-01-01

    Presents demonstrations of chemical reactions by employing different features of various compounds that can be altered after a chemical change occurs. Experimental activities include para- and dia-magnetism in chemical reactions, aluminum reaction with base, reaction of acid with carbonates, use of electrochemical cells for demonstrating chemical…

  17. Experimental Demonstrations in Teaching Chemical Reactions.

    ERIC Educational Resources Information Center

    Hugerat, Muhamad; Basheer, Sobhi

    2001-01-01

    Presents demonstrations of chemical reactions by employing different features of various compounds that can be altered after a chemical change occurs. Experimental activities include para- and dia-magnetism in chemical reactions, aluminum reaction with base, reaction of acid with carbonates, use of electrochemical cells for demonstrating chemical…

  18. Comment on ``Surface restructuring, kinetic oscillations, and chaos in heterogeneous catalytic reactions''

    NASA Astrophysics Data System (ADS)

    Kuzovkov, V. N.; Kortlüke, O.; von Niessen, W.

    2001-02-01

    In a recent article Zhdanov studied the oscillating NO+H2 reaction on the Pt(100) single-crystal surface [V. P. Zhdanov, Phys. Rev. E 59, 6292 (1999)]. We have scrutinized his model and found fundamental errors in the chemical modeling, in the modeling of the surface reconstruction and in the simulation procedure itself.

  19. Experimental assessment of the sensitiveness of an electrochemical oscillator towards chemical perturbations.

    PubMed

    Ferreira, Graziela C A; Batista, Bruno C; Varela, Hamilton

    2012-01-01

    In this study we address the problem of the response of a (electro)chemical oscillator towards chemical perturbations of different magnitudes. The chemical perturbation was achieved by addition of distinct amounts of trifluoromethanesulfonate (TFMSA), a rather stable and non-specifically adsorbing anion, and the system under investigation was the methanol electro-oxidation reaction under both stationary and oscillatory regimes. Increasing the anion concentration resulted in a decrease in the reaction rates of methanol oxidation and a general decrease in the parameter window where oscillations occurred. Furthermore, the addition of TFMSA was found to decrease the induction period and the total duration of oscillations. The mechanism underlying these observations was derived mathematically and revealed that inhibition in the methanol oxidation through blockage of active sites was found to further accelerate the intrinsic non-stationarity of the unperturbed system. Altogether, the presented results are among the few concerning the experimental assessment of the sensitiveness of an oscillator towards chemical perturbations. The universal nature of the complex chemical oscillator investigated here might be used for reference when studying the dynamics of other less accessible perturbed networks of (bio)chemical reactions.

  20. Experimental Assessment of the Sensitiveness of an Electrochemical Oscillator towards Chemical Perturbations

    PubMed Central

    Ferreira, Graziela C. A.; Batista, Bruno C.; Varela, Hamilton

    2012-01-01

    In this study we address the problem of the response of a (electro)chemical oscillator towards chemical perturbations of different magnitudes. The chemical perturbation was achieved by addition of distinct amounts of trifluoromethanesulfonate (TFMSA), a rather stable and non-specifically adsorbing anion, and the system under investigation was the methanol electro-oxidation reaction under both stationary and oscillatory regimes. Increasing the anion concentration resulted in a decrease in the reaction rates of methanol oxidation and a general decrease in the parameter window where oscillations occurred. Furthermore, the addition of TFMSA was found to decrease the induction period and the total duration of oscillations. The mechanism underlying these observations was derived mathematically and revealed that inhibition in the methanol oxidation through blockage of active sites was found to further accelerate the intrinsic non-stationarity of the unperturbed system. Altogether, the presented results are among the few concerning the experimental assessment of the sensitiveness of an oscillator towards chemical perturbations. The universal nature of the complex chemical oscillator investigated here might be used for reference when studying the dynamics of other less accessible perturbed networks of (bio)chemical reactions. PMID:23185559

  1. [Recent results in research on oscillatory chemical reactions].

    PubMed

    Poros, Eszter; Kurin-Csörgei, Krisztina

    2014-01-01

    The mechanisms of the complicated periodical phenomenas in the nature (e.g. hearth beat, sleep cycle, circadian rhythms, etc) could be understood with using the laws of nonlinear chemical systems. In this article the newest result in the research of the subfield of nonlinear chemical dynamics aimed at constructing oscillatory chemical reactions, which are novel either in composition or in configuration, are presented. In the introductory part the concept of chemical periodicity is defined, then the forms as it can appear in time and space and the methods of their study are discussed. Detailed description of the experimental work that has resulted in two significant discoveries is provided. A method was developed to design pH-oscillators which are capable of operating under close conditions. The batch pH-oscillators are more convenient to use in some proposed applications than the equivalent CSTR variant. A redox oscillator that is new in composition was found. The permanganate oxidation of some amino acids was shown to take place according to oscillatory kinetics in a narrow range of the experimental parameters. The KMnO4 - glycine - Na2HPO4 system represents the first example in the family of manganese based oscillators where amino acids is involved. In the conclusion formal analogies between the simple chemical and some more complicated biological oscillatory phenomena are mentioned and the possibility of modeling periodic processes with the use of information gained from the studies of chemical oscillations is pointed out.

  2. The role of Ce(III) in BZ oscillating reactions

    NASA Astrophysics Data System (ADS)

    Nogueira, Paulo A.; Varela, Hamilton; Faria, Roberto B.

    2012-03-01

    Herein we present results on the oscillatory dynamics in the bromate-oxalic acid-acetone-Ce(III)/Ce(IV) system in batch and also in a CSTR. We show that Ce(III) is the necessary reactant to allow the emergence of oscillations. In batch, oscillations occur with Ce(III) and also with Ce(IV), but no induction period is observed with Ce(III). In a CSTR, no oscillations were found using a freshly prepared Ce(IV), but only when the cerium-containing solution was aged, allowing partial conversion of Ce(IV) to Ce(III) by reaction with acetone.

  3. Dynamical regimes of two frequency different chemical oscillators coupled via pulse inhibitory coupling with time delay

    NASA Astrophysics Data System (ADS)

    Proskurkin, I. S.; Vanag, V. K.

    2015-02-01

    Resonance regimes of two frequency different chemical oscillators coupled via pulsed inhibitory coupling with time delay τ have been studied theoretically and experimentally. The Belousov-Zhabotinsky reaction is used as a chemical oscillator. Regions of the 1: 1, 2: 3, 1: 2, 2: 5, and 1: 3 resonances, as well as complex oscillations and a regime in which one oscillator is suppressed have been found in the parameter plane "the ratio between the T 2/ T 1-τ." For the 1: 2 resonance, a sharp transition from one synchronized regime (called "0/0.5") to the other one (called "0.2/0.7") has been found. This transition (reminiscent to the transition between in-phase and anti-phase oscillations in case of the 1: 1 resonance) is controlled by time delay τ and the coupling strength.

  4. (Laser enhanced chemical reaction studies)

    SciTech Connect

    Not Available

    1992-01-01

    Experimental studies of dynamic molecular processes are described with particular emphasis on the use of a powerful infrared diode laser probe technique developed in our laboratory. This technique allows us to determine the final states of CO{sub 2} (and other molecules) produced by collisions, photofragmentation, or chemical reactions with a spectral resolution of 0.0003 cm{sup {minus}1} and a time resolution of 10{sup {minus}7} sec. Such high spectral resolution provides a detailed picture of the vibrational and rotational states of molecules produced by these dynamic events. We have used this experimental method to probe collisions between hot hydrogen/deuterium atoms and CO{sub 2}, between O({sup 1}D) atoms and CO{sub 2}, to study the final states of DC1 molecules produced as a result of the reactions of hot Cl atoms, and to investigate the dynamics of the reaction between OH and CO molecules. Advances in our techniques over the past two years have allowed us to identify and study more than 200 final rotational states in ten different vibrational levels of CO{sub 2} encompassing all 3 normal modes, many overtones, and combination states of the molecule. We have extended the technique to probe a variety of new molecules such as OCS, N{sub 2}O, DCl, and CS{sub 2}. All of this work is aimed at providing experimental tests for polyatomic molecule potential energy surfaces, chemical transition states in complex systems, and theories of reaction dynamic in molecules with more than 3 atoms.

  5. A reversible nanoconfined chemical reaction.

    PubMed

    Nielsen, Thomas K; Bösenberg, Ulrike; Gosalawit, Rapee; Dornheim, Martin; Cerenius, Yngve; Besenbacher, Flemming; Jensen, Torben R

    2010-07-27

    Hydrogen is recognized as a potential, extremely interesting energy carrier system, which can facilitate efficient utilization of unevenly distributed renewable energy. A major challenge in a future "hydrogen economy" is the development of a safe, compact, robust, and efficient means of hydrogen storage, in particular, for mobile applications. Here we report on a new concept for hydrogen storage using nanoconfined reversible chemical reactions. LiBH4 and MgH2 nanoparticles are embedded in a nanoporous carbon aerogel scaffold with pore size Dmax approximately 21 nm and react during release of hydrogen and form MgB2. The hydrogen desorption kinetics is significantly improved compared to bulk conditions, and the nanoconfined system has a high degree of reversibility and stability and possibly also improved thermodynamic properties. This new scheme of nanoconfined chemistry may have a wide range of interesting applications in the future, for example, within the merging area of chemical storage of renewable energy.

  6. A true chemical clock: Serially coupled chlorite iodide oscillators

    NASA Astrophysics Data System (ADS)

    Long, David A.; Chodroff, Leah; O'Neal, Tim M.; Hemkin, Sheryl

    2007-10-01

    A set of serially coupled flow reactors are modeled which contain chlorite-iodide oscillators. By independently varying the reactor flow rates it is possible to produce oscillatory systems with differing periods where the ratio of the period of oscillation between reactors is always an integer value. This system was thoroughly examined and utilized to produce a 'true' chemical clock whose three reactors oscillate with a frequency of minutes, hours, and days.

  7. Learning to predict chemical reactions.

    PubMed

    Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

    2011-09-26

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  8. Learning to Predict Chemical Reactions

    PubMed Central

    Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

    2011-01-01

    Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

  9. Effect of initial substrate concentration of the Belousov-Zhabotinsky reaction on self-oscillation for microgel system.

    PubMed

    Suzuki, Daisuke; Yoshida, Ryo

    2008-10-09

    Self-oscillation for the microgel particles ( approximately 200 nm in diameter) was studied by changing initial substrate concentrations (i.e., malonic acid, sodium bromate, and nitric acid) of the Belousov-Zhabotinsky (BZ) reaction that is used for chemical energy for the self-oscillation. The cross-linked microgels are composed of N-isopropylacrylamide and ruthenium tris(2,2'-bipyridine), Ru(bpy) 3, which is a catalyst for the BZ reaction. Comparing with the homogeneous, stirred solution of the bulk solution for the BZ reaction, swelling/deswelling oscillation of the microgels showed longer induction period, different dependence of initial substrate concentrations on oscillation period, and different oscillation rhythm. The change in oscillation for the microgels can be understood by considering the microgel network effect.

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

    PubMed

    Tian, Tianhai

    2013-01-01

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

  11. Renormalized reaction and relaxation rates for harmonic oscillator model

    NASA Astrophysics Data System (ADS)

    Gorbachev, Yuriy E.

    2017-07-01

    The thermal dissociation process is considered within the method of solving the kinetic equations for spatially inhomogeneous reactive gas mixtures developed in the previous papers. For harmonic oscillator model explicit expressions for reaction and relaxation rates in the renormalized form are derived.

  12. Chemical reactions in endoreversible thermodynamics

    NASA Astrophysics Data System (ADS)

    Wagner, Katharina; Hoffmann, Karl Heinz

    2016-01-01

    Endoreversible thermodynamics is a theory for the (approximate) description of thermodynamic non-equilibrium systems, which allows us to capture the ever present irreversibilities of real processes. For instance in heat engines the dissipation due to finite heat transport capabilities, as well as the resulting limitations in the energy fluxes, can be incorporated into the theory. It has thus been very successful in closing the gap between observed and theoretically predicted efficiencies. Here an extension of the theory is provided, with which chemical reactions can be included in the formalism. This opens up a wide field of applications for endoreversible modeling and the investigation of dissipative processes, for instance in fuel cells or batteries.

  13. Uncovering Oscillations, Complexity, and Chaos in Chemical Kinetics Using Mathematica

    NASA Astrophysics Data System (ADS)

    Ferreira, M. M. C.; Ferreira, W. C., Jr.; Lino, A. C. S.; Porto, M. E. G.

    1999-06-01

    Unlike reactions with no peculiar temporal behavior, in oscillatory reactions concentrations can rise and fall spontaneously in a cyclic or disorganized fashion. In this article, the software Mathematica is used for a theoretical study of kinetic mechanisms of oscillating and chaotic reactions. A first simple example is introduced through a three-step reaction, called the Lotka model, which exhibits a temporal behavior characterized by damped oscillations. The phase plane method of dynamic systems theory is introduced for a geometric interpretation of the reaction kinetics without solving the differential rate equations. The equations are later numerically solved using the built-in routine NDSolve and the results are plotted. The next example, still with a very simple mechanism, is the Lotka-Volterra model reaction, which oscillates indefinitely. The kinetic process and rate equations are also represented by a three-step reaction mechanism. The most important difference between this and the former reaction is that the undamped oscillation has two autocatalytic steps instead of one. The periods of oscillations are obtained by using the discrete Fourier transform (DFT)-a well-known tool in spectroscopy, although not so common in this context. In the last section, it is shown how a simple model of biochemical interactions can be useful to understand the complex behavior of important biological systems. The model consists of two allosteric enzymes coupled in series and activated by its own products. This reaction scheme is important for explaining many metabolic mechanisms, such as the glycolytic oscillations in muscles, yeast glycolysis, and the periodic synthesis of cyclic AMP. A few of many possible dynamic behaviors are exemplified through a prototype glycolytic enzymatic reaction proposed by Decroly and Goldbeter. By simply modifying the initial concentrations, limit cycles, chaos, and birhythmicity are computationally obtained and visualized.

  14. Reaction Decoder Tool (RDT): extracting features from chemical reactions

    PubMed Central

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W.; Holliday, Gemma L.; Steinbeck, Christoph; Thornton, Janet M.

    2016-01-01

    Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder Contact: asad@ebi.ac.uk or s9asad@gmail.com PMID:27153692

  15. Reaction Decoder Tool (RDT): extracting features from chemical reactions.

    PubMed

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

    2016-07-01

    Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

  16. 2005 Chemical Reactions at Surfaces

    SciTech Connect

    Cynthia M. Friend

    2006-03-14

    The Gordon Research Conference (GRC) on 2005 Chemical Reactions at Surfaces was held at Ventura Beach Marriott, Ventura California from February 13, 2005 through February 18, 2005. The Conference was well-attended with 124 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

  17. Linear nonequilibrium thermodynamics of reversible periodic processes and chemical oscillations.

    PubMed

    Heimburg, Thomas

    2017-07-05

    Onsager's phenomenological equations successfully describe irreversible thermodynamic processes. They assume a symmetric coupling matrix between thermodynamic fluxes and forces. It is easily shown that the antisymmetric part of a coupling matrix does not contribute to dissipation. Therefore, entropy production is exclusively governed by the symmetric matrix even in the presence of antisymmetric terms. In this paper we focus on the antisymmetric contributions which describe isentropic oscillations with well-defined equations of motion. The formalism contains variables that are equivalent to momenta and coefficients that are analogous to inertial mass. We apply this formalism to simple problems with known answers such as an oscillating piston containing an ideal gas, and oscillations in an LC-circuit. One can extend this formalism to other pairs of variables, including chemical systems with oscillations. In isentropic thermodynamic systems all extensive and intensive variables including temperature can display oscillations reminiscent of adiabatic waves.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  20. Analysis of precision in chemical oscillators: implications for circadian clocks

    NASA Astrophysics Data System (ADS)

    d'Eysmond, Thomas; De Simone, Alessandro; Naef, Felix

    2013-10-01

    Biochemical reaction networks often exhibit spontaneous self-sustained oscillations. An example is the circadian oscillator that lies at the heart of daily rhythms in behavior and physiology in most organisms including humans. While the period of these oscillators evolved so that it resonates with the 24 h daily environmental cycles, the precision of the oscillator (quantified via the Q factor) is another relevant property of these cell-autonomous oscillators. Since this quantity can be measured in individual cells, it is of interest to better understand how this property behaves across mathematical models of these oscillators. Current theoretical schemes for computing the Q factors show limitations for both high-dimensional models and in the vicinity of Hopf bifurcations. Here, we derive low-noise approximations that lead to numerically stable schemes also in high-dimensional models. In addition, we generalize normal form reductions that are appropriate near Hopf bifurcations. Applying our approximations to two models of circadian clocks, we show that while the low-noise regime is faithfully recapitulated, increasing the level of noise leads to species-dependent precision. We emphasize that subcomponents of the oscillator gradually decouple from the core oscillator as noise increases, which allows us to identify the subnetworks responsible for robust rhythms.

  1. Link weight evolution in a network of coupled chemical oscillators

    NASA Astrophysics Data System (ADS)

    Ke, Hua; Tinsley, Mark R.; Steele, Aaron; Wang, Fang; Showalter, Kenneth

    2014-05-01

    Link weight evolution is studied in a network of coupled chemical oscillators. Oscillators are perturbed by adjustments in imposed light intensity based on excitatory or inhibitory links to other oscillators undergoing excitation. Experimental and modeling studies demonstrate that the network is capable of producing sustained coordinated activity. The individual nodes of the network exhibit incoherent firing events; however, a dominant frequency can be discerned within the collective signal by Fourier analysis. The introduction of spike-timing-dependent plasticity yields a network that evolves to a stable unimodal link weight distribution.

  2. Butterfly effect in a chemical oscillator

    NASA Astrophysics Data System (ADS)

    Budroni, M. A.; Wodlei, F.; Rustici, M.

    2014-07-01

    The strong sensitivity of aperiodic dynamics to initial conditions is one of the fingerprinting features of chaotic systems. While this dependence can be directly verified by means of numerical approaches, it is quite elusive and difficult to be isolated in real experimental systems. In this paper, we discuss a didactic and self-consistent method to show the divergent behaviour between two infinitesimally different solutions of the famous Belousov-Zhabotinsky oscillator simultaneously undergoing a transition to a chaotic regime. Experimental data are also used to give an intuitive visualization of the essential meaning of a Lyapunov exponent, which allows for a more quantitative characterization of the chaotic transient.

  3. Chemical reactions in low-g

    NASA Technical Reports Server (NTRS)

    Grodzka, P. G.; Facemire, B. R.

    1978-01-01

    The Apollo-Soyuz flight experiment, 'Chemical Foams' demonstrated that foams and air/liquid dispersions are much more stable in low-gravity than on the ground. It thus should be possible to conduct unique chemical reactions in space foams. The low-g results and subsequent ground work on the formaldehyde clock reaction indicate that the reaction is strongly influenced by (1) dissociated and undissociated solution species being adsorbed at solid/liquid and gas/liquid surfaces and (2) chemical reaction rates apparently being affected by long-range forces determined by the liquid mass and the extent and nature of all surface interfaces.

  4. Chemical reactions in low-g

    NASA Technical Reports Server (NTRS)

    Grodzka, P. G.; Facemire, B. R.

    1978-01-01

    The Apollo-Soyuz flight experiment, 'Chemical Foams' demonstrated that foams and air/liquid dispersions are much more stable in low-gravity than on the ground. It thus should be possible to conduct unique chemical reactions in space foams. The low-g results and subsequent ground work on the formaldehyde clock reaction indicate that the reaction is strongly influenced by (1) dissociated and undissociated solution species being adsorbed at solid/liquid and gas/liquid surfaces and (2) chemical reaction rates apparently being affected by long-range forces determined by the liquid mass and the extent and nature of all surface interfaces.

  5. Microfabricated electrochemiluminescence cell for chemical reaction detection

    DOEpatents

    Northrup, M. Allen; Hsueh, Yun-Tai; Smith, Rosemary L.

    2003-01-01

    A detector cell for a silicon-based or non-silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The detector cell is an electrochemiluminescence cell constructed of layers of silicon with a cover layer of glass, with spaced electrodes located intermediate various layers forming the cell. The cell includes a cavity formed therein and fluid inlets for directing reaction fluid therein. The reaction chamber and detector cell may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The ECL cell may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  6. 'GREENER' CHEMICAL SYNTHESES USING ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    Microwave (MW) irradiation in conjunction with water as reaction media has proven to be a greener chemical approach for expeditious N-alkylation reactions of amines and hydrazines wherein the reactions under mildly basic conditions afford tertiary amines and double N-alkylation t...

  7. Modelling Students' Visualisation of Chemical Reaction

    ERIC Educational Resources Information Center

    Cheng, Maurice M. W.; Gilbert, John K.

    2017-01-01

    This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…

  8. 'GREENER' CHEMICAL SYNTHESES USING ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    Microwave (MW) irradiation in conjunction with water as reaction media has proven to be a greener chemical approach for expeditious N-alkylation reactions of amines and hydrazines wherein the reactions under mildly basic conditions afford tertiary amines and double N-alkylation t...

  9. Self-oscillating gels driven by the Belousov-Zhabotinsky reaction as novel smart materials.

    PubMed

    Yoshida, Ryo

    2010-08-17

    So far stimuli-responsive polymer gels and their application to smart materials have been widely studied; this research has contributed to progress in gel science and engineering. For their development as a novel biomimetic polymer, studies of polymers with an autonomous self-oscillating function have been carried out since the first reports in 1996. The development of novel self-oscillating polymers and gels have been successful utilizing the oscillating reaction, called the Belousov-Zhabotinsky (BZ) reaction, which is recognized as a chemical model for understanding several autonomous phenomena in biological systems. The self-oscillating polymer is composed of a poly(N-isopropylacrylamide) network in which the catalyst for the BZ reaction is covalently immobilized. In the presence of the reactants, the polymer undergoes spontaneous cyclic soluble-insoluble changes or swelling-deswelling changes (in the case of gel) without any on-off switching of external stimuli. Potential applications of the self-socillating polymers and gels include several kinds of functional material systems, such as biomimetic actuators and mass transport surface.

  10. Chemical memory with states coded in light controlled oscillations of interacting Belousov-Zhabotinsky droplets.

    PubMed

    Gizynski, Konrad; Gorecki, Jerzy

    2017-03-01

    The information storing potential of droplets, in which an oscillatory, photosensitive Belousov-Zhabotinsky (BZ) reaction proceeds, is investigated experimentally. We consider coupled oscillations in pairs and triplets of droplets. Droplets are surrounded by a solution of lipids in decane. Oscillations synchronize via diffusion of an activator through a lipid bilayer. The reaction in each droplet can be individually controlled by illumination with blue light through an optical fiber. We found that in pairs of BZ droplets, only the in-phase and the forcing oscillation modes are stable, however switching between these modes is not reliable. In triplets of droplets, switching between two different, stable rotational modes (clockwise and anticlockwise) can be easily implemented. Therefore, such a system is an excellent candidate for a light controlled, reliable, one bit chemical memory unit.

  11. Chlorine dioxide-iodide-methyl acetoacetate oscillation reaction investigated by UV-vis and online FTIR spectrophotometric method.

    PubMed

    Shi, Laishun; Wang, Xiaomei; Li, Na; Liu, Jie; Yan, Chunying

    2012-01-01

    In order to study the chemical oscillatory behavior and mechanism of a new chlorine dioxide-iodide ion-methyl acetoacetate reaction system, a series of experiments were done by using UV-Vis and online FTIR spectrophotometric method. The initial concentrations of methyl acetoacetate, chlorine dioxide, potassium iodide, and sulfuric acid and the pH value have great influence on the oscillation observed at wavelength of 289 nm. There is a preoscillatory or induction period, and the amplitude and the number of oscillations are associated with the initial concentration of reactants. The equations for the triiodide ion reaction rate changing with reaction time and the initial concentrations in the oscillation stage were obtained. Oscillation reaction can be accelerated by increasing temperature. The apparent activation energies in terms of the induction period and the oscillation period were 26.02 KJ/mol and 17.65 KJ/mol, respectively. The intermediates were detected by the online FTIR analysis. Based upon the experimental data in this work and in the literature, a plausible reaction mechanism was proposed for the oscillation reaction.

  12. Chlorine Dioxide-Iodide-Methyl Acetoacetate Oscillation Reaction Investigated by UV-Vis and Online FTIR Spectrophotometric Method

    PubMed Central

    Shi, Laishun; Wang, Xiaomei; Li, Na; Liu, Jie; Yan, Chunying

    2012-01-01

    In order to study the chemical oscillatory behavior and mechanism of a new chlorine dioxide-iodide ion-methyl acetoacetate reaction system, a series of experiments were done by using UV-Vis and online FTIR spectrophotometric method. The initial concentrations of methyl acetoacetate, chlorine dioxide, potassium iodide, and sulfuric acid and the pH value have great influence on the oscillation observed at wavelength of 289 nm. There is a preoscillatory or induction period, and the amplitude and the number of oscillations are associated with the initial concentration of reactants. The equations for the triiodide ion reaction rate changing with reaction time and the initial concentrations in the oscillation stage were obtained. Oscillation reaction can be accelerated by increasing temperature. The apparent activation energies in terms of the induction period and the oscillation period were 26.02 KJ/mol and 17.65 KJ/mol, respectively. The intermediates were detected by the online FTIR analysis. Based upon the experimental data in this work and in the literature, a plausible reaction mechanism was proposed for the oscillation reaction. PMID:22454614

  13. Nature-Inspired Chemical Reaction Optimisation Algorithms.

    PubMed

    Siddique, Nazmul; Adeli, Hojjat

    2017-01-01

    Nature-inspired meta-heuristic algorithms have dominated the scientific literature in the areas of machine learning and cognitive computing paradigm in the last three decades. Chemical reaction optimisation (CRO) is a population-based meta-heuristic algorithm based on the principles of chemical reaction. A chemical reaction is seen as a process of transforming the reactants (or molecules) through a sequence of reactions into products. This process of transformation is implemented in the CRO algorithm to solve optimisation problems. This article starts with an overview of the chemical reactions and how it is applied to the optimisation problem. A review of CRO and its variants is presented in the paper. Guidelines from the literature on the effective choice of CRO parameters for solution of optimisation problems are summarised.

  14. Chemical potential and reaction electronic flux in symmetry controlled reactions.

    PubMed

    Vogt-Geisse, Stefan; Toro-Labbé, Alejandro

    2016-07-15

    In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc.

  15. Chemical-reaction model for Mexican wave

    NASA Astrophysics Data System (ADS)

    Nagatani, Takashi

    2003-05-01

    We present a chemical-reaction model to describe the Mexican wave ( La Ola) in football stadia. The spectator's action is described in terms of chemical reactions. The model is governed by three reaction rates k 1, k 2, and k3. We study the nonlinear waves on one- and two-dimensional lattices. The Mexican wave is formulated as a clockwise forwardly propagating wave. Waves are growing or disappear, depending on the values of reaction rates. In the specific case of k1= k2= k3=1, the nonlinear-wave equation produces a propagating pulse like soliton.

  16. Scanning electrochemical microscopy of Belousov-Zhabotinsky reaction: how confined oscillations reveal short lived radicals and auto-catalytic species.

    PubMed

    Stockmann, T Jane; Noël, Jean-Marc; Ristori, Sandra; Combellas, Catherine; Abou-Hassan, Ali; Rossi, Federico; Kanoufi, Frédéric

    2015-10-06

    Oscillating chemical reactions, encapsulated within artificial vesicles have been demonstrated as a powerful analogy of living cells for the investigation of chemical communication and morphogenesis. However, little is understood with regards to the influence of confinement on the reactivity of such systems. Herein, the effect of confinement on the Belousov-Zhabotinsky (BZ) oscillating reaction in bulk solution, (employing ferroin as a catalyst and malonic acid as the organic substrate) is investigated using scanning electrochemical microscopy (SECM) toward different insulating surfaces such as glass, silanized glass, or PTFE. An unexpected increase in the amplitude of the BZ reaction at a tip-substrate distance of ∼12-15 μm is observed. By simulating different reaction mechanisms, from simple EC' catalysis to more sophisticated Oregonator or even an 11-reaction scheme, it is shown that such behavior reveals the intervention of redox catalysis processes and particularly the short-lived highly reactive radical intermediate BrO2(•) indirectly detected at micromolar concentrations. The reinspection of the EC' mechanism shows that the homogeneous catalysis route is confirmed and kinetically characterized from SECM toward an insulating substrate, with promising potentiality in many systems. More specifically to the complex chemical case of BZ reactions, the mechanism is understood from the envelope curves of the oscillations, which are assessed in the absence of the oscillation (absence of organic substrate).

  17. Vibrational Participation in Chemical Reactions.

    DTIC Science & Technology

    1986-08-22

    Cesaro Xue-Feng Yang .. V-. V 8. IV. BIBLIOGRAPHY, AFOSR-SPONSORED RESEARCH, 1981 - 1984 1981 Vibrational Excitation of Ozone and Molecular Fluorine...Phys. Chem. 87, 2142 (1983). G.C. Pimentel, S.N. Cesaro and H. Frei. 11. Selective Vibronic Excitation of Singlet Oxygen-Furan Reactions in Cryogenic

  18. Modeling of turbulent chemical reaction

    NASA Technical Reports Server (NTRS)

    Chen, J.-Y.

    1995-01-01

    Viewgraphs are presented on modeling turbulent reacting flows, regimes of turbulent combustion, regimes of premixed and regimes of non-premixed turbulent combustion, chemical closure models, flamelet model, conditional moment closure (CMC), NO(x) emissions from turbulent H2 jet flames, probability density function (PDF), departures from chemical equilibrium, mixing models for PDF methods, comparison of predicted and measured H2O mass fractions in turbulent nonpremixed jet flames, experimental evidence of preferential diffusion in turbulent jet flames, and computation of turbulent reacting flows.

  19. Microfabricated sleeve devices for chemical reactions

    SciTech Connect

    Northrup, M. Allen

    2003-01-01

    A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and non-silicon based materials to provide the thermal properties desired. For example, the chamber may combine a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  20. Chemical Reactions at Surfaces. Final Progress Report

    SciTech Connect

    2003-02-21

    The Gordon Research Conference (GRC) on Chemical Reactions at Surfaces was held at Holiday Inn, Ventura, California, 2/16-21/03. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  1. Chemical Reactions in Turbulent Mixing Flows

    DTIC Science & Technology

    1993-07-15

    investigations of turbulent mixing, chemical reaction and combustion processes in turbulent, subsonic and supersonic flows. The program was comprised of...34) n•4I Abstract The purpose of this research is to conduct fundamental investigations of tur- bulent mixing, chemical reaction and combustion processes ...Another issue to consider is that different data- processing used on the different sets of data might result in differences between sets of data. To this end

  2. Explorations into Chemical Reactions and Biochemical Pathways.

    PubMed

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered.

  3. Kinetic studies of elementary chemical reactions

    SciTech Connect

    Durant, J.L. Jr.

    1993-12-01

    This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

  4. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.

  5. Entropy Generation in a Chemical Reaction

    ERIC Educational Resources Information Center

    Miranda, E. N.

    2010-01-01

    Entropy generation in a chemical reaction is analysed without using the general formalism of non-equilibrium thermodynamics at a level adequate for advanced undergraduates. In a first approach to the problem, the phenomenological kinetic equation of an elementary first-order reaction is used to show that entropy production is always positive. A…

  6. Chemical Principles Revisited: Annotating Reaction Equations.

    ERIC Educational Resources Information Center

    Tykodi, R. J.

    1987-01-01

    Urges chemistry teachers to have students annotate the chemical reactions in aqueous-solutions that they see in their textbooks and witness in the laboratory. Suggests this will help students recognize the reaction type more readily. Examples are given for gas formation, precipitate formation, redox interaction, acid-base interaction, and…

  7. Entropy Generation in a Chemical Reaction

    ERIC Educational Resources Information Center

    Miranda, E. N.

    2010-01-01

    Entropy generation in a chemical reaction is analysed without using the general formalism of non-equilibrium thermodynamics at a level adequate for advanced undergraduates. In a first approach to the problem, the phenomenological kinetic equation of an elementary first-order reaction is used to show that entropy production is always positive. A…

  8. The quantum dynamics of chemical reactions

    NASA Astrophysics Data System (ADS)

    Kuppermann, A.

    1983-03-01

    In this project, we developed accurate and approximate methods for calculating cross sections of elementary reactions. These methods were applied to systems of importance for the fundamental aspects of chemical dynamics and for advanced technologies of interest to the United States Air Force. The application included calculations of three-atom exchange reactions, break-up and three-body recombination collisions and vibrational quenching by reaction. These calculations improved our understanding of such processes and permitted an assessment of some approximate methods.

  9. Chemical Reactions in Turbulent Mixing Flows

    DTIC Science & Technology

    1989-10-15

    GROUP Turbulence, shear layers, jets, mixing, combustion , 21 ni numerical simulation, light detection diagnostics 21 02 9. ABSTRACT (Conmmna on...mixing chemical reactions and combustion processes in turbulent, subsonic and supersonic flows. This program is comprised of several efforts. In...permit the full chemical kinetics of the combustion process to be incorporated. Our recent analytical efforts have concentrated on a 20

  10. Ultrafast Dynamics of Chemical Reactions.

    DTIC Science & Technology

    2007-11-02

    Michael R. Berman 11 SUPPLEMENTARY NOTES 12a D!STRIBUTION AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE 13 Ap’-,T,,,ACT `’,Ii "•--200words) The research and...Caltech), Professor K. Wilson (UC, San Diego), and Professor J. Polanyi (Toronto). 3 6. Publications (1995/1996) Books Collected Works (up to 1994...1995) Direct Observation of The Transition State J. C. Polanyi and A. H. Zewail Accounts of Chemical Research (Holy-Grail Special Issue), 28,119 (1995

  11. Light Scattering from Systems with Chemical Oscillations and Dissipative Structures.

    DTIC Science & Technology

    splitting in the chemical lines and dispersive (non-Lorentzian) contributions. Two model reaction mechanisms, the Volterra - Lotka model and the Prigogine-Lefever model, are examined in detail. (Author)

  12. Topologically invariant reaction coordinates for simulating multistate chemical reactions.

    PubMed

    Mones, Letif; Csányi, Gábor

    2012-12-27

    Evaluating free energy profiles of chemical reactions in complex environments such as solvents and enzymes requires extensive sampling, which is usually performed by potential of mean force (PMF) techniques. The reliability of the sampling depends not only on the applied PMF method but also the reaction coordinate space within the dynamics is biased. In contrast to simple geometrical collective variables that depend only on the positions of the atomic coordinates of the reactants, the E(gap) reaction coordinate (the energy difference obtained by evaluating a suitable force field using reactant and product state topologies) has the unique property that it is able to take environmental effects into account leading to better convergence, a more faithful description of the transition state ensemble and therefore more accurate free energy profiles. However, E(gap) requires predefined topologies and is therefore inapplicable for multistate reactions, in which the barrier between the chemically equivalent topologies is comparable to the reaction activation barrier, because undesired "side reactions" occur. In this article, we introduce a new energy-based collective variable by generalizing the E(gap) reaction coordinate such that it becomes invariant to equivalent topologies and show that it yields more well behaved free energy profiles than simpler geometrical reaction coordinates.

  13. Intracellular click reaction with a fluorescent chemical Ca2+ indicator to prolong its cytosolic retention.

    PubMed

    Takei, Yoshiaki; Murata, Atsushi; Yamagishi, Kento; Arai, Satoshi; Nakamura, Hideki; Inoue, Takafumi; Takeoka, Shinji

    2013-08-25

    The powerful strategy of "intracellular click reaction" was used to retain a chemical Ca(2+) indicator in the cytosol. Specifically, a novel clickable Ca(2+) indicator "N3-fura-2 AM" was coupled with dibenzylcyclooctyl-modified biomacromolecules via copper-free click reaction in living cells and Ca(2+) oscillation was observed for an extended period of time.

  14. Chemical Reactions in Supercritical Carbon Dioxide

    NASA Astrophysics Data System (ADS)

    Wai, Chien M.; Hunt, Fred; Ji, Min; Chen, Xiaoyuan

    1998-12-01

    Utilizing supercritical fluids as environmentally benign solvents for chemical synthesis is one of the new approaches in the "greening" of chemistry. Carbon dioxide is the most widely used gas for supercritical fluid studies because of its moderate critical constants, nontoxic nature, and availability in pure form. One unique property of supercritical carbon dioxide (sc-CO2) is its high solubility for fluorinated compounds. Thus sc-CO2 can be used to replace Freons that are conventionally used as solvents for synthesis of perfluoro-polymers. Another property of sc-CO2 is its miscibility with gases such as H2. Heterogeneous reactions involving these gases may become homogeneous reactions in sc-CO2. Reactions in sc-CO2 may offer several advantages including controlling phase behavior and products, increasing speed of reactions, and obtaining specific reaction channels. This paper describes the following nine types of chemical reactions reported in the literature utilizing sc-CO2 as a solvent to illustrate the unique properties of the supercritical fluid reaction systems: (i) hydrogenation and hydroformylation, (ii) synthesis of organometallic compounds, (iii) metal chelation and extraction, (iv) preparation of inorganic nanoparticles, (v) stereo-selectivity of lipase-catalyzed reactions, (vi) asymmetric catalytic hydrogenation, (vii) polymerization, (viii) Diels-Alder reaction, and (ix) free radical reactions.

  15. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1994-01-01

    Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

  16. Chemical reactions confined within carbon nanotubes.

    PubMed

    Miners, Scott A; Rance, Graham A; Khlobystov, Andrei N

    2016-08-22

    In this critical review, we survey the wide range of chemical reactions that have been confined within carbon nanotubes, particularly emphasising how the pairwise interactions between the catalysts, reactants, transition states and products of a particular molecular transformation with the host nanotube can be used to control the yields and distributions of products of chemical reactions. We demonstrate that nanoscale confinement within carbon nanotubes enables the control of catalyst activity, morphology and stability, influences the local concentration of reactants and products thus affecting equilibria, rates and selectivity, pre-arranges the reactants for desired reactions and alters the relative stability of isomeric products. We critically evaluate the relative advantages and disadvantages of the confinement of chemical reactions inside carbon nanotubes from a chemical perspective and describe how further developments in the controlled synthesis of carbon nanotubes and the incorporation of multifunctionality are essential for the development of this ever-expanding field, ultimately leading to the effective control of the pathways of chemical reactions through the rational design of multi-functional carbon nanoreactors.

  17. Anatomy of an Elementary Chemical Reaction

    NASA Astrophysics Data System (ADS)

    Alexander, Andrew J.; Zare, Richard N.

    1998-09-01

    The alchemists of old sought the knowledge to transform one material to another-for example, base metals into gold-as a path to the elixir of life. As chemists have concerned themselves with the transformation from compound to compound, so they have become involved in trying to uncover the structures of molecules and the pathways that reactions follow. Classically, the study of reaction mechanisms in chemistry encompasses reaction kinetics, the study of velocities or rates of reactions, and reaction dynamics, the study of the nanoscopic motion and rearrangement of atoms during a reactive event. An essential aim of this article is to bring the reader to a favorable vantage point with a brief introduction to reactive dynamics, and from there to describe some examples of recent strategies that have been employed to promote a fundamental understanding of the anatomy of elementary chemical reactions. In the final section we ponder future directions for this rapidly evolving field of research.

  18. Phase-lag synchronization in networks of coupled chemical oscillators.

    PubMed

    Totz, Jan F; Snari, Razan; Yengi, Desmond; Tinsley, Mark R; Engel, Harald; Showalter, Kenneth

    2015-08-01

    Chemical oscillators with a broad frequency distribution are photochemically coupled in network topologies. Experiments and simulations show that the network synchronization occurs by phase-lag synchronization of clusters of oscillators with zero- or nearly zero-lag synchronization. Symmetry also plays a role in the synchronization, the extent of which is explored as a function of coupling strength, frequency distribution, and the highest frequency oscillator location. The phase-lag synchronization occurs through connected synchronized clusters, with the highest frequency node or nodes setting the frequency of the entire network. The synchronized clusters successively "fire," with a constant phase difference between them. For low heterogeneity and high coupling strength, the synchronized clusters are made up of one or more clusters of nodes with the same permutation symmetries. As heterogeneity is increased or coupling strength decreased, the phase-lag synchronization occurs partially through clusters of nodes sharing the same permutation symmetries. As heterogeneity is further increased or coupling strength decreased, partial synchronization and, finally, independent unsynchronized oscillations are observed. The relationships between these classes of behavior are explored with numerical simulations, which agree well with the experimentally observed behavior.

  19. Aerosol simulation including chemical and nuclear reactions

    SciTech Connect

    Marwil, E.S.; Lemmon, E.C.

    1985-01-01

    The numerical simulation of aerosol transport, including the effects of chemical and nuclear reactions presents a challenging dynamic accounting problem. Particles of different sizes agglomerate and settle out due to various mechanisms, such as diffusion, diffusiophoresis, thermophoresis, gravitational settling, turbulent acceleration, and centrifugal acceleration. Particles also change size, due to the condensation and evaporation of materials on the particle. Heterogeneous chemical reactions occur at the interface between a particle and the suspending medium, or a surface and the gas in the aerosol. Homogeneous chemical reactions occur within the aersol suspending medium, within a particle, and on a surface. These reactions may include a phase change. Nuclear reactions occur in all locations. These spontaneous transmutations from one element form to another occur at greatly varying rates and may result in phase or chemical changes which complicate the accounting process. This paper presents an approach for inclusion of these effects on the transport of aerosols. The accounting system is very complex and results in a large set of stiff ordinary differential equations (ODEs). The techniques for numerical solution of these ODEs require special attention to achieve their solution in an efficient and affordable manner. 4 refs.

  20. Theoretical study of chemical reactions in solution

    SciTech Connect

    Yokogawa, D.

    2015-12-31

    Quantum chemical calculations in solution are becoming more and more important in chemistry. Reference interaction site model self-consistent field (RISM-SCF) is one of the powerful approaches to perform quantum chemical calculations in solution. In this work, we developed a new generation of RISM-SCF, where a robust fitting method was newly introduced. We applied the new method to tautomerization reaction of cytosine in aqueous phase. Our calculation reproduced experimentally obtained relative stabilities and relative free energies correctly.

  1. Chemical Demonstrations with Consumer Chemicals: The Black and White Reaction

    NASA Astrophysics Data System (ADS)

    Wright, Stephen W.

    2002-01-01

    A color-change reaction is described in which two colorless solutions are combined to afford a black mixture. Two more colorless solutions are combined to afford a white mixture. The black and white mixtures are then combined to afford a clear, colorless solution. The reaction uses chemicals that are readily available on the retail market: vitamin C, tincture of iodine, vinegar, ammonia, bleach, Epsom salt, and laundry starch.

  2. Classification of Chemical Reactions: Stages of Expertise

    ERIC Educational Resources Information Center

    Stains, Marilyne; Talanquer, Vicente

    2008-01-01

    In this study we explore the strategies that undergraduate and graduate chemistry students use when engaged in classification tasks involving symbolic and microscopic (particulate) representations of different chemical reactions. We were specifically interested in characterizing the basic features to which students pay attention when classifying…

  3. Computer Animation of a Chemical Reaction.

    ERIC Educational Resources Information Center

    Eaker, Charles W.; Jacobs, Edwin L.

    1982-01-01

    Taking a prototype chemical reaction (molecular hydrogen plus hydrogen atom), constructs an accurate semiempirical, generalized diatomics-in-molecules potential energy surface, calculates motions of these atoms on this surface using REACTS trajectory program, and presents results as moving picture on a microcomputer graphics system. Provides…

  4. Classification of Chemical Reactions: Stages of Expertise

    ERIC Educational Resources Information Center

    Stains, Marilyne; Talanquer, Vicente

    2008-01-01

    In this study we explore the strategies that undergraduate and graduate chemistry students use when engaged in classification tasks involving symbolic and microscopic (particulate) representations of different chemical reactions. We were specifically interested in characterizing the basic features to which students pay attention when classifying…

  5. Some simple bifurcation sets of an extended Van der Pol model and their relation to chemical oscillators

    NASA Astrophysics Data System (ADS)

    Koper, Marc T. M.

    1995-04-01

    Some typical bifurcation sets of a generalized autonomous Van der Pol-type model are discussed as archetypes of phase diagrams occurring in nonlinear dynamical systems. The relevance of the obtained bifurcation sets is exemplified by several experimental and numerical results from the literature of oscillating chemical reactions.

  6. Visualization of chemical reaction dynamics: Toward understanding complex polyatomic reactions

    PubMed Central

    SUZUKI, Toshinori

    2013-01-01

    Polyatomic molecules have several electronic states that have similar energies. Consequently, their chemical dynamics often involve nonadiabatic transitions between multiple potential energy surfaces. Elucidating the complex reactions of polyatomic molecules is one of the most important tasks of theoretical and experimental studies of chemical dynamics. This paper describes our recent experimental studies of the multidimensional multisurface dynamics of polyatomic molecules based on two-dimensional ion/electron imaging. It also discusses ultrafast photoelectron spectroscopy of liquids for elucidating nonadiabatic electronic dynamics in aqueous solutions. PMID:23318678

  7. Visualization of chemical reaction dynamics: toward understanding complex polyatomic reactions.

    PubMed

    Suzuki, Toshinori

    2013-01-01

    Polyatomic molecules have several electronic states that have similar energies. Consequently, their chemical dynamics often involve nonadiabatic transitions between multiple potential energy surfaces. Elucidating the complex reactions of polyatomic molecules is one of the most important tasks of theoretical and experimental studies of chemical dynamics. This paper describes our recent experimental studies of the multidimensional multisurface dynamics of polyatomic molecules based on two-dimensional ion/electron imaging. It also discusses ultrafast photoelectron spectroscopy of liquids for elucidating nonadiabatic electronic dynamics in aqueous solutions. (Communicated by Hiroo INOKUCHI, M.J.A.)

  8. Computer simulation of spatial coupling in chemical oscillations of CO oxidation on two Pd(110) single crystals

    NASA Astrophysics Data System (ADS)

    Park, I. J.; Woo, S. I.

    1993-09-01

    Gas-phase coupling between two Pd(110) single crystals in a UHV CO oxidation reaction in a continuous stirred tank reactor (CSTR) has been simulated by solving gas-phase mass balance equations with kinetic rate equations. This work was motivated by the experimental results which show that the frequency of partial pressure change in carbon monoxide is the same as the frequency of the work function change in the oscillation region and that the coupling between the two crystals occurred entirely via CO partial pressure. The computer simulation described here gives qualitative agreement with the experimental results. The change in the oscillatory region originating from the coupling of chemical oscillators which are slightly different to each other is successfully demonstrated by this model. The coupling of two oscillators having a simple periodic oscillation to produce mixed-mode oscillation was also successfully simulated.

  9. Lagrangian descriptors of driven chemical reaction manifolds

    NASA Astrophysics Data System (ADS)

    Craven, Galen T.; Junginger, Andrej; Hernandez, Rigoberto

    2017-08-01

    The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015), 10.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.

  10. Lagrangian descriptors of driven chemical reaction manifolds.

    PubMed

    Craven, Galen T; Junginger, Andrej; Hernandez, Rigoberto

    2017-08-01

    The persistence of a transition state structure in systems driven by time-dependent environments allows the application of modern reaction rate theories to solution-phase and nonequilibrium chemical reactions. However, identifying this structure is problematic in driven systems and has been limited by theories built on series expansion about a saddle point. Recently, it has been shown that to obtain formally exact rates for reactions in thermal environments, a transition state trajectory must be constructed. Here, using optimized Lagrangian descriptors [G. T. Craven and R. Hernandez, Phys. Rev. Lett. 115, 148301 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.148301], we obtain this so-called distinguished trajectory and the associated moving reaction manifolds on model energy surfaces subject to various driving and dissipative conditions. In particular, we demonstrate that this is exact for harmonic barriers in one dimension and this verification gives impetus to the application of Lagrangian descriptor-based methods in diverse classes of chemical reactions. The development of these objects is paramount in the theory of reaction dynamics as the transition state structure and its underlying network of manifolds directly dictate reactivity and selectivity.

  11. Documentation of Chemical Reactions. I. A Faceted Classification

    ERIC Educational Resources Information Center

    Osinga, M.; Verrijn Stuart, A. A.

    1973-01-01

    Existing methods for coding chemical compounds are discussed and evaluated as to their suitability for documentation of chemical reactions, a new classification for chemical reactions is presented, and possibilities of automatic encoding are studied. (24 references) (Author)

  12. Chemical Reactions at Surfaces [Conference summary report

    SciTech Connect

    Henderson, Michael; Gray, Nancy Ryan

    2010-04-14

    Chemical reactions at surfaces underlie some of the most important processes of today, including catalysis, energy conversion, microelectronics, human health and the environment. Understanding surface chemical reactions at a fundamental level is at the core of the field of surface science. The Gordon Research Conference on Chemical Reactions at Surfaces is one of the premiere meetings in the field. The program this year will cover a broad range of topics, including heterogeneous catalysis and surface chemistry, surfaces in environmental chemistry and energy conversion, reactions at the liquid-solid and liquid-gas interface, electronic materials growth and surface modification, biological interfaces, and electrons and photons at surfaces. An exciting program is planned, with contributions from outstanding speakers and discussion leaders from the international scientific community. The conference provides a dynamic environment with ample time for discussion and interaction. Attendees are encouraged to present posters; the poster sessions are historically well attended and stimulate additional discussions. The conference provides an excellent opportunity for junior researchers (e.g. graduate students or postdocs) to present their work and interact with established leaders in the field.

  13. Chemical reactions in reverse micelle systems

    DOEpatents

    Matson, Dean W.; Fulton, John L.; Smith, Richard D.; Consani, Keith A.

    1993-08-24

    This invention is directed to conducting chemical reactions in reverse micelle or microemulsion systems comprising a substantially discontinuous phase including a polar fluid, typically an aqueous fluid, and a microemulsion promoter, typically a surfactant, for facilitating the formation of reverse micelles in the system. The system further includes a substantially continuous phase including a non-polar or low-polarity fluid material which is a gas under standard temperature and pressure and has a critical density, and which is generally a water-insoluble fluid in a near critical or supercritical state. Thus, the microemulsion system is maintained at a pressure and temperature such that the density of the non-polar or low-polarity fluid exceeds the critical density thereof. The method of carrying out chemical reactions generally comprises forming a first reverse micelle system including an aqueous fluid including reverse micelles in a water-insoluble fluid in the supercritical state. Then, a first reactant is introduced into the first reverse micelle system, and a chemical reaction is carried out with the first reactant to form a reaction product. In general, the first reactant can be incorporated into, and the product formed in, the reverse micelles. A second reactant can also be incorporated in the first reverse micelle system which is capable of reacting with the first reactant to form a product.

  14. Chemical computing with reaction-diffusion processes.

    PubMed

    Gorecki, J; Gizynski, K; Guzowski, J; Gorecka, J N; Garstecki, P; Gruenert, G; Dittrich, P

    2015-07-28

    Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  15. Uncertainty Quantification for Nonlinear Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Srinivasan, G.; Robinson, B. A.; Aceves, A. B.; Tartakovsky, D. M.

    2006-12-01

    Systems of coupled chemical reactions are greatly affected by the inherent uncertainties in natural phenomena. These uncertainties can be parametric in nature due to measurement errors or insufficient data. Modeling uncertainties also arise at the molecular level when determining what fraction of the population of each chemical species participates in a chemical reaction at any given time. We present different methods used to quantify both modeling and parametric uncertainties. The application we focus on is that of chemical reactions in the subsurface that greatly affect the transport of contaminants in groundwater. The example considered here is the sorption of Neptunium Np-237 through a competitive ion exchange process. Np-237 is a key radio-nuclide of concern for the Yucca Mountain High Level Waste storage site due to its relatively long half-life, high solubility and low sorption properties. By quantifying the effects of modeling and parametric uncertainties, we can estimate the error associated with Np-237 sorptivity and hence its transport.

  16. Shock-driven chemical reaction in phenylacetylene

    NASA Astrophysics Data System (ADS)

    Dattelbaum, Dana; Sheffield, Stephen; Coe, Joshua; Shock and Detonation Physics Team; Physics and Chemistry of Materials Team

    2013-06-01

    Phenylacetylene (PA) comprises a covalently-linked benzene ring and acetylene moiety, presenting an interesting molecular structure for study of shock driven chemical reactions. In the present work, gas gun-driven embedded electromagnetic gauging experiments produced in situ particle velocity wave profiles at multiple Lagrangian positions at several shock input conditions. The input shock wave evolves over time and distance into a complex multiple wave structure, with a fast risetime 2nd wave, slower risetime 3rd wave, and unusual wave dynamics in the 1st wave. From the shock and particle velocities, the Hugoniot reaction condition, and intermediate and final states associated with the chemical reactions have been obtained. For example, at shock inputs just above the cusp condition, an induction time of 200 ns was observed, with the evolved first wave traveling at Us = 4.2 km/s, P = 5.6 GPa; reaction rates of a few to 10 microsec-1 were inferred. A thermodynamically complete unreacted equation of state was calibrated to estimate the temperature rise along the shock locus. Use of this EOS with the measured wave risetimes yielded highly state-sensitive global reaction rates.

  17. MRI of chemical reactions and processes.

    PubMed

    Britton, Melanie M

    2017-08-01

    As magnetic resonance imaging (MRI) can spatially resolve a wealth of molecular information available from nuclear magnetic resonance (NMR), it is able to non-invasively visualise the composition, properties and reactions of a broad range of spatially-heterogeneous molecular systems. Hence, MRI is increasingly finding applications in the study of chemical reactions and processes in a diverse range of environments and technologies. This article will explain the basic principles of MRI and how it can be used to visualise chemical composition and molecular properties, providing an overview of the variety of information available. Examples are drawn from the disciplines of chemistry, chemical engineering, environmental science, physics, electrochemistry and materials science. The review introduces a range of techniques used to produce image contrast, along with the chemical and molecular insight accessible through them. Methods for mapping the distribution of chemical species, using chemical shift imaging or spatially-resolved spectroscopy, are reviewed, as well as methods for visualising physical state, temperature, current density, flow velocities and molecular diffusion. Strategies for imaging materials with low signal intensity, such as those containing gases or low sensitivity nuclei, using compressed sensing, para-hydrogen or polarisation transfer, are discussed. Systems are presented which encapsulate the diversity of chemical and physical parameters observable by MRI, including one- and two-phase flow in porous media, chemical pattern formation, phase transformations and hydrodynamic (fingering) instabilities. Lastly, the emerging area of electrochemical MRI is discussed, with studies presented on the visualisation of electrochemical deposition and dissolution processes during corrosion and the operation of batteries, supercapacitors and fuel cells. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  18. Concordant chemical reaction networks and the Species-Reaction Graph.

    PubMed

    Shinar, Guy; Feinberg, Martin

    2013-01-01

    In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network's Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams.

  19. Concordant Chemical Reaction Networks and the Species-Reaction Graph

    PubMed Central

    Shinar, Guy; Feinberg, Martin

    2015-01-01

    In a recent paper it was shown that, for chemical reaction networks possessing a subtle structural property called concordance, dynamical behavior of a very circumscribed (and largely stable) kind is enforced, so long as the kinetics lies within the very broad and natural weakly monotonic class. In particular, multiple equilibria are precluded, as are degenerate positive equilibria. Moreover, under certain circumstances, also related to concordance, all real eigenvalues associated with a positive equilibrium are negative. Although concordance of a reaction network can be decided by readily available computational means, we show here that, when a nondegenerate network’s Species-Reaction Graph satisfies certain mild conditions, concordance and its dynamical consequences are ensured. These conditions are weaker than earlier ones invoked to establish kinetic system injectivity, which, in turn, is just one ramification of network concordance. Because the Species-Reaction Graph resembles pathway depictions often drawn by biochemists, results here expand the possibility of inferring significant dynamical information directly from standard biochemical reaction diagrams. PMID:22940368

  20. Minimum Energy Pathways for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Walch, S. P.; Langhoff, S. R. (Technical Monitor)

    1995-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

  1. Theoretical studies of chemical reaction dynamics

    SciTech Connect

    Schatz, G.C.

    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.

  2. Quantum Theory of Fast Chemical Reactions

    SciTech Connect

    Light, John C

    2007-07-30

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

  3. Chemical reactions directed Peptide self-assembly.

    PubMed

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-05-13

    Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

  4. Chemical Reactions Directed Peptide Self-Assembly

    PubMed Central

    Rasale, Dnyaneshwar B.; Das, Apurba K.

    2015-01-01

    Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly. PMID:25984603

  5. Chemical Reaction Networks for Computing Polynomials.

    PubMed

    Salehi, Sayed Ahmad; Parhi, Keshab K; Riedel, Marc D

    2017-01-20

    Chemical reaction networks (CRNs) provide a fundamental model in the study of molecular systems. Widely used as formalism for the analysis of chemical and biochemical systems, CRNs have received renewed attention as a model for molecular computation. This paper demonstrates that, with a new encoding, CRNs can compute any set of polynomial functions subject only to the limitation that these functions must map the unit interval to itself. These polynomials can be expressed as linear combinations of Bernstein basis polynomials with positive coefficients less than or equal to 1. In the proposed encoding approach, each variable is represented using two molecular types: a type-0 and a type-1. The value is the ratio of the concentration of type-1 molecules to the sum of the concentrations of type-0 and type-1 molecules. The proposed encoding naturally exploits the expansion of a power-form polynomial into a Bernstein polynomial. Molecular encoders for converting any input in a standard representation to the fractional representation as well as decoders for converting the computed output from the fractional to a standard representation are presented. The method is illustrated first for generic CRNs; then chemical reactions designed for an example are mapped to DNA strand-displacement reactions.

  6. Suppression of Ostwald Ripening by Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Zwicker, David; Hyman, Anthony A.; Jülicher, Frank

    2015-03-01

    Emulsions consisting of droplets immersed in a fluid are typically unstable and coarsen over time. One important coarsening process is Ostwald ripening, which is driven by the surface tension of the droplets. Ostwald ripening must thus be suppressed to stabilize emulsions, e.g. to control the properties of pharmaceuticals, food, or cosmetics. Suppression of Ostwald ripening is also important in biological cells, which contain stable liquid-like compartments, e.g. germ granules, Cajal-bodies, and centrosomes. Such systems are often driven away from equilibrium by chemical reactions and can thus be called active emulsions. Here, we show that non-equilibrium chemical reactions can suppress Ostwald Ripening, leading to stable, monodisperse emulsions. We derive analytical approximations of the typical droplet size, droplet count, and time scale of the dynamics from a coarse-grained description of the droplet dynamics. We also compare these results to numerical simulations of the continuous concentration fields. Generally, we thus show how chemical reactions can be used to stabilize emulsions and to control their properties in technology and nature.

  7. Excited state quenching via "unsuccessful" chemical reactions.

    PubMed

    Sinicropi, Adalgisa; Nau, Werner M; Olivucci, Massimo

    2002-08-01

    We discuss the results of recent photochemical reaction path computations on 1n,pi* azoalkanes interacting with a single quencher molecule. We provide computational and experimental evidence that there are two basic mechanisms for the true quenching of 1n,pi* states both based on unsuccessful chemical reactions. The first mechanism is based upon an unsuccessful hydrogen atom transfer and may occur through two different (direct and stepwise) routes. The second mechanism is based on an unsuccessful charge transfer reaction that occurs exclusively in a direct fashion. We show that the efficiency of the two quenching mechanisms is substantially due to the existence of two different types of conical intersections between the excited and ground state potential energy surfaces of the reacting bimolecular system.

  8. Stochastic thermodynamics of chemical reaction networks.

    PubMed

    Schmiedl, Tim; Seifert, Udo

    2007-01-28

    For chemical reaction networks in a dilute solution described by a master equation, the authors define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction events. A first-law like energy balance relates internal energy, applied (chemical) work, and dissipated heat for every single reaction. Entropy production along a single trajectory involves a sum over changes in the entropy of the network itself and the entropy of the medium. The latter is given by the exchanged heat identified through the first law. Total entropy production is constrained by an integral fluctuation theorem for networks arbitrarily driven by time-dependent rates and a detailed fluctuation theorem for networks in the steady state. Further exact relations such as a generalized Jarzynski relation and a generalized Clausius inequality are discussed. The authors illustrate these results for a three-species cyclic reaction network which exhibits nonequilibrium steady states as well as transitions between different steady states.

  9. Novel tubing microreactor for monitoring chemical reactions.

    PubMed

    Nielsen, Charles A; Chrisman, Ray W; LaPointe, Robert E; Miller, Theodore E

    2002-07-01

    There is an expanding interest in small-scale methods to evaluate catalysts and chemical reactions at a variety of conditions, ranging up to 6.9 MPa (1000 psig) and 300 degrees C. Multiwell parallel batch techniques are most commonly applied in high-throughput screening systems. In contrast, we describe here a rapid, serial, highly controllable method based on LC-type steel tubing rated for high pressures. The tube, containing a variety of flowing ingredients, such as carrier solvents, catalyst formulations, and reactants, is self-heated ohmically using electrical current from a power supply monitored and regulated with a precision of 0.01%. An array of voltage taps arranged along its length serves to sense the real-time temperature profile of the tube. Reactions are seen as temperature pulses progressing through the reactor, in zones of 200 microL each, and tracked with a temperature precision of 0.1 degrees C. A unique pressure controller was devised to maintain constant reactor pressures despite effluent viscosity fluctuations due to polymerization. Several chemical reaction systems have been characterized to date, including decomposition reactions of di-tert-butyl peroxide, polymerizations of styrene, formation of polyethylene from ethylene, and copolymerization of ethylene with 1-octene. For ethylene polymerization, the amount of mass of polymer formed is proportional to the responses observed.

  10. Stochastic flux analysis of chemical reaction networks.

    PubMed

    Kahramanoğulları, Ozan; Lynch, James F

    2013-12-07

    Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.

  11. Stochastic flux analysis of chemical reaction networks

    PubMed Central

    2013-01-01

    Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

  12. Spatially organized dynamical states in chemical oscillator networks: synchronization, dynamical differentiation, and chimera patterns.

    PubMed

    Wickramasinghe, Mahesh; Kiss, István Z

    2013-01-01

    Dynamical processes in many engineered and living systems take place on complex networks of discrete dynamical units. We present laboratory experiments with a networked chemical system of nickel electrodissolution in which synchronization patterns are recorded in systems with smooth periodic, relaxation periodic, and chaotic oscillators organized in networks composed of up to twenty dynamical units and 140 connections. The reaction system formed domains of synchronization patterns that are strongly affected by the architecture of the network. Spatially organized partial synchronization could be observed either due to densely connected network nodes or through the 'chimera' symmetry breaking mechanism. Relaxation periodic and chaotic oscillators formed structures by dynamical differentiation. We have identified effects of network structure on pattern selection (through permutation symmetry and coupling directness) and on formation of hierarchical and 'fuzzy' clusters. With chaotic oscillators we provide experimental evidence that critical coupling strengths at which transition to identical synchronization occurs can be interpreted by experiments with a pair of oscillators and analysis of the eigenvalues of the Laplacian connectivity matrix. The experiments thus provide an insight into the extent of the impact of the architecture of a network on self-organized synchronization patterns.

  13. Chemical Reactions in a Sonoluminescing Bubble

    NASA Astrophysics Data System (ADS)

    Yasui, Kyuichi

    1997-09-01

    Rates of chemical reactions in an air bubble are calculatednumerically under a condition of the single-bubble sonoluminescence(SBSL) and that of non-light-emission. In the calculations, effect of non-equilibrium evaporation and condensationof water vapor at the bubble wall andthat of thermal conduction both inside and outside the bubbleare taken into account.Numerical calculations reveal that appreciable amounts of OH, H2O2, HO2, O3, H2, H, and O moleculesare created in a bubble under the condition of SBSL.The amounts of chemical products containing nitrogen such as NOx, NHx, and HNOx are much less than those of the above products at least in the first few acoustic cycles.Numerical calculations also reveal that no chemical reactionstake place under a condition of non-light-emission.Connection with sonoluminescence is also discussed.

  14. Chemical reactions in shear-free turbulence

    NASA Astrophysics Data System (ADS)

    de Bruyn Kops, Stephen M.; Riley, James J.

    2000-11-01

    Understanding and predicting the reaction of chemical species in shear-free turbulence is important in research addressing natural as well as technological problems. In the configuration considered here, two initially separated species mix and react downstream of a turbulence-generating grid in a wind tunnel. Results are reported from high resolution, direct numerical simulations in which the evolution of the conserved scalar field accurately matches that of the temperature field in existing laboratory experiments. Superimposed on the flow are passive, single-step, temperature-dependent reactions with a wide range of activation energies and stoichiometric ratios. Several aspects of the flow are investigated here with the conclusions that (1) reactions in which r ne 1 are more accurately modeled by frozen and equilibrium chemistry limits than are reactions in which r=1; (2) an existing definition of a reduced Damköhler number that includes temperature and stoichiometry effects is a very good measure of reaction rate; and (3) existing theoretical models for the coherence and phase of fuel-oxidizer cross-spectra and the spectrum of the equilibrium fuel mass fraction when r=1 yield accurate predictions. (Supported by NSF and AFOSR.)

  15. A new type of bromate oscillator: the bromate-iodide reaction in a stirred-flow reactor

    SciTech Connect

    Alamgir, M.; De Kepper, P.; Orban, M.; Epstein, I.R.

    1983-05-04

    Sustained oscillations and bistability have been observed in the reaction between bromate and iodide in acidic solution in a stirred tank reactor at 25/sup 0/C. This reaction appears to be the first bromate oscillator that requires a mechanism more analogous to that of chlorite oscillators than to that of other bromate systems such as the Belousov-Zhobotinskii reaction.

  16. The smallest chemical reaction system with bistability

    PubMed Central

    Wilhelm, Thomas

    2009-01-01

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

  17. Surface restructuring and kinetic oscillations in heterogeneous catalytic reactions

    NASA Astrophysics Data System (ADS)

    Zhdanov, V. P.

    1999-12-01

    We extend our earlier Monte Carlo simulations of isothermal kinetic oscillations in the NO-H2/Pt(100) system [V. P. Zhdanov, Phys. Rev. E 59, 6292 (1999)]. The analysis, based on a lattice-gas model describing surface restructuring in terms of the statistical theory of first-order phase transitions, is primarily focused on adsorbate-diffusion-mediated synchronization of oscillations. The conventional condition for synchronization, (Dτ)1/2>L (D is the diffusion coefficient, τ the oscillation period, and L the lattice size), is proved to considerably underestimate the role of surface diffusion. Due to the formation of mesoscopic islands, well developed oscillations are found to be possible in the cases when the left part of this condition is much lower than the right part.

  18. Chemical and radiation-chemical radical reactions in lignocellulose materials

    NASA Astrophysics Data System (ADS)

    Kuzina, Svetlana I.; Shilova, Irina A.; Mikhailov, Al'fa I.

    2011-09-01

    Chemical and radiation-chemical radical reactions in lignocellulose materials were explored by 3-cm and 2-mm ESR spectroscopy. Background (intrinsic) singlet signals at g=2.003 from wood pulp and lignin and those arising during reaction of lignocellulose materials with acids and chlorine were attributed to radicals with conjugated CC bonds. The 2-mm ESR signal with 3D anisotropy of g-factor from o-semiquinone radical ions formed in reaction of lignin with NaOH was recorded for the first time. The singlet signals derived from cellulose γ-irradiated at 77 K and marked out during post-thermal reactions were assigned to radicals with conjugated bonds. In wetted cellulose, a triplet signal with αβH≅2.7 mT and imposed quadruplet structure (0.5-0.7 mT) from three γ-protons was detected at 300 K and attributed to С 4-radicals. The triplet signals derived from С 2- and С 3-radicals in pyranose cycles of cellulose exhibited higher values of αβH (3.0-3.2 mT) and lower thermal stability (up to 250 K). In radiolyzed cotton pulp, detected were ESR signals derived from formyl radicals formed upon rupture of the С 5С 6 bond in pyranose cycles. Heating up irradiated samples under О 2 was accompanied by formation of peroxide radicals. Photoinduced recombination of trapped electrons with С 1-radicals was found to proceed as a chain reaction with a kinetic length of about 25 units. Photolysis ( λ≥360 nm) of radiolyzed cellulose enhanced the disclosure of pyranose cycles and, as a result, the evolution of CO 2 by a factor of 2-2.5.

  19. Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

    DTIC Science & Technology

    1989-09-01

    following six elemen- taxy reactions: (2.1) CH3CHO --> CH3 + CHO Acceso , " (2.2) CHO --> CO + H NTIS Cq-.’ d- (2.3) CH3 + CH3CHO --> CH4 + CH3CO (2.4) CH3CO...1981 [2] Feinberg, M. Chemical Oscillations, Multiple Equilibria, and Reaction Network Structure. In Dynamics and Modelling of Reactive Systems, W. E

  20. Effect of noise correlation on noise-induced oscillation frequency in the photosensitive Belousov-Zhabotinsky reaction in a continuous stirred tank reactor.

    PubMed

    Simakov, David S A; Pérez-Mercader, Juan

    2013-12-27

    We report on the experimental study of noise-induced oscillations in the photosensitive Ru(bpy)3(2+)-catalyzed Belousov-Zhabotinsky reaction in a continuous stirred tank reactor (CSTR). In the absence of deterministic oscillations and any external periodic forcing, oscillations appear when the system is perturbed by stochastic fluctuations in light irradiation with sufficiently high amplitude in the vicinity of the bifurcation point. The frequency distribution of the noise-induced oscillations is strongly affected by noise correlation. There is a shift of the noise-induced oscillation frequency toward higher frequencies for an intermediate range of the noise correlation exponent, indicating the occurrence of coherence resonance. Our findings indicate that, in principle, noise correlation can be used to direct chemical reactions toward certain behavior.

  1. Quantum dynamics of fast chemical reactions

    SciTech Connect

    Light, J.C.

    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.

  2. Chimera and phase-cluster states in populations of coupled chemical oscillators

    NASA Astrophysics Data System (ADS)

    Tinsley, Mark R.; Nkomo, Simbarashe; Showalter, Kenneth

    2012-09-01

    Populations of coupled oscillators may exhibit two coexisting subpopulations, one with synchronized oscillations and the other with unsynchronized oscillations, even though all of the oscillators are coupled to each other in an equivalent manner. This phenomenon, discovered about ten years ago in theoretical studies, was then further characterized and named the chimera state after the Greek mythological creature made up of different animals. The highly counterintuitive coexistence of coherent and incoherent oscillations in populations of identical oscillators, each with an equivalent coupling structure, inspired great interest and a flurry of theoretical activity. Here we report on experimental studies of chimera states and their relation to other synchronization states in populations of coupled chemical oscillators. Our experiments with coupled Belousov-Zhabotinsky oscillators and corresponding simulations reveal chimera behaviour that differs significantly from the behaviour found in theoretical studies of phase-oscillator models.

  3. [Laser enhanced chemical reaction studies]. [Progress report

    SciTech Connect

    Not Available

    1992-04-01

    Experimental studies of dynamic molecular processes are described with particular emphasis on the use of a powerful infrared diode laser probe technique developed in our laboratory. This technique allows us to determine the final states of CO{sub 2} (and other molecules) produced by collisions, photofragmentation, or chemical reactions with a spectral resolution of 0.0003 cm{sup {minus}1} and a time resolution of 10{sup {minus}7} sec. Such high spectral resolution provides a detailed picture of the vibrational and rotational states of molecules produced by these dynamic events. We have used this experimental method to probe collisions between hot hydrogen/deuterium atoms and CO{sub 2}, between O({sup 1}D) atoms and CO{sub 2}, to study the final states of DC1 molecules produced as a result of the reactions of hot Cl atoms, and to investigate the dynamics of the reaction between OH and CO molecules. Advances in our techniques over the past two years have allowed us to identify and study more than 200 final rotational states in ten different vibrational levels of CO{sub 2} encompassing all 3 normal modes, many overtones, and combination states of the molecule. We have extended the technique to probe a variety of new molecules such as OCS, N{sub 2}O, DCl, and CS{sub 2}. All of this work is aimed at providing experimental tests for polyatomic molecule potential energy surfaces, chemical transition states in complex systems, and theories of reaction dynamic in molecules with more than 3 atoms.

  4. Law of Localization in Chemical Reaction Networks

    NASA Astrophysics Data System (ADS)

    Okada, Takashi; Mochizuki, Atsushi

    2016-07-01

    In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g., metabolic pathways. Here we developed a theory to predict the sensitivity, i.e., the responses of concentrations and fluxes to perturbations of enzymes, from network structure alone. Nonzero response patterns turn out to exhibit two characteristic features, localization and hierarchy. We present a general theorem connecting sensitivity with network topology that explains these characteristic patterns. Our results imply that network topology is an origin of biological robustness. Finally, we suggest a strategy to determine real networks from experimental measurements.

  5. Depth oscillations of electronuclear reaction yield initiated by relativistic planar channeled electrons: quantum versus classical calculations

    NASA Astrophysics Data System (ADS)

    Eikhorn, Yu. L.; Korotchenko, K. B.; Pivovarov, Yu. L.; Tukhfatullin, T. A.

    2017-07-01

    The first experiment on electronuclear reaction initated by axially channeled 700 MeV electrons in a Si crystal [1] revealed remarkable depth oscillations of reaction yield. The effect was satisfactory explained [2] by computer simulations using binary collisions model. In this work the oscillations effect is investigated for planar channeled electrons in a Si crystal using the new computer code BCM-1.0 which allows both classical and quantum calculations of channeled electrons flux density.

  6. Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system

    PubMed Central

    Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

    2016-01-01

    The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion–fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies. PMID:26786848

  7. Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system.

    PubMed

    Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

    2016-01-20

    The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion-fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies.

  8. Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system

    NASA Astrophysics Data System (ADS)

    Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

    2016-01-01

    The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion-fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies.

  9. Strategies for chemical reaction searching in SciFinder

    PubMed

    Ridley

    2000-09-01

    The bibliographic, chemical structure, and chemical reaction databases produced by Chemical Abstracts Service allow a number of possibilities for chemical reaction searching. While these same databases may be searched through the STN network, many end-users find the intuitive software interface SciFinder simpler, but there still are issues to address. Searching may be performed through keywords, chemical structures, or chemical reactions, and the answers may vary with respect to precision and comprehension. Often combinations of search options may be needed to best solve the problem. Retrosynthetic analyses are easily performed in the chemical reaction database and can give unique insights into synthetic alternatives.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  12. Mathematical model of reaction rate oscillations on a chain of nm-sized catalyst particles

    NASA Astrophysics Data System (ADS)

    Peskov, N. V.; Slinko, M. M.; Jaeger, N. I.

    2003-05-01

    The model of reaction rate oscillations over the surface of nanoparticles embedded into zeolite matrix is numerically investigated. The reaction rate oscillations on each particle are described by a lumped model. The reactions on separate particles interact via the gas diffusion through the pores, which is modeled in the frame of the Maxwell-Stefan approach. The reaction reveals a complex dynamical behavior if a nonhomogeneous distribution of reagent concentrations exists along the chain of particles with a sufficiently large gradient near the ends of the chain.

  13. Autonomous Oscillation of Polymer Chains Induced by the Belousov–Zhabotinsky Reaction

    PubMed Central

    Hara, Yusuke; Takenaka, Yoshiko

    2014-01-01

    We investigated the self-oscillating behaviors of two types of polymer chains induced by the Belousov–Zhabotinsky (BZ) reaction. One consisted of N-isopropylacrylamide (NIPAAm) and the Ru catalyst of the BZ reaction, and the other consisted of NIPAAm, the Ru catalyst, and acrylamide-2-methylpropanesulfonic acid (AMPS) with a negatively charged domain as a solubility control site. A comparison of the two types of self-oscillation systems showed that the anionic AMPS portion of the polymer chain significantly affected the self-oscillating behavior under strongly acidic condition. The periods of self-oscillation for the two types of self-oscillating polymer chains were investigated by changing the initial concentrations of the three BZ substrates and the temperature. As a result, it was demonstrated that the period of self-oscillation could be controlled by the concentration of the BZ substrates and the temperature. Furthermore, the activation energies of the two types of the self-oscillating polymer chains gave similar values as normal BZ reactions, i.e., not including the self-oscillating polymer system with a Ru moiety. In addition, it was clarified the activation energy was hardly affected by the initial concentration of the three BZ substrates. PMID:24434841

  14. Autonomous oscillation of polymer chains induced by the Belousov-Zhabotinsky reaction.

    PubMed

    Hara, Yusuke; Takenaka, Yoshiko

    2014-01-15

    We investigated the self-oscillating behaviors of two types of polymer chains induced by the Belousov-Zhabotinsky (BZ) reaction. One consisted of N-isopropylacrylamide (NIPAAm) and the Ru catalyst of the BZ reaction, and the other consisted of NIPAAm, the Ru catalyst, and acrylamide-2-methylpropanesulfonic acid (AMPS) with a negatively charged domain as a solubility control site. A comparison of the two types of self-oscillation systems showed that the anionic AMPS portion of the polymer chain significantly affected the self-oscillating behavior under strongly acidic condition. The periods of self-oscillation for the two types of self-oscillating polymer chains were investigated by changing the initial concentrations of the three BZ substrates and the temperature. As a result, it was demonstrated that the period of self-oscillation could be controlled by the concentration of the BZ substrates and the temperature. Furthermore, the activation energies of the two types of the self-oscillating polymer chains gave similar values as normal BZ reactions, i.e., not including the self-oscillating polymer system with a Ru moiety. In addition, it was clarified the activation energy was hardly affected by the initial concentration of the three BZ substrates.

  15. pH oscillations in the BrO3--SO3(2-)/HSO3- reaction in a CSTR.

    PubMed

    Szantó, Tibor G; Rabai, Gyula

    2005-06-23

    Large-amplitude pH oscillations have been measured during the oxidation of sulfur (IV) species by the bromate ion in aqueous solution in a continuous-flow stirred tank reactor in the absence of any additional oxidizing or reducing reagent. The source of the oscillation in this simple chemical reaction is a two-way oxidation of sulfur (IV) by the bromate ion: (1) the hydrogen-ion-producing self-accelerating oxidation to sulfur (VI) (SO4(2-)), and (2) a hydrogen-ion-consuming oxidation to sulfur (V) (S2O6(2-)). In such a way, both the H+-producing and H+-consuming composite processes required for a pH oscillator take place in parallel in a reaction between two reagents in this system. A simple reaction scheme, consisting of the protonation equilibria of SO3(2-) and HSO3-, the oxidation of HSO3- and H2SO3 by BrO3- to SO4(2-), and the oxidation of H2SO3 to S2O6(2-) has successfully been used to simulate the observed dynamical behavior. Simulation with this simple scheme shows that oscillations can be calculated even if only about 1% of sulfur (IV) is oxidized to S2O6(2-) along with the main product SO4(2-). Agreement between calculated and measured dynamical behavior is found to be quite good. Increasing temperature decreases both the period length of oscillations in a CSTR and the Landolt time measured in a closed reactor. No temperature compensation of the oscillatory frequency is found in this reaction.

  16. Coexistence of wave propagation and oscillation in the photosensitive Belousov-Zhabotinsky reaction on a circular route.

    PubMed

    Nakata, Satoshi; Morishima, Sayaka; Ichino, Takatoshi; Kitahata, Hiroyuki

    2006-12-21

    The photosensitive Belousov-Zhabotinsky (BZ) reaction was investigated on a circular ring, which was drawn using computer software and then projected on a film soaked with BZ solution using a liquid-crystal projector. Under the initial conditions, a chemical wave propagated with a constant velocity on the black ring under a bright background. When the background was rapidly changed to dark, coexistence of the oscillation on part of the ring and propagation of the chemical wave on the other part was observed. These experimental results are discussed in relation to the nature of the photosensitive BZ reaction and theoretically reproduced based on a reaction-diffusion system using the modified Oregonator model.

  17. Quantum theory of chemical reaction rates

    SciTech Connect

    Miller, W.H. |

    1994-10-01

    If one wishes to describe a chemical reaction at the most detailed level possible, i.e., its state-to-state differential scattering cross section, then it is necessary to solve the Schroedinger equation to obtain the S-matrix as a function of total energy E and total angular momentum J, in terms of which the cross sections can be calculated as given by equation (1) in the paper. All other physically observable attributes of the reaction can be derived from the cross sections. Often, in fact, one is primarily interested in the least detailed quantity which characterizes the reaction, namely its thermal rate constant, which is obtained by integrating Eq. (1) over all scattering angles, summing over all product quantum states, and Boltzmann-averaging over all initial quantum states of reactants. With the proper weighting factors, all of these averages are conveniently contained in the cumulative reaction probability (CRP), which is defined by equation (2) and in terms of which the thermal rate constant is given by equation (3). Thus, having carried out a full state-to-state scattering calculation to obtain the S-matrix, one can obtain the CRP from Eq. (2), and then rate constant from Eq. (3), but this seems like ``overkill``; i.e., if one only wants the rate constant, it would clearly be desirable to have a theory that allows one to calculate it, or the CRP, more directly than via Eq. (2), yet also correctly, i.e., without inherent approximations. Such a theory is the subject of this paper.

  18. Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity.

    PubMed

    Himeoka, Yusuke; Kaneko, Kunihiko

    2016-04-05

    Cells generally convert nutrient resources to products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although these processes occur under conditions of dynamic metabolism, most studies of cellular thermodynamic efficiency have been restricted to examining steady states; thus, the relevance of dynamics to this efficiency has not yet been elucidated. Here, we develop a simple model of metabolic reactions with anabolism-catabolism coupling catalyzed by enzymes. Through application of external oscillation in the enzyme abundances, the thermodynamic efficiency of metabolism was found to be improved. This result is in strong contrast with that observed in the oscillatory input, in which the efficiency always decreased with oscillation. This improvement was effectively achieved by separating the anabolic and catabolic reactions, which tend to disequilibrate each other, and taking advantage of the temporal oscillations so that each of the antagonistic reactions could progress near equilibrium. In this case, anti-phase oscillation between the reaction flux and chemical affinity through oscillation of enzyme abundances is essential. This improvement was also confirmed in a model capable of generating autonomous oscillations in enzyme abundances. Finally, the possible relevance of the improvement in thermodynamic efficiency is discussed with respect to the potential for manipulation of metabolic oscillations in microorganisms.

  19. Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity

    NASA Astrophysics Data System (ADS)

    Himeoka, Yusuke; Kaneko, Kunihiko

    2016-04-01

    Cells generally convert nutrient resources to products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although these processes occur under conditions of dynamic metabolism, most studies of cellular thermodynamic efficiency have been restricted to examining steady states; thus, the relevance of dynamics to this efficiency has not yet been elucidated. Here, we develop a simple model of metabolic reactions with anabolism-catabolism coupling catalyzed by enzymes. Through application of external oscillation in the enzyme abundances, the thermodynamic efficiency of metabolism was found to be improved. This result is in strong contrast with that observed in the oscillatory input, in which the efficiency always decreased with oscillation. This improvement was effectively achieved by separating the anabolic and catabolic reactions, which tend to disequilibrate each other, and taking advantage of the temporal oscillations so that each of the antagonistic reactions could progress near equilibrium. In this case, anti-phase oscillation between the reaction flux and chemical affinity through oscillation of enzyme abundances is essential. This improvement was also confirmed in a model capable of generating autonomous oscillations in enzyme abundances. Finally, the possible relevance of the improvement in thermodynamic efficiency is discussed with respect to the potential for manipulation of metabolic oscillations in microorganisms.

  20. Chemical communication and dynamics of droplet emulsions in networks of Belousov-Zhabotinsky micro-oscillators produced by microfluidics.

    PubMed

    Torbensen, Kristian; Rossi, Federico; Ristori, Sandra; Abou-Hassan, Ali

    2017-03-29

    Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes. Droplets can thus be regarded as single units, able to generate chemical messengers that diffuse in the environment and hence can interact with other compartments. The Belousov-Zhabotinsky (BZ) reaction is a well-known chemical oscillator largely used as a model for complex nonlinear phenomena, including chemical, physical and biological examples. When the BZ-reaction is encapsulated inside microcompartments, its chemical intermediates can serve as messengers by diffusing among different microcompartments, to trigger specific reactions leading to a collective behavior between the elements. The geometry and constitution of the diffusion pathways play an important role in governing the collective behaviour of the system. In this context, microfluidics is not only a versatile tool for mastering the encapsulation process of the BZ-reaction in monodisperse microcompartments, but also for creating geometries and networks with well defined boundaries. The individual compartments can be engineered with selected properties using different surfactants in the case of simple emulsions, or with specific membrane properties in the case of liposomes. Furthermore, it enables the arrangement of these microcompartments in various geometric configurations, where the diffusive coupling pathways between individual compartments are both spatially and chemically well-defined. In this tutorial paper, we review a

  1. Multistable Phase Patterns of Spatially Structured Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Giver, Michael; Goldstein, Daniel; Chakraborty, Bulbul

    2014-03-01

    Recent experiments of two-dimensional microfluidic arrays of droplets containing Belousov-Zhabotinsky reactants show a rich variety of spatio-temporal patterns. Using optical techniques a variety of boundary conditions can be set within the system, including finite rings of droplets. These experiments have provided an interesting and easily reproducible system for probing the effects of nonlinearities and fluctuations in a spatially extended system. Motivated by this experimental set up, we study a simple model of chemical oscillators in the highly nonlinear excitable regime in order to gain insight into the mechanism giving rise to the observed multistable attractors. We map the attractor space of a simple two species activator-inhibitor model coupled via three different coupling mechanism: simple inhibitor diffusion, inhibitor diffusion through an inhomogenous medium where active droplets are separated by inactive holding cells, and coupling through diffusion of an inert signaling species, which arrises through a coarse graining of the inhomogenous medium. Once the attractor space of the mean-field level model has been mapped, we check the robustness of the attractors when subject to intrinsic noise.

  2. Solving moment hierarchies for chemical reaction networks

    NASA Astrophysics Data System (ADS)

    Krishnamurthy, Supriya; Smith, Eric

    2017-10-01

    The study of chemical reaction networks (CRN’s) is a very active field. Earlier well-known results (Feinberg 1987 Chem. Enc. Sci. 42 2229, Anderson et al 2010 Bull. Math. Biol. 72 1947) identify a topological quantity called deficiency, for any CRN, which, when exactly equal to zero, leads to a unique factorized steady-state for these networks. No results exist however for the steady states of non-zero-deficiency networks. In this paper, we show how to write the full moment-hierarchy for any non-zero-deficiency CRN obeying mass-action kinetics, in terms of equations for the factorial moments. Using these, we can recursively predict values for lower moments from higher moments, reversing the procedure usually used to solve moment hierarchies. We show, for non-trivial examples, that in this manner we can predict any moment of interest, for CRN’s with non-zero deficiency and non-factorizable steady states.

  3. Extracting Chemical Reactions from Biological Literature

    DTIC Science & Technology

    2014-05-16

    noun   phrase , and prepositional  phrase ) are relevant to the  reaction. An extremely general top down pattern may match any sentence that contains these...illuminates an important aspect of our pattern­based  approach . Patterns are designed to capture commonalities in  phrases  used to describe chemical...limitations in our  approach  and outline future works (Section 7) before concluding.  2. Related Works  Semantic relationship extraction is the task of

  4. Identification of two-step chemical mechanisms using small temperature oscillations and a single tagged species

    NASA Astrophysics Data System (ADS)

    Closa, F.; Gosse, C.; Jullien, L.; Lemarchand, A.

    2015-05-01

    In order to identify two-step chemical mechanisms, we propose a method based on a small temperature modulation and on the analysis of the concentration oscillations of a single tagged species involved in the first step. The thermokinetic parameters of the first reaction step are first determined. Then, we build test functions that are constant only if the chemical system actually possesses some assumed two-step mechanism. Next, if the test functions plotted using experimental data are actually even, the mechanism is attributed and the obtained constant values provide the rate constants and enthalpy of reaction of the second step. The advantage of the protocol is to use the first step as a probe reaction to reveal the dynamics of the second step, which can hence be relieved of any tagging. The protocol is anticipated to apply to many mechanisms of biological relevance. As far as ligand binding is considered, our approach can address receptor conformational changes or dimerization as well as competition with or modulation by a second partner. The method can also be used to screen libraries of untagged compounds, relying on a tracer whose concentration can be spectroscopically monitored

  5. Silicon-based sleeve devices for chemical reactions

    DOEpatents

    Northrup, M.A.; Mariella, R.P. Jr.; Carrano, A.V.; Balch, J.W.

    1996-12-31

    A silicon-based sleeve type chemical reaction chamber is described that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis. 32 figs.

  6. Silicon-based sleeve devices for chemical reactions

    DOEpatents

    Northrup, M. Allen; Mariella, Jr., Raymond P.; Carrano, Anthony V.; Balch, Joseph W.

    1996-01-01

    A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

  7. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models.

    PubMed

    Liberman, M A; Kiverin, A D; Ivanov, M F

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  8. Regimes of chemical reaction waves initiated by nonuniform initial conditions for detailed chemical reaction models

    NASA Astrophysics Data System (ADS)

    Liberman, M. A.; Kiverin, A. D.; Ivanov, M. F.

    2012-05-01

    Regimes of chemical reaction wave propagation initiated by initial temperature nonuniformity in gaseous mixtures, whose chemistry is governed by chain-branching kinetics, are studied using a multispecies transport model and a detailed chemical model. Possible regimes of reaction wave propagation are identified for stoichiometric hydrogen-oxygen and hydrogen-air mixtures in a wide range of initial pressures and temperature levels, depending on the initial non-uniformity steepness. The limits of the regimes of reaction wave propagation depend upon the values of the spontaneous wave speed and the characteristic velocities of the problem. It is shown that one-step kinetics cannot reproduce either quantitative neither qualitative features of the ignition process in real gaseous mixtures because the difference between the induction time and the time when the exothermic reaction begins significantly affects the ignition, evolution, and coupling of the spontaneous reaction wave and the pressure wave, especially at lower temperatures. We show that all the regimes initiated by the temperature gradient occur for much shallower temperature gradients than predicted by a one-step model. The difference is very large for lower initial pressures and for slowly reacting mixtures. In this way the paper provides an answer to questions, important in practice, about the ignition energy, its distribution, and the scale of the initial nonuniformity required for ignition in one or another regime of combustion wave propagation.

  9. Dual-frequency oscillations induced by acidity in Belousov-Zhabotinskii reactions with aldosugars as substrates

    NASA Astrophysics Data System (ADS)

    Li, Hexing; Jin, Ronghua; Dai, Weilin; Deng, Jingfa

    1997-08-01

    Depending on the initial concentration of H 2SO 4, two types of dual-frequency oscillations have been observed in Belousov-Zhabotinskii type reactions catalyzed by Mn 2+ with acetone and aldosugars (arabinose, glucose, galactose, lactose or maltose) as coupled substrates in a batch reactor. No such dual-frequency oscillations have been found when a ketosugar like fructose was used instead of an aldosugar as the substrate; or acetone was replaced by N 2 flow. No oscillations were observed when Ce 3+ was used instead of Mn 2+. The reaction products of aldosugars in different oscillating regimes have been analyzed. The dual-frequency oscillatory patterns have been discussed according to the roles of the substrates and their derivatives formed at different acidity.

  10. Plasmon-driven sequential chemical reactions in an aqueous environment.

    PubMed

    Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

    2014-06-24

    Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H(+) in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight.

  11. Plasmon-driven sequential chemical reactions in an aqueous environment

    PubMed Central

    Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

    2014-01-01

    Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H+ in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight. PMID:24958029

  12. Plasmon-driven sequential chemical reactions in an aqueous environment

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Wang, Peijie; Zhang, Zhenglong; Fang, Yurui; Sun, Mengtao

    2014-06-01

    Plasmon-driven sequential chemical reactions were successfully realized in an aqueous environment. In an electrochemical environment, sequential chemical reactions were driven by an applied potential and laser irradiation. Furthermore, the rate of the chemical reaction was controlled via pH, which provides indirect evidence that the hot electrons generated from plasmon decay play an important role in plasmon-driven chemical reactions. In acidic conditions, the hot electrons were captured by the abundant H+ in the aqueous environment, which prevented the chemical reaction. The developed plasmon-driven chemical reactions in an aqueous environment will significantly expand the applications of plasmon chemistry and may provide a promising avenue for green chemistry using plasmon catalysis in aqueous environments under irradiation by sunlight.

  13. The effect of flow rate on the oscillatory activation energy of an oscillating reaction

    NASA Astrophysics Data System (ADS)

    Monteiro, Emily V.; Varela, Hamilton; Faria, Roberto B.

    2017-09-01

    The simultaneous influence of temperature and flow rate (k0) in the oscillatory regime of the bromate-oxalic acid-acetone-Ce(III) oscillating reaction was investigated. The influence of temperature was evaluated in terms of the oscillatory activation energy (Eω), which was determined at different flow rates. Increasing k0, the oscillatory activation energy is decreased, tending to a limit value, Eω∞. The sensitivity of Eω with k0 is described by the parameter η = dEω/d(1/k0). Eω∞ and η are global properties of any particular oscillating reaction and describes a correlation between the dynamical behavior and temperature, and should be used when comparing different oscillating reactions.

  14. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    PubMed

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  15. Heterogeneous chemical reactions: Preparation of monodisperse latexes

    NASA Technical Reports Server (NTRS)

    Vanderhoff, J. W.; Micale, F. J.; El-Aasser, M. S.; Sterk, A. A.; Bethke, G. W.

    1977-01-01

    It is demonstrated that a photoinitiated emulsion polymerization can be carried out to a significant conversion in a SPAR rocket prototype polymerization vessel within the six minutes allowed for the experiment. The percentage of conversion was determined by both dilatometry and gravimetric methods with good agreement. The experimental results lead to the following conclusions: (1) emulsion polymerizations can be carried out to conversions as high as 75%, using a stable micellized styrene-SLS system plus photoinitiator; (2) dilatometry can be used to accurately determine both the rate and conversion of polymerization; (3) thermal expansion due to the light source and heat of reaction is small and can be corrected for if necessary; (4) although seeded emulsion polymerizations are unfavorable in photoinitiation, as opposed to chemical initiation, polymerizations can be carried out to at least 15% conversion using 7940A seed particles, with 0.05% solids; and (5) photoinitiation should be used to initiate polymerization in the SPAR rocket experiments because of the mechanical simplicity of the experiment.

  16. Reaction rate oscillations during catalytic CO oxidation: A brief overview

    NASA Astrophysics Data System (ADS)

    Tsotsis, T. T.; Sane, R. C.

    1987-04-01

    It is not the intent here to present a comprehensive review of the dynamic behavior of the catalytic oxidation of CO. This reaction is one of the most widely studied in the field of catalysis. A review paper by Engel and Ertl has examined the basic kinetic and mechanistic aspects, and a comprehensive paper by Razon and Schmitz was recently devoted to its dynamic behavior. Those interested in further study of the subject should consult these reviews and a number of general review papers on catalytic reaction dynamics. The goal is to present a brief overview of certain interesting aspects of the dynamic behavior of this reaction and to discuss a few questions and issues, which are still the subject of study and debate.

  17. Reaction rate oscillations during catalytic CO oxidation: A brief overview

    NASA Technical Reports Server (NTRS)

    Tsotsis, T. T.; Sane, R. C.

    1987-01-01

    It is not the intent here to present a comprehensive review of the dynamic behavior of the catalytic oxidation of CO. This reaction is one of the most widely studied in the field of catalysis. A review paper by Engel and Ertl has examined the basic kinetic and mechanistic aspects, and a comprehensive paper by Razon and Schmitz was recently devoted to its dynamic behavior. Those interested in further study of the subject should consult these reviews and a number of general review papers on catalytic reaction dynamics. The goal is to present a brief overview of certain interesting aspects of the dynamic behavior of this reaction and to discuss a few questions and issues, which are still the subject of study and debate.

  18. Spectroscopy and reactions of molecules important in chemical evolution

    NASA Technical Reports Server (NTRS)

    Becker, R. S.

    1974-01-01

    The research includes: (1) hot hydrogen atom reactions in terms of the nature of products produced, mechanism of the reactions and the implication and application of such reactions for molecules existing in interstellar clouds, in planetary atmospheres, and in chemical evolution; (2) photochemical reactions that can lead to molecules important in chemical evolution, interstellar clouds and as constituents in planetary atmospheres; and (3) spectroscopic and theoretical properties of biomolecules and their precursors and where possible, use these to understand their photochemical behavior.

  19. GREEN CHEMICAL SYNTHESIS THROUGH CATALYSIS AND ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    Green chemical synthesis through catalysis and alternate reaction conditions

    Encompassing green chemistry techniques and methodologies, we have initiated several projects at the National Risk Management Research laboratory that focus on the design and development of chemic...

  20. Prediction and Prevention of Chemical Reaction Hazards: Learning by Simulation.

    ERIC Educational Resources Information Center

    Shacham, Mordechai; Brauner, Neima; Cutlip, Michael B.

    2001-01-01

    Points out that chemical hazards are the major cause of accidents in chemical industry and describes a safety teaching approach using a simulation. Explains a problem statement on exothermic liquid-phase reactions. (YDS)

  1. GREEN CHEMICAL SYNTHESIS THROUGH CATALYSIS AND ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    Green chemical synthesis through catalysis and alternate reaction conditions

    Encompassing green chemistry techniques and methodologies, we have initiated several projects at the National Risk Management Research laboratory that focus on the design and development of chemic...

  2. Prediction and Prevention of Chemical Reaction Hazards: Learning by Simulation.

    ERIC Educational Resources Information Center

    Shacham, Mordechai; Brauner, Neima; Cutlip, Michael B.

    2001-01-01

    Points out that chemical hazards are the major cause of accidents in chemical industry and describes a safety teaching approach using a simulation. Explains a problem statement on exothermic liquid-phase reactions. (YDS)

  3. Shaking Catalysts Accelerating Chemical Reaction in Micro Reactors

    NASA Astrophysics Data System (ADS)

    Suzumori, Koichi; Nagata, Takashi; Kanda, Takefumi; Sakata, Yusaku; Muto, Akinori

    Efficient uniform mixing is an essential process for chemical reaction. However, it is difficult to fabricate many tiny stirrers on reactor chips. This paper shows a new method promoting high-efficient chemical reaction in micro chamber. To stir chemicals and to accelerate reaction catalytic particles are driven electrostatically in micro chamber. Two driving methods have been evaluated; AC drive and DC drive. Evaluation of chemical reactions revealed the effect of this developed devices. In addition conveyance system of catalytic particles is necessary for particles exchange.

  4. Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations

    PubMed Central

    Baum, Katharina; Kofahl, Bente; Steuer, Ralf; Wolf, Jana

    2016-01-01

    Oscillations occur in a wide variety of cellular processes, for example in calcium and p53 signaling responses, in metabolic pathways or within gene-regulatory networks, e.g. the circadian system. Since it is of central importance to understand the influence of perturbations on the dynamics of these systems a number of experimental and theoretical studies have examined their robustness. The period of circadian oscillations has been found to be very robust and to provide reliable timing. For intracellular calcium oscillations the period has been shown to be very sensitive and to allow for frequency-encoded signaling. We here apply a comprehensive computational approach to study the robustness of period and amplitude of oscillatory systems. We employ different prototype oscillator models and a large number of parameter sets obtained by random sampling. This framework is used to examine the effect of three design principles on the sensitivities towards perturbations of the kinetic parameters. We find that a prototype oscillator with negative feedback has lower period sensitivities than a prototype oscillator relying on positive feedback, but on average higher amplitude sensitivities. For both oscillator types, the use of Michaelis-Menten instead of mass action kinetics in all degradation and conversion reactions leads to an increase in period as well as amplitude sensitivities. We observe moderate changes in sensitivities if replacing mass conversion reactions by purely regulatory reactions. These insights are validated for a set of established models of various cellular rhythms. Overall, our work highlights the importance of reaction kinetics and feedback type for the variability of period and amplitude and therefore for the establishment of predictive models. PMID:28027301

  5. Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations.

    PubMed

    Baum, Katharina; Politi, Antonio Z; Kofahl, Bente; Steuer, Ralf; Wolf, Jana

    2016-12-01

    Oscillations occur in a wide variety of cellular processes, for example in calcium and p53 signaling responses, in metabolic pathways or within gene-regulatory networks, e.g. the circadian system. Since it is of central importance to understand the influence of perturbations on the dynamics of these systems a number of experimental and theoretical studies have examined their robustness. The period of circadian oscillations has been found to be very robust and to provide reliable timing. For intracellular calcium oscillations the period has been shown to be very sensitive and to allow for frequency-encoded signaling. We here apply a comprehensive computational approach to study the robustness of period and amplitude of oscillatory systems. We employ different prototype oscillator models and a large number of parameter sets obtained by random sampling. This framework is used to examine the effect of three design principles on the sensitivities towards perturbations of the kinetic parameters. We find that a prototype oscillator with negative feedback has lower period sensitivities than a prototype oscillator relying on positive feedback, but on average higher amplitude sensitivities. For both oscillator types, the use of Michaelis-Menten instead of mass action kinetics in all degradation and conversion reactions leads to an increase in period as well as amplitude sensitivities. We observe moderate changes in sensitivities if replacing mass conversion reactions by purely regulatory reactions. These insights are validated for a set of established models of various cellular rhythms. Overall, our work highlights the importance of reaction kinetics and feedback type for the variability of period and amplitude and therefore for the establishment of predictive models.

  6. Classification of chemical reactions and chemoinformatic processing of enzymatic transformations.

    PubMed

    Latino, Diogo A R S; Aires-de-Sousa, João

    2011-01-01

    The automatic perception of chemical similarities between chemical reactions is required for a variety of applications in chemistry and connected fields, namely with databases of metabolic reactions. Classification of enzymatic reactions is required, e.g., for genome-scale reconstruction (or comparison) of metabolic pathways, computer-aided validation of classification systems, or comparison of enzymatic mechanisms. This chapter presents different current approaches for the representation of chemical reactions enabling automatic reaction classification. Representations based on the encoding of the reaction center are illustrated, which use physicochemical features, Reaction Classification (RC) numbers, or Condensed Reaction Graphs (CRG). Representation of differences between the structures of products and reactants include reaction signatures, fingerprint differences, and the MOLMAP approach. The approaches are illustrated with applications to real datasets.

  7. New Possibilities for Magnetic Control of Chemical and Biochemical Reactions.

    PubMed

    Buchachenko, Anatoly; Lawler, Ronald G

    2017-02-20

    Chemistry is controlled by Coulomb energy; magnetic energy is lower by many orders of magnitude and may be confidently ignored in the energy balance of chemical reactions. The situation becomes less clear, however, when reaction rates are considered. In this case, magnetic perturbations of nearly degenerate energy surface crossings may produce observable, and sometimes even dramatic, effects on reactions rates, product yields, and spectroscopic transitions. A case in point that has been studied for nearly five decades is electron spin-selective chemistry via the intermediacy of radical pairs. Magnetic fields, external (permanent or oscillating) and the internal magnetic fields of magnetic nuclei, have been shown to overcome electron spin selection rules for pairs of reactive paramagnetic intermediates, catalyzing or inhibiting chemical reaction pathways. The accelerating effects of magnetic stimulation may therefore be considered to be magnetic catalysis. This type of catalysis is most commonly observed for reactions of a relatively long-lived radical pair containing two weakly interacting electron spins formed by dissociation of molecules or by electron transfer. The pair may exist in singlet (total electron spin is zero) or triplet (total spin is unity) spin states. In virtually all cases, only the singlet state yields stable reaction products. Magnetic interactions with nuclear spins or applied fields may therefore affect the reactivity of radical pairs by changing the angular momentum of the pairs. Magnetic catalysis, first detected via its effect on spin state populations in nuclear and electron spin resonance, has been shown to function in a great variety of well-characterized reactions of organic free radicals. Considerably less well studied are examples suggesting that the basic mechanism may also explain magnetic effects that stimulate ATP synthesis, eliminating ATP deficiency in cardiac diseases, control cell proliferation, killing cancer cells, and

  8. Semiclassical methods in chemical reaction dynamics

    SciTech Connect

    Keshavamurthy, Srihari

    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.

  9. Incidents of chemical reactions in cell equipment

    SciTech Connect

    Baldwin, N.M.; Barlow, C.R.

    1991-12-31

    Strongly exothermic reactions can occur between equipment structural components and process gases under certain accident conditions in the diffusion enrichment cascades. This paper describes the conditions required for initiation of these reactions, and describes the range of such reactions experienced over nearly 50 years of equipment operation in the US uranium enrichment program. Factors are cited which can promote or limit the destructive extent of these reactions, and process operations are described which are designed to control the reactions to minimize equipment damage, downtime, and the possibility of material releases.

  10. Transient complex oscillations in a closed chemical system with coupled autocatalysis

    NASA Astrophysics Data System (ADS)

    Zhao, Jinpei; Chen, Yu; Wang, Jichang

    2005-03-01

    In this study, hydroquinone was introduced to the classic Belousov-Zhabotinsky (BZ) reaction to build up coupled autocatalytic feedbacks. Various complex dynamical behaviors including successive period-adding bifurcations, irregular oscillations, and frequency modulations were observed in the coupled reaction system. Not only the complexity of oscillations but also the time period during which complex oscillations persist were found to depend greatly on the initial concentration of hydroquinone, which was expected to manifest the coupling strength in the studied system. Dependence of the observed transient complex oscillations on concentrations of ferroin, sulfuric acid, bromate, and malonic acid was also characterized systematically. Numerical simulations with a modified BZ model via incorporating reactions involving hydroquinone and products of hydroquinone qualitatively reproduced the influence of hydroquinone seen in experiments.

  11. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1990-01-01

    The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.

  12. Chemical Looping Combustion Reactions and Systems

    SciTech Connect

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2014-03-01

    , they performed a sensitivity analysis for velocity, height and polydispersity and compared results against literature data for experimental studies of CLC beds with no reaction. Finally, they present an optimization space using simple non-reactive configurations. In Subtask 5.3, through a series of experimental studies, behavior of a variety of oxygen carriers with different loadings and manufacturing techniques was evaluated under both oxidizing and reducing conditions. The influences of temperature, degree of carrier conversion and thermodynamic driving force resulting from the difference between equilibrium and system O{sub 2} partial pressures were evaluated through several experimental campaigns, and generalized models accounting for these influences were developed to describe oxidation and oxygen release. Conversion of three solid fuels with widely ranging reactivities was studied in a small fluidized bed system, and all but the least reactive fuel (petcoke) were rapidly converted by oxygen liberated from the CLOU carrier. Attrition propensity of a variety of carriers was also studied, and the carriers produced by freeze granulation or impregnation of preformed substrates displayed the lowest rates of attrition. Subtask 5.4 focused on gathering kinetic data for a copper-based oxygen carrier to assist with modeling of a functioning chemical looping reactor. The kinetics team was also responsible for the development and analysis of supported copper oxygen carrier material.

  13. Chemical Demonstrations with Consumer Chemicals: The Black and White Reaction.

    ERIC Educational Resources Information Center

    Wright, Stephen W.

    2002-01-01

    Describes a dramatic chemical demonstration in which chemicals that are black and white combine to produce a colorless liquid. Reactants include tincture of iodine, bleach, white vinegar, Epsom salt, vitamin C tablets, and liquid laundry starch. (DDR)

  14. Chemical Demonstrations with Consumer Chemicals: The Black and White Reaction.

    ERIC Educational Resources Information Center

    Wright, Stephen W.

    2002-01-01

    Describes a dramatic chemical demonstration in which chemicals that are black and white combine to produce a colorless liquid. Reactants include tincture of iodine, bleach, white vinegar, Epsom salt, vitamin C tablets, and liquid laundry starch. (DDR)

  15. Carbon dioxide evolution in a Belousov-Zhabotinsky type oscillating reaction with acetonedicarboxylic acid.

    PubMed

    Sevcík, Peter; Misicák, Daniel; Adamcíková, L'ubica

    2007-10-11

    Oscillations in the platinum redox potential during the reaction of bromate ions with acetonedicarboxylic acid catalyzed by Mn(II) ions were observed. The volume of gaseous carbon dioxide produced was measured. A nonoscillatory course was found both at the slow and rapid stirring rates for carbon dioxide evolution. The perturbation experiments suggest supersaturation during the Belousov-Zhabotinsky reaction with acetonedicarboxylic acid. Possible reasons for such observations are discussed.

  16. Experimental Evidence of Localized Oscillations in the Photosensitive Chlorine Dioxide-Iodine-Malonic Acid Reaction

    NASA Astrophysics Data System (ADS)

    Míguez, David G.; Alonso, Sergio; Muñuzuri, Alberto P.; Sagués, Francesc

    2006-10-01

    The interaction between Hopf and Turing modes has been the subject of active research in recent years. We present here experimental evidence of the existence of mixed Turing-Hopf modes in a two-dimensional system. Using the photosensitive chlorine dioxide-iodine-malonic acid reaction (CDIMA) and external constant background illumination as a control parameter, standing spots oscillating in amplitude and with hexagonal ordering were observed. Numerical simulations in the Lengyel-Epstein model for the CDIMA reaction confirmed the results.

  17. Stereodynamics: From elementary processes to macroscopic chemical reactions

    SciTech Connect

    Kasai, Toshio; Che, Dock-Chil; Tsai, Po-Yu; Lin, King-Chuen; Palazzetti, Federico; Aquilanti, Vincenzo

    2015-12-31

    This paper aims at discussing new facets on stereodynamical behaviors in chemical reactions, i.e. the effects of molecular orientation and alignment on reactive processes. Further topics on macroscopic processes involving deviations from Arrhenius behavior in the temperature dependence of chemical reactions and chirality effects in collisions are also discussed.

  18. Chemical kinetics computer program for static and flow reactions

    NASA Technical Reports Server (NTRS)

    Bittker, D. A.; Scullin, V. J.

    1972-01-01

    General chemical kinetics computer program for complex gas mixtures has been developed. Program can be used for any homogeneous reaction in either one dimensional flow or static system. It is flexible, accurate, and easy to use. It can be used for any chemical system for which species thermodynamic data and reaction rate constant data are known.

  19. Demonstrating Energy Migration in Coupled Oscillators: A Central Concept in the Theory of Unimolecular Reactions

    ERIC Educational Resources Information Center

    Marcotte, Ronald E.

    2005-01-01

    This physical chemistry lecture demonstration is designed to aid the understanding of intramolecular energy transfer processes as part of the presentation of the theory of unimolecular reaction rates. Coupled pendulums are used to show the rate of migration of energy between oscillators under resonant and nonresonant conditions with varying…

  20. Demonstrating Energy Migration in Coupled Oscillators: A Central Concept in the Theory of Unimolecular Reactions

    ERIC Educational Resources Information Center

    Marcotte, Ronald E.

    2005-01-01

    This physical chemistry lecture demonstration is designed to aid the understanding of intramolecular energy transfer processes as part of the presentation of the theory of unimolecular reaction rates. Coupled pendulums are used to show the rate of migration of energy between oscillators under resonant and nonresonant conditions with varying…

  1. Negative Temperature Coefficient in Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Leenson, I. A.; Sergeev, Gleb B.

    1984-05-01

    A systematic analysis of reactions whose rate decreases with increase of temperature is presented. The possibility of a negative temperature coefficient in the elementary reactions is examined from the standpoint of the transition state theory and of collision theory. The mechanisms of complex reactions in which the temperature dependence of the rate is anomalous are discussed, and possible reasons for the anomaly are examined. The bibliography contains 175 references.

  2. Mesoscale simulations of shockwave energy dissipation via chemical reactions.

    PubMed

    Antillon, Edwin; Strachan, Alejandro

    2015-02-28

    We use a particle-based mesoscale model that incorporates chemical reactions at a coarse-grained level to study the response of materials that undergo volume-reducing chemical reactions under shockwave-loading conditions. We find that such chemical reactions can attenuate the shockwave and characterize how the parameters of the chemical model affect this behavior. The simulations show that the magnitude of the volume collapse and velocity at which the chemistry propagates are critical to weaken the shock, whereas the energetics in the reactions play only a minor role. Shock loading results in transient states where the material is away from local equilibrium and, interestingly, chemical reactions can nucleate under such non-equilibrium states. Thus, the timescales for equilibration between the various degrees of freedom in the material affect the shock-induced chemistry and its ability to attenuate the propagating shock.

  3. Chemical and genomic evolution of enzyme-catalyzed reaction networks.

    PubMed

    Kanehisa, Minoru

    2013-09-02

    There is a tendency that a unit of enzyme genes in an operon-like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway. Our recent analysis shows that this and other genomic units correspond to chemical units reflecting chemical logic of organic reactions. From all known metabolic pathways in the KEGG database we identified chemical units, called reaction modules, as the conserved sequences of chemical structure transformation patterns of small molecules. The extracted patterns suggest co-evolution of genomic units and chemical units. While the core of the metabolic network may have evolved with mechanisms involving individual enzymes and reactions, its extension may have been driven by modular units of enzymes and reactions. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  4. Versatile Dual Photoresponsive System for Precise Control of Chemical Reactions.

    PubMed

    Xu, Can; Bing, Wei; Wang, Faming; Ren, Jinsong; Qu, Xiaogang

    2017-08-22

    A versatile method for photoregulation of chemical reactions was developed through a combination of near-infrared (NIR) and ultraviolet (UV) light sensitive materials. This regulatory effect was achieved through photoresponsive modulation of reaction temperature and pH values, two prominent factors influencing reaction kinetics. Photothermal nanomaterial graphene oxide (GO) and photobase reagent malachite green carbinol base (MGCB) were selected for temperature and pH regulation, respectively. Using nanocatalyst- and enzyme-mediated chemical reactions as model systems, we demonstrated the feasibility and high efficiency of this method. In addition, a photoresponsive, multifunctional "Band-aid"-like hydrogel platform was presented for programmable wound healing. Overall, this simple, efficient, and reversible system was found to be effective for controlling a wide variety of chemical reactions. Our work may provide a method for remote and sustainable control over chemical reactions for industrial and biomedical applications.

  5. Synchronization of Cell Cycle Oscillator by Multi-pulse Chemical Perturbations

    NASA Astrophysics Data System (ADS)

    Lin, Yihan; Li, Ying; Dinner, Aaron; Scherer, Norbert

    2011-03-01

    Oscillators underlie biological rhythms in various organisms and provide a timekeeping mechanism. Cell cycle oscillator, for example, controls the progression of cell cycle stage and drives cyclic reproduction in both prokaryotes and eukaryotes. The understanding of the underlying nonlinear regulatory network allows experimental design of external perturbations to interact and control cell cycle oscillation. We have previously demonstrated in experiment and in simulation that the cell cycle coherence of a model bacterium can be progressively tuned by the level of a histidine kinase. Here, we present our recent effort to synchronize the division of a population of bacterium cells by external pulsatile chemical perturbations. We were able to synchronize the cell population by phase-locking approach: the external oscillator (i.e. periodic perturbation) entrains the internal cell cycle oscillator which is in analogous to the phase-locking of circadian clock to external light/dark oscillator. We explored the ranges of frequencies for two external oscillators of different amplitudes where phase-locking occurred. To our surprise, non-periodic chemical perturbations could also cause synchronization of a cell population, suggesting a Markovian cell cycle oscillation dynamics.

  6. Steric Control of Complex Chemical Reactions

    DTIC Science & Technology

    2014-05-31

    reactants. When the infrared (IR) laser was directed in the source chamber to excite the methane reactants, we probed the stereodynamics by...The reaction of Cl + CH4 is of great importance in atmosphere chemistry as being a primary competing process to the ozone -hole catalytic reaction

  7. An Analysis of the Algebraic Method for Balancing Chemical Reactions.

    ERIC Educational Resources Information Center

    Olson, John A.

    1997-01-01

    Analyzes the algebraic method for balancing chemical reactions. Introduces a third general condition that involves a balance between the total amount of oxidation and reduction. Requires the specification of oxidation states for all elements throughout the reaction. Describes the general conditions, the mathematical treatment, redox reactions, and…

  8. Chemical redox reactions in ES-MS: Study of electrode reactions

    SciTech Connect

    Zhou, Feimeng; VAn Berkel, G.J.

    1995-12-31

    The authors previously demonstrated that chemical redox reactions can be used to ionize neutral commpounds for electrospray mass spectrometric (ES-MS) detection. Two different compounds, viz, C{sub 60}F{sub 48} and {beta}-carotene were used to demonstrate the utility of chemical redox reactions with on-line ES-MS for the elucidation of mechanisms of complicated electron transfer reactions and for the kinetic study of electrode reactions in which relatively short-lived intermediates are involved.

  9. Formal modeling of a system of chemical reactions under uncertainty.

    PubMed

    Ghosh, Krishnendu; Schlipf, John

    2014-10-01

    We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

  10. The How and Why of Chemical Reactions

    ERIC Educational Resources Information Center

    Schubert, Leo

    1970-01-01

    Presents a discussion of some of the fundamental concepts in thermodynamics and quantum mechanics including entropy, enthalpy, free energy, the partition function, chemical kinetics, transition state theory, the making and breaking of chemical bonds, electronegativity, ion sizes, intermolecular energies and of their role in explaining the nature…

  11. FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

  12. The How and Why of Chemical Reactions

    ERIC Educational Resources Information Center

    Schubert, Leo

    1970-01-01

    Presents a discussion of some of the fundamental concepts in thermodynamics and quantum mechanics including entropy, enthalpy, free energy, the partition function, chemical kinetics, transition state theory, the making and breaking of chemical bonds, electronegativity, ion sizes, intermolecular energies and of their role in explaining the nature…

  13. FACILITATED CHEMICAL SYNTHESIS UNDER ALTERNATE REACTION CONDITIONS

    EPA Science Inventory

    The chemical research in the late 1990's witnessed a paradigm shift towards "environmentally-friendly chemistry" more popularly known as "green chemistry" due to the increasing environmental concerns and legislative requirements to curb the release of chemical waste into the atmo...

  14. Modular verification of chemical reaction network encodings via serializability analysis.

    PubMed

    Lakin, Matthew R; Stefanovic, Darko; Phillips, Andrew

    2016-06-13

    Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a "commit reaction" that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of "extra tolerance", which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited.

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

    NASA Astrophysics Data System (ADS)

    Yang, Xueming

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

  16. Chemical Reaction Experiment for the Undergraduate Laboratory.

    ERIC Educational Resources Information Center

    Kwon, K. C.; And Others

    1987-01-01

    Provides an overview of an experiment on reaction kinetics of the anthracene-hydrogen system. Includes a description of the laboratory equipment, procedures, and data analysis requirements. Points out the advantages of the recommended technique. (ML)

  17. Kinetics of Chemical Reactions in Flames

    NASA Technical Reports Server (NTRS)

    Zeldovich, Y.; Semenov, N.

    1946-01-01

    In part I of the paper the theory of flame propagation is developed along the lines followed by Frank-Kamenetsky and one of the writers. The development of chain processes in flames is considered. A basis is given for the application of the method of stationary concentrations to reactions in flames; reactions with branching chains are analyzed. The case of a diffusion coefficient different from the coefficient of temperature conductivity is considered.

  18. Chemical tailoring of teicoplanin with site-selective reactions.

    PubMed

    Pathak, Tejas P; Miller, Scott J

    2013-06-05

    Semisynthesis of natural product derivatives combines the power of fermentation with orthogonal chemical reactions. Yet, chemical modification of complex structures represents an unmet challenge, as poor selectivity often undermines efficiency. The complex antibiotic teicoplanin eradicates bacterial infections. However, as resistance emerges, the demand for improved analogues grows. We have discovered chemical reactions that achieve site-selective alteration of teicoplanin. Utilizing peptide-based additives that alter reaction selectivities, certain bromo-teicoplanins are accessible. These new compounds are also scaffolds for selective cross-coupling reactions, enabling further molecular diversification. These studies enable two-step access to glycopeptide analogues not available through either biosynthesis or rapid total chemical synthesis alone. The new compounds exhibit a spectrum of activities, revealing that selective chemical alteration of teicoplanin may lead to analogues with attenuated or enhanced antibacterial properties, in particular against vancomycin- and teicoplanin-resistant strains.

  19. An autonomous organic reaction search engine for chemical reactivity

    PubMed Central

    Dragone, Vincenza; Sans, Victor; Henson, Alon B.; Granda, Jaroslaw M.; Cronin, Leroy

    2017-01-01

    The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways. PMID:28598440

  20. An autonomous organic reaction search engine for chemical reactivity

    NASA Astrophysics Data System (ADS)

    Dragone, Vincenza; Sans, Victor; Henson, Alon B.; Granda, Jaroslaw M.; Cronin, Leroy

    2017-06-01

    The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways.

  1. An autonomous organic reaction search engine for chemical reactivity.

    PubMed

    Dragone, Vincenza; Sans, Victor; Henson, Alon B; Granda, Jaroslaw M; Cronin, Leroy

    2017-06-09

    The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways.

  2. Flow-distributed oscillations: Stationary chemical waves in a reacting flow

    NASA Astrophysics Data System (ADS)

    Kærn, Mads; Menzinger, Michael

    1999-10-01

    A recent prediction of stationary waves in open, reacting flows is experimentally verified. We show that stationary waves are generated by a mechanism whereby the flow carries a time-oscillating subelement, behaving like a batch reactor, through space while a fixed boundary condition at the inflow locks the phase of the oscillation. This mechanism can generate stationary patterns when all diffusion coefficients are equal. The experimental system is the ferroin-catalyzed Belousov-Zhabotinsky reaction in a tubular reactor, fed by the outflow of a continuous flow stirred tank reactor (CSTR). Parameter conditions are such that the concentrations are constant in the CSTR while they oscillate in the flow tube.

  3. Modular verification of chemical reaction network encodings via serializability analysis

    PubMed Central

    Lakin, Matthew R.; Stefanovic, Darko; Phillips, Andrew

    2015-01-01

    Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a “commit reaction” that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of “extra tolerance”, which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited. PMID:27325906

  4. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.

    1992-01-01

    The work on the NH + NO system which was described in the last progress report was written up and a draft of the manuscript is included in the appendix. The appendix also contains a draft of a manuscript on an Ar + H + H surface. New work which was completed in the last six months includes the following: (1) calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction; (2) calculations for the NH2 + O reaction; (3) calculations for the CH3 + O2 reaction; and (4) calculations for CH3O and the two decomposition channels--CH2OH and H + H2CO. Detailed descriptions of this work will be given in manuscripts; however, brief descriptions of the CH3 + OH and CH3 + O2 projects are given.

  5. Morphological changes of amphiphilic molecular assemblies induced by chemical reactions.

    PubMed

    Nakagawa, Koh M; Noguchi, Hiroshi

    2015-02-04

    Shape transformations of amphiphilic molecular assemblies induced by chemical reactions are studied using coarse-grained molecular simulations. A binding reaction between hydrophilic and hydrophobic molecules is considered. It is found that the reaction induces transformation of an oil droplet to a tubular vesicle via bicelles and vesicles with discoidal arms. The discoidal arms close into vesicles, which are subsequently fused into the tubular vesicle. Under the chemical reaction, the bicelle-to-vesicle transition occurs at smaller sizes than in the absence of the hydrophobic molecules. It is revealed that the enhancement of this transition is due to embedded hydrophobic particles that reduce the membrane bending rigidity.

  6. Non-equilibrium effects in high temperature chemical reactions

    NASA Technical Reports Server (NTRS)

    Johnson, Richard E.

    1987-01-01

    Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

  7. Communication: Control of chemical reactions using electric field gradients.

    PubMed

    Deshmukh, Shivaraj D; Tsori, Yoav

    2016-05-21

    We examine theoretically a new idea for spatial and temporal control of chemical reactions. When chemical reactions take place in a mixture of solvents, an external electric field can alter the local mixture composition, thereby accelerating or decelerating the rate of reaction. The spatial distribution of electric field strength can be non-trivial and depends on the arrangement of the electrodes producing it. In the absence of electric field, the mixture is homogeneous and the reaction takes place uniformly in the reactor volume. When an electric field is applied, the solvents separate and the reactants are concentrated in the same phase or separate to different phases, depending on their relative miscibility in the solvents, and this can have a large effect on the kinetics of the reaction. This method could provide an alternative way to control runaway reactions and to increase the reaction rate without using catalysts.

  8. Developing Secondary Students' Conceptions of Chemical Reactions: The Introduction of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Van Driel, Jan H.; De Vos, Wobbe; Verloop, Nico; Dekkers, Hetty

    1998-01-01

    Describes an empirical study concerning the introduction of the concept of chemical equilibrium in chemistry classrooms in a way which challenges students' initial conceptions of chemical reactions. Contains 23 references. (DDR)

  9. Developing Secondary Students' Conceptions of Chemical Reactions: The Introduction of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Van Driel, Jan H.; De Vos, Wobbe; Verloop, Nico; Dekkers, Hetty

    1998-01-01

    Describes an empirical study concerning the introduction of the concept of chemical equilibrium in chemistry classrooms in a way which challenges students' initial conceptions of chemical reactions. Contains 23 references. (DDR)

  10. Mineralization of hazardous chemicals by heme reaction

    SciTech Connect

    Kang, G.; Jung, J.; Park, K.; Stevens, D.K.

    1995-12-31

    The catalytic degradation of pentachlorophenol contaminated soil by heme and hydrogen peroxide has been reported. Here we studied evidence for the mechanism and mineralization by the heme catalyzed reaction for hazardous organopollutants. Ferryl heme radical and non-radical ferryl heme were generated rapidly by the interaction of heme and hydrogen peroxide (H{sub 2}O{sub 2}). The activated heme radical could initiate the oxidation of 5-aminosalicylic acid (5-ASA). The reactions by heme with H{sub 2}O{sub 2} could support the redox cycling between the ferryl species of heme and 5-ASA as the mechanistic routes of the heme catalyzed reaction. Hazardous compounds such as pentachlorophenol, phenanthrene and benzota[a]pyrene were mineralized 20, 6, and 7%, respectively, with 30 mM heme and 1500 mM H{sub 2}O{sub 2} after 24 hr reaction. This catalyzed degradation of organopollutants could be used as a novel technology for hazardous waste remediation.

  11. Steric Control of Complex Chemical Reactions - 1

    DTIC Science & Technology

    2011-12-26

    their contrasting behaviors upon vibrational and translational excitations can serve as benchmark for gaining deeper insights into polyatomic reaction...equipped with a uniquely designed ion velocity map imaging detector capable of measuring the product pair correlation. The ultrafast femtosecond laser...From A + BC to Polyatomic Systems” K. Liu, Adv. in Chem. Phys. 149, (in press). Invited Review Invited talks at Conferences (* denoting

  12. A chemometric method to identify enzymatic reactions leading to the transition from glycolytic oscillations to waves

    NASA Astrophysics Data System (ADS)

    Zimányi, László; Khoroshyy, Petro; Mair, Thomas

    2010-06-01

    In the present work we demonstrate that FTIR-spectroscopy is a powerful tool for the time resolved and noninvasive measurement of multi-substrate/product interactions in complex metabolic networks as exemplified by the oscillating glycolysis in a yeast extract. Based on a spectral library constructed from the pure glycolytic intermediates, chemometric analysis of the complex spectra allowed us the identification of many of these intermediates. Singular value decomposition and multiple level wavelet decomposition were used to separate drifting substances from oscillating ones. This enabled us to identify slow and fast variables of glycolytic oscillations. Most importantly, we can attribute a qualitative change in the positive feedback regulation of the autocatalytic reaction to the transition from homogeneous oscillations to travelling waves. During the oscillatory phase the enzyme phosphofructokinase is mainly activated by its own product ADP, whereas the transition to waves is accompanied with a shift of the positive feedback from ADP to AMP. This indicates that the overall energetic state of the yeast extract determines the transition between spatially homogeneous oscillations and travelling waves.

  13. Femtosecond Diffraction and Spectroscopy of Chemical Reactions

    DTIC Science & Technology

    2008-03-31

    bifurcation into phytical and chemical channels, redefines structural dynamics of the energy landscape in radiationless processes. Paper 6. In this... acid bilayers. In 4DUEM we are now able, using timed single-electron packets, to image nano-to-micro scale structures of materials and biological

  14. Experiments on Rate of Chemical Reactions.

    ERIC Educational Resources Information Center

    United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand).

    This laboratory manual, part of a series of instruction books on basic experimental chemistry, is designed to provide the secondary school students of developing countries in Asia with laboratory experiences that bring out the fundamental concepts and ideas of chemical kinetics. Taking into consideration the possibility of limited facilities of…

  15. Force-activated reactivity switch in a bimolecular chemical reaction.

    PubMed

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

    2009-06-01

    The effect of mechanical force on the free-energy surface that governs a chemical reaction is largely unknown. The combination of protein engineering with single-molecule force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by nucleophiles in a bimolecular substitution reaction (S(N)2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity 'switch' at ∼500 pN, after which the accelerating effect of force on the rate of an S(N)2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in S(N)2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule.

  16. 29. NORTHWEST VIEW OF BOILER FEEDWATER CHEMICAL REACTION TANKS, WITH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    29. NORTHWEST VIEW OF BOILER FEEDWATER CHEMICAL REACTION TANKS, WITH FORMER GENERAL OFFICE BUILDING IN BACKGROUND. - U.S. Steel Duquesne Works, Fuel & Utilities Plant, Along Monongahela River, Duquesne, Allegheny County, PA

  17. Solvent-starved conditions in confinement cause chemical oscillations excited by passage of a cathodic delamination front.

    PubMed

    Iqbal, Danish; Sarfraz, Adnan; Stratmann, Martin; Erbe, Andreas

    2015-11-18

    After passage of a delamination front at a polymer/zinc interface, pH oscillations and oscillations in the quantity of corrosion products are observed. The reason for these oscillations is the low quantity of water in the confined reaction volume, water consumption by oxygen reduction, and water regeneration after precipitation of ZnO.

  18. Computed Potential Energy Surfaces for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A manuscript describing the calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction, which were described in the last progress report, has been accepted for publication in J. Chem. Phys., and a copy of the manuscript is included in the appendix. The production of (1)CH2 in this reaction is important in hydrocarbon combustion since (1)CH2 is highly reactive and would be expected to insert into N2, possibly leading to a new source for prompt NO(x) (vide infra). During the last six months new calculations have been carried out for the NH2 + NO system, which is important in the thermal de-NO(x) process.

  19. Nucleic Acid Templated Reactions for Chemical Biology.

    PubMed

    Di Pisa, Margherita; Seitz, Oliver

    2017-06-21

    Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  20. Chemical reactions simulated by ground-water-quality models

    USGS Publications Warehouse

    Grove, David B.; Stollenwerk, Kenneth G.

    1987-01-01

    Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

  1. Ferroin-induced complex oscillations in the bromate-hydroquinone photochemical reaction.

    PubMed

    Li, Nan; Wang, Jichang

    2009-06-04

    This study presents an experimental investigation on the dynamics of the ferroin-bromate-hydroquinone photoreaction, in which two isolated oscillatory regimes emerge due to the presence of ferroin. Oscillations within the two isolated regimes exhibit different dependence on light intensity and initial compositions of the reaction solution. A phase diagram outlining the occurrence of the new oscillatory regime has been established in the bromate-ferroin concentration plane. As opposed to the ferroin-free system, in which there is nearly no difference in the reaction behavior whether benzoquinone or hydroquinone is used as the starting reactant, here the two-staged oscillatory behavior can only be obtained with hydroquinone as the initial reagent. This observation suggests that the reduction of ferriin by hydroquinone and the autocatalytic oxidation of ferroin by acidic bromate may have played a major role in the new oscillation window.

  2. Colloidal Assemblies Effect on Chemical Reactions.

    DTIC Science & Technology

    1986-07-01

    MICROEMULSIONS - SURFACTANTS - OXIDATION - PHOTOCATALYSIS - DEGRADATION - HALOAROMATIC COMPOUNDS - REACTION MECHANISM - KINETICS 20. ABmT’AcT (cthwe - 0...phase model accounting for the observed rate constants was proposed. The complexing and extracting properties of a functionalized surfactant family...micelles were studied. The proper conditions for an efficient iron(III) complexation and extraction were determined. SECURY C - fa ;c --r 2 - SECURITY

  3. Chemical reactions of organic compounds on clay surfaces.

    PubMed Central

    Soma, Y; Soma, M

    1989-01-01

    Chemical reactions of organic compounds including pesticides at the interlayer and exterior surfaces of clay minerals and with soil organic matter are reviewed. Representative reactions under moderate conditions possibly occurring in natural soils are described. Attempts have been made to clarify the importance of the chemical nature of molecules, their structures and their functional groups, and the Brönsted or Lewis acidity of clay minerals. PMID:2533556

  4. Coherent Radiative Control of Chemical Reactions

    DTIC Science & Technology

    1992-01-01

    effective were determined and successful control was displayed using a model of Stilbene isomerization. F. Control over Chemically Distinct Products...than, the stilbene molecule for which Si(t>to) = Ia(to)Il14ru-(I’ f = 1, II11 (3) there is a vast array of data available art for which...mechanical o calculation of ground and first excited electronic potential surfaces _o for trans- and cis- stilbene . To minimize computational cost we 0

  5. Phase Waves in Oscillatory Chemical Reactions.

    DTIC Science & Technology

    number of waves emitted from a center of heterogeneous catalysis , the rate of wave emission. the lifetime of each wave, the asymptotic wave pattern, the...A theory is presented for the effect of heterogeneity on an oscillatory chemically reactive system in a stable limit cycle such as in heterogeneous ... catalysis . A perturbation technique is developed free of secular behavior for the solution of the non-linear partial differential equations. The

  6. Modelling of chemical reactions in plasma

    NASA Astrophysics Data System (ADS)

    Aktaev, N. E.; Remnev, G. E.; Yalovets, A. P.

    2017-01-01

    The paper is devoted to theoretical investigation of interaction of pulsed high current electron beam with gas substance. As a result of the interaction the formation of chemical active plasma can be observed. One of the key parameter for theoretical analyze of the process is the electron distribution function. Within the framework of the Boltzmann approach we obtained the dynamical equation for electron distribution function depending on the electron energy, coordinate and time.

  7. Quantifying chemical reactions by using mixing analysis.

    PubMed

    Jurado, Anna; Vázquez-Suñé, Enric; Carrera, Jesús; Tubau, Isabel; Pujades, Estanislao

    2015-01-01

    This work is motivated by a sound understanding of the chemical processes that affect the organic pollutants in an urban aquifer. We propose an approach to quantify such processes using mixing calculations. The methodology consists of the following steps: (1) identification of the recharge sources (end-members) and selection of the species (conservative and non-conservative) to be used, (2) identification of the chemical processes and (3) evaluation of mixing ratios including the chemical processes. This methodology has been applied in the Besòs River Delta (NE Barcelona, Spain), where the River Besòs is the main aquifer recharge source. A total number of 51 groundwater samples were collected from July 2007 to May 2010 during four field campaigns. Three river end-members were necessary to explain the temporal variability of the River Besòs: one river end-member is from the wet periods (W1) and two are from dry periods (D1 and D2). This methodology has proved to be useful not only to compute the mixing ratios but also to quantify processes such as calcite and magnesite dissolution, aerobic respiration and denitrification undergone at each observation point.

  8. Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

    PubMed

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-12

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  9. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

    NASA Astrophysics Data System (ADS)

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-11-01

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

  10. Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

    PubMed Central

    Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

    2014-01-01

    Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism. PMID:25387603

  11. Accelerated Chemical Reactions and Organic Synthesis in Leidenfrost Droplets.

    PubMed

    Bain, Ryan M; Pulliam, Christopher J; Thery, Fabien; Cooks, R Graham

    2016-08-22

    Leidenfrost levitated droplets can be used to accelerate chemical reactions in processes that appear similar to reaction acceleration in charged microdroplets produced by electrospray ionization. Reaction acceleration in Leidenfrost droplets is demonstrated for a base-catalyzed Claisen-Schmidt condensation, hydrazone formation from precharged and neutral ketones, and for the Katritzky pyrylium into pyridinium conversion under various reaction conditions. Comparisons with bulk reactions gave intermediate acceleration factors (2-50). By keeping the volume of the Leidenfrost droplets constant, it was shown that interfacial effects contribute to acceleration; this was confirmed by decreased reaction rates in the presence of a surfactant. The ability to multiplex Leidenfrost microreactors, to extract product into an immiscible solvent during reaction, and to use Leidenfrost droplets as reaction vessels to synthesize milligram quantities of product is also demonstrated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Plasmonic smart dust for probing local chemical reactions.

    PubMed

    Tittl, Andreas; Yin, Xinghui; Giessen, Harald; Tian, Xiang-Dong; Tian, Zhong-Qun; Kremers, Christian; Chigrin, Dmitry N; Liu, Na

    2013-04-10

    Locally probing chemical reactions or catalytic processes on surfaces under realistic reaction conditions has remained one of the main challenges in materials science and heterogeneous catalysis. Where conventional surface interrogation techniques usually require high-vacuum conditions or ensemble average measurements, plasmonic nanoparticles excel in extreme light focusing and can produce highly confined electromagnetic fields in subwavelength volumes without the need for complex near-field microscopes. Here, we demonstrate an all-optical probing technique based on plasmonic smart dust for monitoring local chemical reactions in real time. The silica shell-isolated gold nanoparticles that form the smart dust can work as strong light concentrators and optically report subtle environmental changes at their pinning sites on the probed surface during reaction processes. As a model system, we investigate the hydrogen dissociation and subsequent uptake trajectory in palladium with both "dust-on-film" and "film-on-dust" platforms. Using time-resolved single particle measurements, we demonstrate that our technique can in situ encode chemical reaction information as optical signals for a variety of surface morphologies. The presented technique offers a unique scheme for real-time, label-free, and high-resolution probing of local reaction kinetics in a plethora of important chemical reactions on surfaces, paving the way toward the development of inexpensive and high-output reaction sensors for real-world applications.

  13. Is the simplest chemical reaction really so simple?

    PubMed

    Jankunas, Justin; Sneha, Mahima; Zare, Richard N; Bouakline, Foudhil; Althorpe, Stuart C; Herráez-Aguilar, Diego; Aoiz, F Javier

    2014-01-07

    Modern computational methods have become so powerful for predicting the outcome for the H + H2 → H2 + H bimolecular exchange reaction that it might seem further experiments are not needed. Nevertheless, experiments have led the way to cause theorists to look more deeply into this simplest of all chemical reactions. The findings are less simple.

  14. Is the simplest chemical reaction really so simple?

    PubMed Central

    Jankunas, Justin; Sneha, Mahima; Zare, Richard N.; Bouakline, Foudhil; Althorpe, Stuart C.; Herráez-Aguilar, Diego; Aoiz, F. Javier

    2014-01-01

    Modern computational methods have become so powerful for predicting the outcome for the H + H2 → H2 + H bimolecular exchange reaction that it might seem further experiments are not needed. Nevertheless, experiments have led the way to cause theorists to look more deeply into this simplest of all chemical reactions. The findings are less simple. PMID:24367084

  15. Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

    ERIC Educational Resources Information Center

    Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.

    2011-01-01

    Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

  16. Understanding Chemical Reaction Kinetics and Equilibrium with Interlocking Building Blocks

    ERIC Educational Resources Information Center

    Cloonan, Carrie A.; Nichol, Carolyn A.; Hutchinson, John S.

    2011-01-01

    Chemical reaction kinetics and equilibrium are essential core concepts of chemistry but are challenging topics for many students, both at the high school and undergraduate university level. Visualization at the molecular level is valuable to aid understanding of reaction kinetics and equilibrium. This activity provides a discovery-based method to…

  17. Chemical reactions driven by concentrated solar energy

    NASA Astrophysics Data System (ADS)

    Levy, Moshe

    Solar energy can be used for driving endothermic reactions, either photochemically or thermally. The fraction of the solar spectrum that can be photochemically active is quite small. Therefore, it is desirable to be able to combine photochemical and thermal processes in order to increase the overall efficiency. Two thermally driven reactions are being studied: oil shale gasification and methane reforming. In both cases, the major part of the work was done in opaque metal reactors where photochemical reactions cannot take place. We then proceeded working in transparent quartz reactors. The results are preliminary, but they seem to indicate that there may be some photochemical enhancement. The experimental solar facilities used for this work include the 30 kW Schaeffer Solar Furnace and the 3 MW Solar Central Receiver in operation at the Weizmann Institute. The furnace consists of a 96 sq. m flat heliostat, that follows the sun by computer control. It reflects the solar radiation onto a spherical concentrator, 7.3 m in diameter, with a rim angle of 65 degrees. The furnace was characterized by radiometric and calorimetric measurements to show a solar concentration ratio of over 10,000 suns. The central receiver consists of 64 concave heliostats, 54 sq. m each, arranged in a north field and facing a 52 m high tower. The tower has five target levels that can be used simultaneously. The experiments with the shale gasification were carried out at the lowest level, 20 m above ground, which has the lowest solar efficiency and is assigned for low power experiments. We used secondary concentrators to boost the solar flux.

  18. Design and development of computer-aided chemical systems: representation and balance of inorganic chemical reactions

    PubMed

    Ruiz; Martinez-Pedrajas; Gomez-Nieto

    2000-05-01

    A model for the tracking of inorganic chemical reactions is proposed. Designed to acquire, process, and solve a great number of inorganic reactions, this model will hopefully contribute to the development of powerful computer-aided chemistry teaching systems for use within or without the environment of a virtual laboratory. Using full representation of an inorganic reaction to allow the extraction of chemical knowledge, incomplete reactions (where species are absent) may be completed by adding the necessary species, and reactions may be solved and balanced. Various types of reaction are classified, and a layer-based model is defined for the solution of different reaction types, establishing the basis for the construction of a system which, based on a wide set of production rules, is capable of solving an incomplete inorganic chemical reaction.

  19. Chemical Reactions in Turbulent Mixing Flows.

    DTIC Science & Technology

    1987-06-01

    soot particles are also often formed at the reaction interface, so the feasibility study was intenced to determine whether the two sources of particles...buoyancy effects (i.e. gravity is ipored). it can be shown that the disturbance eigentunction , satisfies the equation .0 .....o ... P I ./Pl...34 * (o’’o) *’t [a" U L" + I ’ U’/g ""* where ( )’ corresponds to d/dy. The equation * above reduces to the Rayleigh equation when the -4.0 d ensity is

  20. Laser cutting with chemical reaction assist

    SciTech Connect

    Gettemy, D.J.

    1991-04-08

    This invention is comprised of a method for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation.

  1. Laser cutting with chemical reaction assist

    DOEpatents

    Gettemy, D.J.

    1992-11-17

    A method is described for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation. 1 figure.

  2. Laser cutting with chemical reaction assist

    DOEpatents

    Gettemy, Donald J.

    1992-01-01

    A method for cutting with a laser beam where an oxygen-hydrocarbon reaction is used to provide auxiliary energy to a metal workpiece to supplement the energy supplied by the laser. Oxygen is supplied to the laser focus point on the workpiece by a nozzle through which the laser beam also passes. A liquid hydrocarbon is supplied by coating the workpiece along the cutting path with the hydrocarbon prior to laser irradiation or by spraying a stream of hydrocarbon through a nozzle aimed at a point on the cutting path which is just ahead of the focus point during irradiation.

  3. The Regenerative chemiluminescence of ruthenium complexes in self-Oscillating reactions

    SciTech Connect

    Karavaev, A.D.; Kazakov, V.P.; Khokhlova, N.L.; Tolstikov, G.A.; Yakshin, V.V.

    1985-09-20

    A method for the activation of chemiluminescence intensity is discussed; the method involves the use of an avtivator which itself undergoes cyclic oxidation-reduction transformations resulting in chemical excitation and constant regeneration in the system. The authors feel that it is specifically this process which provides for the strong amplification in the CL intensity upon the addition of tris-w,w'-dapprox. =pyridylrutheium (DPR) in the self-oscillation oxidation of malonic acid by bromate catalyzed by cerium or manganese ions.

  4. Results of the 2010 Survey on Teaching Chemical Reaction Engineering

    ERIC Educational Resources Information Center

    Silverstein, David L.; Vigeant, Margot A. S.

    2012-01-01

    A survey of faculty teaching the chemical reaction engineering course or sequence during the 2009-2010 academic year at chemical engineering programs in the United States and Canada reveals change in terms of content, timing, and approaches to teaching. The report consists of two parts: first, a statistical and demographic characterization of the…

  5. Results of the 2010 Survey on Teaching Chemical Reaction Engineering

    ERIC Educational Resources Information Center

    Silverstein, David L.; Vigeant, Margot A. S.

    2012-01-01

    A survey of faculty teaching the chemical reaction engineering course or sequence during the 2009-2010 academic year at chemical engineering programs in the United States and Canada reveals change in terms of content, timing, and approaches to teaching. The report consists of two parts: first, a statistical and demographic characterization of the…

  6. Modelling Chemical Reasoning to Predict and Invent Reactions.

    PubMed

    Segler, Marwin H S; Waller, Mark P

    2016-11-11

    The ability to reason beyond established knowledge allows organic chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chemical reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph containing 14.4 million molecules and 8.2 million binary reactions, which represents the bulk of all chemical reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalysed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery.

  7. Elementary reaction modeling of solid oxide electrolysis cells: Main zones for heterogeneous chemical/electrochemical reactions

    NASA Astrophysics Data System (ADS)

    Li, Wenying; Shi, Yixiang; Luo, Yu; Cai, Ningsheng

    2015-01-01

    A theoretical model of solid oxide electrolysis cells considering the heterogeneous elementary reactions, electrochemical reactions and the transport process of mass and charge is applied to study the relative performance of H2O electrolysis, CO2 electrolysis and CO2/H2O co-electrolysis and the competitive behavior of heterogeneous chemical and electrochemical reactions. In cathode, heterogeneous chemical reactions exist near the outside surface and the electrochemical reactions occur near the electrolyte. According to the mathematical analysis, the mass transfer flux D ∇c determines the main zone size of heterogeneous chemical reactions, while the charge transfer flux σ ∇V determines the other one. When the zone size of heterogeneous chemistry is enlarged, more CO2 could react through heterogeneous chemical pathway, and polarization curves of CO2/H2O co-electrolysis could be prone to H2O electrolysis. Meanwhile, when the zone size of electrochemistry is enlarged, more CO2 could react through electrochemical pathway, and polarization curves of CO2/H2O co-electrolysis could be prone to CO2 electrolysis. The relative polarization curves, the ratio of CO2 participating in electrolysis and heterogeneous chemical reactions, the mass and charge transfer flux and heterogeneous chemical/electrochemical reaction main zones are simulated to study the effects of cathode material characteristics (porosity, particle diameter and ionic conductivity) and operating conditions (gas composition and temperature).

  8. Effect of gravity on human spontaneous 10-Hz electroencephalographic oscillations during the arrest reaction.

    PubMed

    Cheron, G; Leroy, A; De Saedeleer, C; Bengoetxea, A; Lipshits, M; Cebolla, A; Servais, L; Dan, B; Berthoz, A; McIntyre, J

    2006-11-22

    Electroencephalographic oscillations at 10 Hz (alpha and mu rhythms) are the most prominent rhythms observed in awake, relaxed (eye-closed) subjects. These oscillations may be considered as a marker of cortical inactivity or an index of the active inhibition of the sensory information. Different cortical sources may participate in the 10-Hz oscillation and appear to be modulated by the sensory context and functional demands. In microgravity, the marked reduction in multimodal graviceptive inputs to cortical networks participating in the representation of space could be expected to affect the 10-Hz activity. The effect of microgravity on this basic oscillation has heretofore not been studied quantitatively. Because the alpha rhythm has a functional role in the regulation of network properties of the visual areas, we hypothesised that the absence of gravity would affect its strength. Here, we report the results of an experiment conducted over the course of 3 space flights, in which we quantified the power of the 10-Hz activity in relation to the arrest reaction (i.e., in 2 distinct physiological states: eyes open and eyes closed). We observed that the power of the spontaneous 10-Hz oscillation recorded in the eyes-closed state in the parieto-occipital (alpha rhythm) and sensorimotor areas (mu rhythm) increased in the absence of gravity. The suppression coefficient during the arrest reaction and the related spectral perturbations produced by eye-opening/closure state transition also increased in on orbit. These results are discussed in terms of current theories on the source and the importance of the alpha rhythm for cognitive function.

  9. Chemical reactions on solid surfaces using molecular beam techniques

    NASA Astrophysics Data System (ADS)

    Palmer, R. L.

    1980-07-01

    Thermal energy molecular beams have been used to study chemical interactions with metal surfaces. Chemisorption of simple molecules such as H2, O2, CH4, C2Hx and CO was investigated on single and polycrystalline surfaces of Pt, Ni, Co, and Ag. Kinetic parameters and reaction mechanisms were determined for model catalytic reactions including CO and C2Hx oxidation and methanation from H2/CO mixtures. Chemical reactions of NOx with CO and D2 on Pt(111) and other surfaces have been surveyed and the kinetics of NO and O2 chemisorption have been measured. The theory of adsorption/desorption kinetics is reviewed and certain deficiencies identified.

  10. Modulation of mechanical resonance by chemical potential oscillation in graphene

    NASA Astrophysics Data System (ADS)

    Chen, Changyao; Deshpande, Vikram V.; Koshino, Mikito; Lee, Sunwoo; Gondarenko, Alexander; MacDonald, Allan H.; Kim, Philip; Hone, James

    2016-03-01

    The classical picture of the force on a capacitor assumes a large density of electronic states, such that the electrochemical potential of charges added to the capacitor is given by the external electrostatic potential and the capacitance is determined purely by geometry. Here we consider capacitively driven motion of a nano-mechanical resonator with a low density of states, in which these assumptions can break down. We find three leading-order corrections to the classical picture: the first of which is a modulation in the static force due to variation in the internal chemical potential; the second and third are changes in the static force and dynamic spring constant due to the rate of change of chemical potential, expressed as the quantum (density of states) capacitance. As a demonstration, we study capacitively driven graphene mechanical resonators, where the chemical potential is modulated independently of the gate voltage using an applied magnetic field to manipulate the energy of electrons residing in discrete Landau levels. In these devices, we observe large periodic frequency shifts consistent with the three corrections to the classical picture. In devices with extremely low strain and disorder, the first correction term dominates and the resonant frequency closely follows the chemical potential. The theoretical model fits the data with only one adjustable parameter representing disorder-broadening of the Landau levels. The underlying electromechanical coupling mechanism is not limited by the particular choice of material, geometry, or mechanism for variation in the chemical potential, and can thus be extended to other low-dimensional systems.

  11. Exact stochastic simulation of coupled chemical reactions with delays

    NASA Astrophysics Data System (ADS)

    Cai, Xiaodong

    2007-03-01

    Gillespie's exact stochastic simulation algorithm (SSA) [J. Phys. Chem. 81, 2350 (1977)] has been widely used to simulate the stochastic dynamics of chemically reacting systems. In this algorithm, it is assumed that all reactions occur instantly. While this is true in many cases, it is also possible that some chemical reactions, such as gene transcription and translation in living cells, take certain time to finish after they are initiated. Thus, the product of such reactions will emerge after certain delays. Apparently, Gillespie's SSA is not an exact algorithm for chemical reaction systems with delays. In this paper, the author develops an exact SSA for chemical reaction systems with delays, based upon the same fundamental premise of stochastic kinetics used by Gillespie in the development of his SSA. He then shows that an algorithm modified from Gillespie's SSA by Barrio et al. [PLOS Comput. Biol. 2, 1017 (2006)] is also an exact SSA for chemical reaction systems with delays, but it needs to generate more random variables than the author's algorithm.

  12. Topological Influence On Network Of Coupled Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Zhao, Jie; Rericha, Erin; Vanderbilt Biophysics Collaboration

    2013-03-01

    Networks of interacting nodes are ubiquitous in biological and communication systems. Recently the manner of the network connections, be it through of activator or inhibitor signals, and the topology of the network has received theoretical attention with the goal of finding networks with optimal synchronization and information transmission properties. In preparation for building an experimental system to examine these predictions, we numerically explore networks of Belousov-Zhabotinsky oscillatory nodes connected through unidirectional links of activator species. We measure the time required for the nodes to synchronize as a function of the network topology. While we observe a trend of smaller synchronization times with increasing first non-zero eigen values, we find that the most important factor in determining synchronization time is the initial phase difference between the oscillators. We find that the synchronization times for a given network topology, as determined from a uniform distribution of initial phase differences, is best described with a skewed Gaussian. To better understand the factors underlying this distribution, we look at the synchronization times in a three-node network as a function of both initial conditions and model parameters.

  13. Chemical kinetic reaction mechanism for the combustion of propane

    NASA Technical Reports Server (NTRS)

    Jachimowski, C. J.

    1984-01-01

    A detailed chemical kinetic reaction mechanism for the combustion of propane is presented and discussed. The mechanism consists of 27 chemical species and 83 elementary chemical reactions. Ignition and combustion data as determined in shock tube studies were used to evaluate the mechanism. Numerical simulation of the shock tube experiments showed that the kinetic behavior predicted by the mechanism for stoichiometric mixtures is in good agrement with the experimental results over the entire temperature range examined (1150-2600K). Sensitivity and theoretical studies carried out using the mechanism revealed that hydrocarbon reactions which are involved in the formation of the HO2 radical and the H2O2 molecule are very important in the mechanism and that the observed nonlinear behavior of ignition delay time with decreasing temperature can be interpreted in terms of the increased importance of the HO2 and H2O2 reactions at the lower temperatures.

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

    PubMed

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

    2014-06-25

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

  15. ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

    PubMed

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

    Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

  16. Protic Ionic Liquids for the Belousov-Zhabotinsky Reaction: Aspects of the BZ Reaction in Protic Ionic Liquids and Its Use for the Autonomous Coil-Globule Oscillation of a Linear Polymer.

    PubMed

    Ueki, Takeshi; Matsukawa, Ko; Masuda, Tsukuru; Yoshida, Ryo

    2017-04-14

    Herein, we describe physicochemical aspects of the Belousov-Zhabotinsky (BZ) reaction in hydrated protic ionic liquids (PILs) combined with different cations with a hydrogen sulfate ([HSO4(-)]) anion. PILs were prepared from sulfuric acid neutralization reactions with 13 different aliphatic amines. The amine structure was selected to investigate the effect of the number of active protons, alkyl chain length (hydrophilicity), and cationic linearity on the BZ mechanism. The pKa values of PILs were significantly higher (pKa = 0.99 ~ 2.49) than those of inorganic acids (H2SO4 = -3, and HNO3 = -1.4), the conventional proton source in a BZ reaction. A periodic redox oscillation was observed in Ru(bpy)3 when appropriate amounts of BZ reaction substrates (NaBrO3 oxidant; malonic acid reductant) were added to the hydrated PILs. A long-lasting BZ oscillation was realized when hydrophilic cations (ammonium, ethylammonium, and dimethylethylammonium) were employed. Interestingly, a large △A5000 (oscillation amplitude of absorbance for the scale of the oscillation stability observed after 5000 s from the initiation of the BZ reaction) was achieved for PILs possessing less than four carbon atoms in their cation structure. The apparent BZ oscillation activation energies (Ea) in the hydrated PILs were estimated as ~40 kJ mol(-1); <30 kJ mol(-1) than that observed in a conventional system. The catalytic reaction in the BZ reaction sub-process suppresses the total activation energy of the reaction. In order to realize long-lasting self-oscillating polymeric materials acting under milder condition, we demonstrated an autonomous coil-globule polymer chain transition (BZ-driven) that directly converts chemical energy to mechanical motion in hydrated PILs without freely diffusing Ru(bpy)3 metal catalyst. Ethylammonium hydrogen sulfate ([ea-H(+)][HSO4(-)]) is selected to utilize as a suitable proton source for the BZ reaction. A well-defined self-oscillating polymer incorporated Ru

  17. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1988-01-01

    The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.

  18. Graph-theoretic methods for the analysis of chemical and biochemical networks. I. Multistability and oscillations in ordinary differential equation models.

    PubMed

    Mincheva, Maya; Roussel, Marc R

    2007-07-01

    A chemical mechanism is a model of a chemical reaction network consisting of a set of elementary reactions that express how molecules react with each other. In classical mass-action kinetics, a mechanism implies a set of ordinary differential equations (ODEs) which govern the time evolution of the concentrations. In this article, ODE models of chemical kinetics that have the potential for multiple positive equilibria or oscillations are studied. We begin by considering some methods of stability analysis based on the digraph of the Jacobian matrix. We then prove two theorems originally given by A. N. Ivanova which correlate the bifurcation structure of a mass-action model to the properties of a bipartite graph with nodes representing chemical species and reactions. We provide several examples of the application of these theorems.

  19. Chemical Looping Combustion Reactions and Systems

    SciTech Connect

    Sarofim, Adel; Lighty, JoAnn; Smith, Philip; Whitty, Kevin; Eyring, Edward; Sahir, Asad; Alvarez, Milo; Hradisky, Michael; Clayton, Chris; Konya, Gabor; Baracki, Richard; Kelly, Kerry

    2011-07-01

    Chemical Looping Combustion (CLC) is one promising fuel-combustion technology, which can facilitate economic CO2 capture in coal-fired power plants. It employs the oxidation/reduction characteristics of a metal, or oxygen carrier, and its oxide, the oxidizing gas (typically air) and the fuel source may be kept separate. This work focused on two classes of oxygen carrier, one that merely undergoes a change in oxidation state, such as Fe3O4/Fe2O3 and one that is converted from its higher to its lower oxidation state by the release of oxygen on heating, i.e., CuO/Cu2O. This topical report discusses the results of four complementary efforts: (1) the development of process and economic models to optimize important design considerations, such as oxygen carrier circulation rate, temperature, residence time; (2) the development of high-performance simulation capabilities for fluidized beds and the collection, parameter identification, and preliminary verification/uncertainty quantification (3) the exploration of operating characteristics in the laboratory-scale bubbling bed reactor, with a focus on the oxygen carrier performance, including reactivity, oxygen carrying capacity, attrition resistance, resistance to deactivation, cost and availability (4) the identification of mechanisms and rates for the copper, cuprous oxide, and cupric oxide system using thermogravimetric analysis.

  20. Automatic NMR-Based Identification of Chemical Reaction Types in Mixtures of Co-Occurring Reactions

    PubMed Central

    Latino, Diogo A. R. S.; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the 1H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the 1H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of the

  1. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    PubMed

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

  2. Taking the plunge: chemical reaction dynamics in liquids.

    PubMed

    Orr-Ewing, Andrew J

    2017-07-06

    The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

  3. An Efficient Chemical Reaction Optimization Algorithm for Multiobjective Optimization.

    PubMed

    Bechikh, Slim; Chaabani, Abir; Ben Said, Lamjed

    2015-10-01

    Recently, a new metaheuristic called chemical reaction optimization was proposed. This search algorithm, inspired by chemical reactions launched during collisions, inherits several features from other metaheuristics such as simulated annealing and particle swarm optimization. This fact has made it, nowadays, one of the most powerful search algorithms in solving mono-objective optimization problems. In this paper, we propose a multiobjective variant of chemical reaction optimization, called nondominated sorting chemical reaction optimization, in an attempt to exploit chemical reaction optimization features in tackling problems involving multiple conflicting criteria. Since our approach is based on nondominated sorting, one of the main contributions of this paper is the proposal of a new quasi-linear average time complexity quick nondominated sorting algorithm; thereby making our multiobjective algorithm efficient from a computational cost viewpoint. The experimental comparisons against several other multiobjective algorithms on a variety of benchmark problems involving various difficulties show the effectiveness and the efficiency of this multiobjective version in providing a well-converged and well-diversified approximation of the Pareto front.

  4. Incorporation of Chemical Reactions into Building-scale Flow

    SciTech Connect

    Humphreys, T D; Jayaweera, T M; Lee, R L

    2003-10-30

    Many hazardous atmospheric releases involve chemical reactions that occur within a few kilometers of the source. Reactions with commonly occurring atmospheric compounds such as the OH radical, can transform and potentially neutralize original release compounds. Especially in these cases, accurately resolving flow around nearby structures and over surrounding topography can be critical to correctly predicting material dispersion, and thus, the extent of any hazard. Accurate prediction of material dispersion around complex geometries near the source of an atmospheric release requires high-resolution computation. Further complications arise if the compounds released undergo chemical reactions which could alter the extent of the main plume. The reaction products form dispersion patterns separate from, and often more complicated than, the original plume. Directions for future work include expanding the library of chemical reaction mechanisms, adding capabilities for aqueous and heterogeneous reactions, and integrating this model within larger-scale models. We plan that the larger-scale models will provide meteorological and chemical boundary conditions, and that this model could provide a source term in larger-scale models, both for momentum and for dispersed compounds.

  5. Matrix isolation as a tool for studying interstellar chemical reactions

    NASA Technical Reports Server (NTRS)

    Ball, David W.; Ortman, Bryan J.; Hauge, Robert H.; Margrave, John L.

    1989-01-01

    Since the identification of the OH radical as an interstellar species, over 50 molecular species were identified as interstellar denizens. While identification of new species appears straightforward, an explanation for their mechanisms of formation is not. Most astronomers concede that large bodies like interstellar dust grains are necessary for adsorption of molecules and their energies of reactions, but many of the mechanistic steps are unknown and speculative. It is proposed that data from matrix isolation experiments involving the reactions of refractory materials (especially C, Si, and Fe atoms and clusters) with small molecules (mainly H2, H2O, CO, CO2) are particularly applicable to explaining mechanistic details of likely interstellar chemical reactions. In many cases, matrix isolation techniques are the sole method of studying such reactions; also in many cases, complexations and bond rearrangements yield molecules never before observed. The study of these reactions thus provides a logical basis for the mechanisms of interstellar reactions. A list of reactions is presented that would simulate interstellar chemical reactions. These reactions were studied using FTIR-matrix isolation techniques.

  6. Asymmetric chemical reactions by polarized quantum beams

    NASA Astrophysics Data System (ADS)

    Takahashi, Jun-Ichi; Kobayashi, Kensei

    One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044

  7. The state space of a model for the Bray-Liebhafsky oscillating reaction

    NASA Astrophysics Data System (ADS)

    Schmitz, G.; Kolar-Anić, Lj.

    2007-09-01

    It has been known for a long time that the decomposition of hydrogen peroxide catalyzed by hydrogen and iodate ions, the Bray-Liebhafsky reaction, can generate oscillations in a batch reactor. Recently, mixed-mode oscillations and chaos have also been observed in a CSTR. The model we had previously proposed to explain the kinetics in a batch reactor can also simulate these new complex behaviors. Time series give only a limited view of the features of the calculated behaviors and more information is obtained studying the properties of the state space. We use projections of the trajectories, calculation of the correlation dimension of the attractor, Poincaré sections, and return maps. As the state space of the model is six-dimensional, we try to answer the questions of whether the projections into a 3D subspace give correct pictures of the real trajectories and whether we have reasons to prefer a special subspace.

  8. Spatial confinement controls self-oscillations in polymer gels undergoing the Belousov-Zhabotinsky reaction.

    PubMed

    Kuksenok, Olga; Yashin, Victor V; Balazs, Anna C

    2009-11-01

    Chemoresponsive gels undergoing the Belousov-Zhabotinsky (BZ) reaction exhibit self-sustained pulsations, which can be harnessed to perform mechanical work. In technological applications, the gels would typically be confined between hard surfaces and thus, it is essential to establish how confinement affects these distinctive oscillations. Using theory and simulation, we pinpoint regions in phase space where the dynamic behavior of BZ gels critically depends on the presence of confining walls. We then illustrate how the wave propagation within thin samples can be tailored by selectively introducing "cut outs" in the bounding surfaces. The oscillations in the latter films are localized in specified areas, so the system contains well-defined oscillatory and nonoscillatory regions. The cut outs provide an effective means of tuning the mechanical action within the film and provide a route for tailoring the functionality of the material.

  9. Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

    NASA Astrophysics Data System (ADS)

    Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

    2016-06-01

    Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

  10. Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.

    PubMed

    de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre

    2012-09-24

    This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

  11. Analysis of the bromate-sulfite-ferrocyanide pH oscillator using the particle filter: toward the automated modeling of complex chemical systems.

    PubMed

    Sato, Naoya; Hasegawa, Hiroshi H; Kimura, Rika; Mori, Yoshihito; Okazaki, Noriaki

    2010-09-23

    This study was aimed at identifying a quantitatively accurate reaction model of the bromate-sulfilte-ferrocyanide (BSF) pH oscillator by using the simulation-based model estimation algorithm known as the particle filter. The Rbai-Kaminaga-Hanazaki (RKH) model proposed for the BSF system was extended by adding the protonation equilibrium of SO42-, for which the particle filter analysis was carried out to optimize the rate constants involved with reference to the measured pH oscillation data. The extended RKH model with the optimized rate constants almost completely reproduced the measured pH oscillations and the state diagram, showing the validity of the present analysis. Chemical oscillators such as the BSF system show drastic switching of the dominant reaction path, which strongly disturbs the convergence of the rate constants if the objective function is defined in a conventional manner to reflect only a single time step datum. In this study, the objective function was defined as the residual sum of squares with respect to pH taken over an interval longer than one oscillatory period, so that all of the relevant reaction steps can contribute to the objective function. This is the first report which exemplifies the effectiveness of the particle filter in the analysis of real complex chemical systems.

  12. The Electronic Flux in Chemical Reactions. Insights on the Mechanism of the Maillard Reaction

    NASA Astrophysics Data System (ADS)

    Flores, Patricio; Gutiérrez-Oliva, Soledad; Herrera, Bárbara; Silva, Eduardo; Toro-Labbé, Alejandro

    2007-11-01

    The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used, together with the reaction force, to shed light on reaction mechanism of the Schiff base formation in the Maillard reaction. By partitioning the reaction coordinate in regions in which different process might be taking place, electronic reordering associated to polarization and transfer has been identified and found to be localized at specific transition state regions where most bond forming and breaking occur.

  13. Structural simplification of chemical reaction networks in partial steady states.

    PubMed

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. A viscosity self-oscillation of polymer solution induced by the Belousov-Zhabotinsky reaction under acid-free condition.

    PubMed

    Hara, Yusuke; Yoshida, Ryo

    2008-06-14

    We succeeded in measuring a viscosity self-oscillation induced by the Belousov-Zhabotinsky (BZ) reaction for a polymer solution on the constant temperature condition under acid-free condition. The polymer chain is consisted of N-isopropylacrylamide, ruthenium complex as a catalyst of the BZ reaction, and an acrylamide-2-methylpropanesulfonic acid (AMPS) as a pH and the solubility control site. The viscosity self-oscillation for the AMPS-containing polymer solution was attributed to the difference between viscosities for the polymer solution in the reduced and oxidized states. The effects of the polymer concentration and the temperature of the polymer solution on the viscosity self-oscillation were investigated. As a result, the viscosity self-oscillating behavior significantly depended on the polymer concentration and the temperature of the polymer solution. The period of the viscosity self-oscillation decreased with increasing temperature in accordance with the Arrenius equation.

  15. STM CONTROL OF CHEMICAL REACTIONS: Single-Molecule Synthesis

    NASA Astrophysics Data System (ADS)

    Hla, Saw-Wai; Rieder, Karl-Heinz

    2003-10-01

    The fascinating advances in single atom/molecule manipulation with a scanning tunneling microscope (STM) tip allow scientists to fabricate atomic-scale structures or to probe chemical and physical properties of matters at an atomic level. Owing to these advances, it has become possible for the basic chemical reaction steps, such as dissociation, diffusion, adsorption, readsorption, and bond-formation processes, to be performed by using the STM tip. Complete sequences of chemical reactions are able to induce at a single-molecule level. New molecules can be constructed from the basic molecular building blocks on a one-molecule-at-a-time basis by using a variety of STM manipulation schemes in a systematic step-by-step manner. These achievements open up entirely new opportunities in nanochemistry and nanochemical technology. In this review, various STM manipulation techniques useful in the single-molecule reaction process are reviewed, and their impact on the future of nanoscience and technology are discussed.

  16. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

    DOE PAGES

    Kale, Seyit; Sode, Olaseni; Weare, Jonathan; ...

    2014-11-07

    Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum undermore » DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.« less

  17. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

    SciTech Connect

    Kale, Seyit; Sode, Olaseni; Weare, Jonathan; Dinner, Aaron R.

    2014-11-07

    Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.

  18. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

    PubMed Central

    2015-01-01

    Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled. PMID:25516726

  19. Maximum probability reaction sequences in stochastic chemical kinetic systems.

    PubMed

    Salehi, Maryam; Perkins, Theodore J

    2010-01-01

    The detailed behavior of many molecular processes in the cell, such as protein folding, protein complex assembly, and gene regulation, transcription and translation, can often be accurately captured by stochastic chemical kinetic models. We investigate a novel computational problem involving these models - that of finding the most-probable sequence of reactions that connects two or more states of the system observed at different times. We describe an efficient method for computing the probability of a given reaction sequence, but argue that computing most-probable reaction sequences is EXPSPACE-hard. We develop exact (exhaustive) and approximate algorithms for finding most-probable reaction sequences. We evaluate these methods on test problems relating to a recently-proposed stochastic model of folding of the Trp-cage peptide. Our results provide new computational tools for analyzing stochastic chemical models, and demonstrate their utility in illuminating the behavior of real-world systems.

  20. Maximum Probability Reaction Sequences in Stochastic Chemical Kinetic Systems

    PubMed Central

    Salehi, Maryam; Perkins, Theodore J.

    2010-01-01

    The detailed behavior of many molecular processes in the cell, such as protein folding, protein complex assembly, and gene regulation, transcription and translation, can often be accurately captured by stochastic chemical kinetic models. We investigate a novel computational problem involving these models – that of finding the most-probable sequence of reactions that connects two or more states of the system observed at different times. We describe an efficient method for computing the probability of a given reaction sequence, but argue that computing most-probable reaction sequences is EXPSPACE-hard. We develop exact (exhaustive) and approximate algorithms for finding most-probable reaction sequences. We evaluate these methods on test problems relating to a recently-proposed stochastic model of folding of the Trp-cage peptide. Our results provide new computational tools for analyzing stochastic chemical models, and demonstrate their utility in illuminating the behavior of real-world systems. PMID:21629860

  1. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

    PubMed

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

    Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

  2. Method and apparatus for controlling gas evolution from chemical reactions

    DOEpatents

    Skorpik, James R.; Dodson, Michael G.

    1999-01-01

    The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846.

  3. Method and apparatus for controlling gas evolution from chemical reactions

    DOEpatents

    Skorpik, J.R.; Dodson, M.G.

    1999-05-25

    The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846. 8 figs.

  4. Chemical reactions in viscous liquids under space conditions

    NASA Astrophysics Data System (ADS)

    Kondyurin, A.; Lauke, B.; Richter, E.

    A long-term human flight needs a large-size space ships with artificial self-regulating ecological life-support system. The best way for creation of large-size space ship is a synthesis of light construction on Earth orbit, that does not need a high energy transportation carriers from Earth surface. The construction can be created by the way of chemical polymerisation reaction under space environment. But the space conditions are very specific for chemical reactions. A high vacuum, high energy particles, X-rays, UV- and VUV-irradiations, atomic oxygen, microgravity have a significant influence on chemical reactions. Polymerisation reactions in liquid active mixture were studied in simulated space environment. The epoxy resins based on Bisphenol A and amine curing agents were investigated under vacuum, microwave plasma discharge and ion beam. An acceleration of polymerisation reaction with free radicals formation was observed. The polymerisation reaction can be carried out under space environment. The study was supported by Alexander von Humboldt Foundation (A. Kondyurin) and European Space Agency, ESTEC (contract 17083/03/NL/Sfe "Space Environmental Effects on the Polymerisation of Composite Structures").

  5. Equilibriumlike behavior in chemical reaction networks far from equilibrium.

    PubMed

    Lubensky, David K

    2010-06-01

    In an equilibrium chemical reaction mixture, the number of molecules present obeys a Poisson distribution. We report that, surprisingly, the same is true of a large class of nonequilibrium reaction networks. In particular, we show that certain topological features imply a Poisson distribution, whatever the reaction rates. Such driven systems also obey an analog of the fluctuation-dissipation theorem. Our results shed light on the fundamental question of when equilibrium concepts might apply to nonequilibrium systems and may have applications to models of noise in biochemical networks.

  6. Uncertainty quantification for quantum chemical models of complex reaction networks.

    PubMed

    Proppe, Jonny; Husch, Tamara; Simm, Gregor N; Reiher, Markus

    2016-12-22

    For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

  7. Modeling Second-Order Chemical Reactions using Cellular Automata

    NASA Astrophysics Data System (ADS)

    Hunter, N. E.; Barton, C. C.; Seybold, P. G.; Rizki, M. M.

    2012-12-01

    Cellular automata (CA) are discrete, agent-based, dynamic, iterated, mathematical computational models used to describe complex physical, biological, and chemical systems. Unlike the more computationally demanding molecular dynamics and Monte Carlo approaches, which use "force fields" to model molecular interactions, CA models employ a set of local rules. The traditional approach for modeling chemical reactions is to solve a set of simultaneous differential rate equations to give deterministic outcomes. CA models yield statistical outcomes for a finite number of ingredients. The deterministic solutions appear as limiting cases for conditions such as a large number of ingredients or a finite number of ingredients and many trials. Here we present a 2-dimensional, probabilistic CA model of a second-order gas phase reaction A + B → C, using a MATLAB basis. Beginning with a random distribution of ingredients A and B, formation of C emerges as the system evolves. The reaction rate can be varied based on the probability of favorable collisions of the reagents A and B. The model permits visualization of the conversion of reagents to products, and allows one to plot concentration vs. time for A, B and C. We test hypothetical reaction conditions such as: limiting reagents, the effects of reaction probabilities, and reagent concentrations on the reaction kinetics. The deterministic solutions of the reactions emerge as statistical averages in the limit of the large number of cells in the array. Modeling results for dynamic processes in the atmosphere will be presented.

  8. Chemical pathways in ultracold reactions of SrF molecules

    SciTech Connect

    Meyer, Edmund R.; Bohn, John L.

    2011-03-15

    We present a theoretical investigation of the chemical reaction SrF + SrF {yields} products, focusing on reactions at ultralow temperatures. We find that bond swapping SrF + SrF {yields} Sr{sub 2} + F{sub 2} is energetically forbidden at these temperatures. Rather, the only energetically allowed reaction is SrF + SrF {yields} SrF{sub 2} + Sr, and even then only singlet states of the SrF{sub 2} trimer can form. A calculation along a reduced reaction path demonstrates that this abstraction reaction is barrierless and proceeds by one SrF molecule ''handing off'' a fluorine atom to the other molecule.

  9. Universality and chaoticity in ultracold K+KRb chemical reactions

    NASA Astrophysics Data System (ADS)

    Croft, J. F. E.; Makrides, C.; Li, M.; Petrov, A.; Kendrick, B. K.; Balakrishnan, N.; Kotochigova, S.

    2017-07-01

    A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysis of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.

  10. Researches on Preliminary Chemical Reactions in Spark-Ignition Engines

    NASA Technical Reports Server (NTRS)

    Muehlner, E.

    1943-01-01

    Chemical reactions can demonstrably occur in a fuel-air mixture compressed in the working cylinder of an Otto-cycle (spark ignition) internal-combustion engine even before the charge is ignited by the flame proceeding from the sparking plug. These are the so-called "prelinminary reactions" ("pre-flame" combustion or oxidation), and an exact knowledge of their characteristic development is of great importance for a correct appreciation of the phenomena of engine-knock (detonation), and consequently for its avoidance. Such reactions can be studied either in a working engine cylinder or in a combustion bomb. The first method necessitates a complicated experimental technique, while the second has the disadvantage of enabling only a single reaction to be studied at one time. Consequently, a new series of experiments was inaugurated, conducted in a motored (externally-driven) experimental engine of mixture-compression type, without ignition, the resulting preliminary reactions being detectable and measurable thermometrically.

  11. Universality and chaoticity in ultracold K+KRb chemical reactions

    PubMed Central

    Croft, J. F. E.; Makrides, C.; Li, M.; Petrov, A.; Kendrick, B. K.; Balakrishnan, N.; Kotochigova, S.

    2017-01-01

    A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysis of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome. PMID:28722014

  12. Reduction of chemical reaction networks through delay distributions

    NASA Astrophysics Data System (ADS)

    Barrio, Manuel; Leier, André; Marquez-Lago, Tatiana T.

    2013-03-01

    Accurate modelling and simulation of dynamic cellular events require two main ingredients: an adequate description of key chemical reactions and simulation of such chemical events in reasonable time spans. Quite logically, posing the right model is a crucial step for any endeavour in Computational Biology. However, more often than not, it is the associated computational costs which actually limit our capabilities of representing complex cellular behaviour. In this paper, we propose a methodology aimed at representing chains of chemical reactions by much simpler, reduced models. The abridgement is achieved by generation of model-specific delay distribution functions, consecutively fed to a delay stochastic simulation algorithm. We show how such delay distributions can be analytically described whenever the system is solely composed of consecutive first-order reactions, with or without additional "backward" bypass reactions, yielding an exact reduction. For models including other types of monomolecular reactions (constitutive synthesis, degradation, or "forward" bypass reactions), we discuss why one must adopt a numerical approach for its accurate stochastic representation, and propose two alternatives for this. In these cases, the accuracy depends on the respective numerical sample size. Our model reduction methodology yields significantly lower computational costs while retaining accuracy. Quite naturally, computational costs increase alongside network size and separation of time scales. Thus, we expect our model reduction methodologies to significantly decrease computational costs in these instances. We anticipate the use of delays in model reduction will greatly alleviate some of the current restrictions in simulating large sets of chemical reactions, largely applicable in pharmaceutical and biological research.

  13. Program Helps To Determine Chemical-Reaction Mechanisms

    NASA Technical Reports Server (NTRS)

    Bittker, D. A.; Radhakrishnan, K.

    1995-01-01

    General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

  14. Program Helps To Determine Chemical-Reaction Mechanisms

    NASA Technical Reports Server (NTRS)

    Bittker, D. A.; Radhakrishnan, K.

    1995-01-01

    General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

  15. Effects of incomplete mixing on chemical reactions under flow heterogeneities.

    NASA Astrophysics Data System (ADS)

    Perez, Lazaro; Hidalgo, Juan J.; Dentz, Marco

    2016-04-01

    Evaluation of the mixing process in aquifers is of primary importance when assessing attenuation of pollutants. In aquifers different hydraulic and chemical properties can increase mixing and spreading of the transported species. Mixing processes control biogeochemical transformations such as precipitation/dissolution reactions or degradation reactions that are fast compared to mass transfer processes. Reactions are local phenomena that fluctuate at the pore scale, but predictions are often made at much larger scales. However, aquifer heterogeities are found at all scales and generates flow heterogeneities which creates complex concentration distributions that enhances mixing. In order to assess the impact of spatial flow heterogeneities at pore scale we study concentration profiles, gradients and reaction rates using a random walk particle tracking (RWPT) method and kernel density estimators to reconstruct concentrations and gradients in two setups. First, we focus on a irreversible bimolecular reaction A+B → C under homogeneous flow to distinguish phenomena of incomplete mixing of reactants from finite-size sampling effects. Second, we analise a fast reversible bimolecular chemical reaction A+B rightleftharpoons C in a laminar Poiseuille flow reactor to determine the difference between local and global reaction rates caused by the incomplete mixing under flow heterogeneities. Simulation results for the first setup differ from the analytical solution of the continuum scale advection-dispersion-reaction equation studied by Gramling et al. (2002), which results in an overstimation quantity of reaction product (C). In the second setup, results show that actual reaction rates are bigger than the obtained from artificially mixing the system by averaging the concentration vertically. - LITERATURE Gramling, C. M.,Harvey, C. F., Meigs, and L. C., (2002). Reactive transport in porous media: A comparison of model prediction with laboratory visualization, Environ. Sci

  16. Reaction Hamiltonian and state-to-state description of chemical reactions

    SciTech Connect

    Ruf, B.A.; Kresin, V.Z.; Lester, W.A. Jr.

    1985-08-01

    A chemical reaction is treated as a quantum transition from reactants to products. A specific reaction Hamiltonian (in second quantization formalism) is introduced. The approach leads to Franck-Condon-like factor, and adiabatic method in the framework of the nuclear motion problems. The influence of reagent vibrational state on the product energy distribution has been studied following the reaction Hamiltonian method. Two different cases (fixed available energy and fixed translational energy) are distinguished. Results for several biomolecular reactions are presented. 40 refs., 5 figs.

  17. Supersonic molecular beam experiments on surface chemical reactions.

    PubMed

    Okada, Michio

    2014-10-01

    The interaction of a molecule and a surface is important in various fields, and in particular in complex systems like biomaterials and their related chemistry. However, the detailed understanding of the elementary steps in the surface chemistry, for example, stereodynamics, is still insufficient even for simple model systems. In this Personal Account, I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams demonstrate a significant role of the translational energy of the incident molecules. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths specific for the hyperthermal energy region, and to develop new methods for the fabrication of thin films. On the other hand, oriented molecular beams also demonstrate the possibility of understanding surface chemical reactions in detail by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for finely monitoring the elementary step of the surface chemical reactions and creating new materials on surfaces.

  18. Prediction of Rate Constants for Catalytic Reactions with Chemical Accuracy.

    PubMed

    Catlow, C Richard A

    2016-08-01

    Ex machina: A computational method for predicting rate constants for reactions within microporous zeolite catalysts with chemical accuracy has recently been reported. A key feature of this method is a stepwise QM/MM approach that allows accuracy to be achieved while using realistic models with accessible computer resources.

  19. Mapping students' ideas about chemical reactions at different educational levels

    NASA Astrophysics Data System (ADS)

    Yan, Fan

    Understanding chemical reactions is crucial in learning chemistry at all educational levels. Nevertheless, research in science education has revealed that many students struggle to understand chemical processes. Improving teaching and learning about chemical reactions demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the discipline. Thus, we have carried out a qualitative study using semi-structured interviews as the main data collection tool to explore students reasoning about reaction mechanism and causality. The participants of this study included students at different levels of training in chemistry: general chemistry students (n=22), organic chemistry students (n=16), first year graduate students (n=13) and Ph.D. candidates (n=14). We identified major conceptual modes along critical dimensions of analysis, and illustrated common ways of reasoning using typical cases. Main findings indicate that although significant progress is observed in student reasoning in some areas, major conceptual difficulties seem to persist even at the more advanced educational levels. In addition, our findings suggest that students struggle to integrate important concepts when thinking about mechanism and causality in chemical reactions. The results of our study are relevant to chemistry educators interested in learning progressions, assessment, and conceptual development.

  20. Chemical Reaction Engineering: Current Status and Future Directions.

    ERIC Educational Resources Information Center

    Dudukovic, M. P.

    1987-01-01

    Describes Chemical Reaction Engineering (CRE) as the discipline that quantifies the interplay of transport phenomena and kinetics in relating reactor performance to operating conditions and input variables. Addresses the current status of CRE in both academic and industrial settings and outlines future trends. (TW)

  1. WATER AS A REACTION MEDIUM FOR CLEAN CHEMICAL PROCESSES.

    EPA Science Inventory

    Green chemistry is a rapid developing new field that provides us a pro-active avenue for the sustainable development of future science and technologies. When designed properly, clean chemical technology can be developed in water as a reaction media. The technologies generated f...

  2. Quantum and semiclassical theories of chemical reaction rates

    SciTech Connect

    Miller, W.H. |

    1995-09-01

    A rigorous quantum mechanical theory (and a semiclassical approximation thereto) is described for calculating chemical reaction rates ``directly``, i.e., without having to solve the complete state-to-state reactive scattering problem. The approach has many vestiges of transition state theory, for which it may be thought of as the rigorous generalization.

  3. Chemical Reaction Engineering: Current Status and Future Directions.

    ERIC Educational Resources Information Center

    Dudukovic, M. P.

    1987-01-01

    Describes Chemical Reaction Engineering (CRE) as the discipline that quantifies the interplay of transport phenomena and kinetics in relating reactor performance to operating conditions and input variables. Addresses the current status of CRE in both academic and industrial settings and outlines future trends. (TW)

  4. Molecular codes in biological and chemical reaction networks.

    PubMed

    Görlich, Dennis; Dittrich, Peter

    2013-01-01

    Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio-) chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries), biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades), an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

  5. WATER AS A REACTION MEDIUM FOR CLEAN CHEMICAL PROCESSES.

    EPA Science Inventory

    Green chemistry is a rapid developing new field that provides us a pro-active avenue for the sustainable development of future science and technologies. When designed properly, clean chemical technology can be developed in water as a reaction media. The technologies generated f...

  6. Perspective: chemical dynamics simulations of non-statistical reaction dynamics.

    PubMed

    Ma, Xinyou; Hase, William L

    2017-04-28

    Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Author(s).

  7. 2011 Chemical Reactions at Surfaces Gordon Research Conference

    SciTech Connect

    Peter Stair

    2011-02-11

    The Gordon Research Conference on Chemical Reactions at Surfaces is dedicated to promoting and advancing the fundamental science of interfacial chemistry and physics by providing surface scientists with the foremost venue for presentation and discussion of research occurring at the frontiers of their fields.

  8. Stabilization of miscible viscous fingering by chemical reaction decreasing viscosity

    NASA Astrophysics Data System (ADS)

    Arai, Shuntaro; Nagatsu, Yuichiro; Shukla, Priyanka; de Wit, Anne

    2016-11-01

    Viscous fingering (VF) occurs when a more viscous fluid is displaced by a less viscous one in porous media or Hele-Shaw cells. In this study, experiment on miscible VF with chemical reaction is conducted by using a Hele-Shaw cell. Here, the chemical reaction takes place between a polymer dissolved in the more viscous solution and hydrochloric acid (HCl) dissolved in the less viscous one in the miscible interface region. The reaction decreases the viscosity of the polymer solution. The experiment shows that the reaction stabilizes VF when the flow rate is small. In the present study, the corresponding numerical simulation is also conducted. The simulation is able to reproduce the experimental results mentioned above when different diffusion coefficients are considered meaning that HCl diffuses faster than the polymer. However, the stabilization cannot be found under conditions of the same diffusivity of the reactants. These numerical results show that the different diffusivity is responsible for the stabilization of miscible VF by the chemical reaction decreasing viscosity.

  9. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

    PubMed

    Holliday, Gemma L; Murray-Rust, Peter; Rzepa, Henry S

    2006-01-01

    A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

  10. The role of chemical reactions in the Chernobyl accident

    SciTech Connect

    Grishanin, E. I.

    2010-12-15

    It is shown that chemical reactions played an essential role in the Chernobyl accident at all of its stages. It is important that the reactor before the explosion was at maximal xenon poisoning, and its reactivity, apparently, was not destroyed by the explosion. The reactivity release due to decay of Xe-235 on the second day after the explosion led to a reactor power of 80-110 MW. Owing to this power, the chemical reactions of reduction of uranium, plutonium, and other metals at a temperature of about 2000 Degree-Sign C occurred in the core. The yield of fission products thus sharply increased. Uranium and other metals flew down in the bottom water communications and rooms. After reduction of the uranium and its separation from the graphite, the chain reaction stopped, the temperature of the core decreased, and the activity yield stopped.

  11. Multiscale stochastic simulations of chemical reactions with regulated scale separation

    SciTech Connect

    Koumoutsakos, Petros; Feigelman, Justin

    2013-07-01

    We present a coupling of multiscale frameworks with accelerated stochastic simulation algorithms for systems of chemical reactions with disparate propensities. The algorithms regulate the propensities of the fast and slow reactions of the system, using alternating micro and macro sub-steps simulated with accelerated algorithms such as τ and R-leaping. The proposed algorithms are shown to provide significant speedups in simulations of stiff systems of chemical reactions with a trade-off in accuracy as controlled by a regulating parameter. More importantly, the error of the methods exhibits a cutoff phenomenon that allows for optimal parameter choices. Numerical experiments demonstrate that hybrid algorithms involving accelerated stochastic simulations can be, in certain cases, more accurate while faster, than their corresponding stochastic simulation algorithm counterparts.

  12. Mixing, chemical reaction and flow field development in ducted rockets

    SciTech Connect

    Vanka, S.P.; Craig, R.R.; Stull, F.D.

    1984-09-01

    Calculations have been made of the three-dimensional mixing, chemical reaction, and flow field development in a typical ducted rocket configuration. The governing partial differential equations are numerically solved by an iterative finite-difference solution procedure. The physical models include the k approx. epsilon turbulence model, one-step reaction, and mixing controlled chemical reaction rate. Radiation is neglected. The mean flow structure, fuel dispersal patterns, and temperature field are presented in detail for a base configuration with 0.058 m (2 in.) dome height, 45/sup 0/ side arm inclination, and with gaseous ethylene injected from the dome plate at an eccentric location. In addition, the influences of the geometrical parameters such as dome height, inclination of the side arms, and location of the fuel injector are studied.

  13. Multiscale stochastic simulations of chemical reactions with regulated scale separation

    NASA Astrophysics Data System (ADS)

    Koumoutsakos, Petros; Feigelman, Justin

    2013-07-01

    We present a coupling of multiscale frameworks with accelerated stochastic simulation algorithms for systems of chemical reactions with disparate propensities. The algorithms regulate the propensities of the fast and slow reactions of the system, using alternating micro and macro sub-steps simulated with accelerated algorithms such as τ and R-leaping. The proposed algorithms are shown to provide significant speedups in simulations of stiff systems of chemical reactions with a trade-off in accuracy as controlled by a regulating parameter. More importantly, the error of the methods exhibits a cutoff phenomenon that allows for optimal parameter choices. Numerical experiments demonstrate that hybrid algorithms involving accelerated stochastic simulations can be, in certain cases, more accurate while faster, than their corresponding stochastic simulation algorithm counterparts.

  14. Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

    PubMed

    Wu, Emilia L

    2010-12-01

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

  15. Photoexcited chemical wave in the ruthenium-catalyzed Belousov-Zhabotinsky reaction.

    PubMed

    Nakata, Satoshi; Matsushita, Mariko; Sato, Taisuke; Suematsu, Nobuhiko J; Kitahata, Hiroyuki; Amemiya, Takashi; Mori, Yoshihito

    2011-07-07

    The excitation of the photosensitive Belousov-Zhabotinsky (BZ) reaction induced by light stimulation was systematically investigated. A stepwise increase in the light intensity induced the excitation, whereas a stepwise decrease did not induce the excitation. The threshold values for the excitation were found to be a function of the initial and final light intensities, time variation in light intensity, and the concentration of NaBrO(3). The experimental results were qualitatively reproduced by a theoretical calculation based on a three-variable Oregonator model modified for the photosensitive BZ reaction. These results suggest that although the steady light irradiation is known to inhibit oscillation and chemical waves in the BZ system under almost all conditions, the stepwise increase in the light irradiation leads to the rapid production of an activator, resulting in the photoexcitation.

  16. Petri Nets - A Mathematical Formalism to Analyze Chemical Reaction Networks.

    PubMed

    Koch, Ina

    2010-12-17

    In this review we introduce and discuss Petri nets - a mathematical formalism to describe and analyze chemical reaction networks. Petri nets were developed to describe concurrency in general systems. We find most applications to technical and financial systems, but since about twenty years also in systems biology to model biochemical systems. This review aims to give a short informal introduction to the basic formalism illustrated by a chemical example, and to discuss possible applications to the analysis of chemical reaction networks, including cheminformatics. We give a short overview about qualitative as well as quantitative modeling Petri net techniques useful in systems biology, summarizing the state-of-the-art in that field and providing the main literature references. Finally, we discuss advantages and limitations of Petri nets and give an outlook to further development.

  17. Diabatic models with transferrable parameters for generalized chemical reactions

    NASA Astrophysics Data System (ADS)

    Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.

    2017-05-01

    Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical

  18. Students' Understandings of Chemical Bonds and the Energetics of Chemical Reactions.

    ERIC Educational Resources Information Center

    Boo, Hong Kwen

    1998-01-01

    Investigates Grade 12 students' understandings of the nature of chemical bonds and the energetics elicited across five familiar chemical reactions following a course of instruction. Discusses the many ways in which students can misconstruct concepts and principles. Contains 63 references. (DDR)

  19. Development of a chemical oxygen - iodine laser with production of atomic iodine in a chemical reaction

    SciTech Connect

    Censky, M; Spalek, O; Jirasek, V; Kodymova, J; Jakubec, I

    2009-11-30

    The alternative method of atomic iodine generation for a chemical oxygen - iodine laser (COIL) in chemical reactions with gaseous reactants is investigated experimentally. The influence of the configuration of iodine atom injection into the laser cavity on the efficiency of the atomic iodine generation and small-signal gain is studied. (lasers)

  20. Students' Understandings of Chemical Bonds and the Energetics of Chemical Reactions.

    ERIC Educational Resources Information Center

    Boo, Hong Kwen

    1998-01-01

    Investigates Grade 12 students' understandings of the nature of chemical bonds and the energetics elicited across five familiar chemical reactions following a course of instruction. Discusses the many ways in which students can misconstruct concepts and principles. Contains 63 references. (DDR)

  1. Interplay between chemical reactions and transport in structured spaces

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2005-07-01

    The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C1,C2,…,CN and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate λ . Tubes connecting containers allow for the exchange of chemicals with the transport rate D . A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

  2. Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping

    PubMed Central

    2009-01-01

    Abstract The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection between robustness and efficiency of simulation. Without robustness guarantees, stochastic simulation seems to require computational time proportional to the total number of reaction events. Even if the concentration (molecular count per volume) stays bounded, the number of reaction events can be linear in the duration of simulated time and total molecular count. We show that the behavior of robust systems can be predicted such that the computational work scales linearly with the duration of simulated time and concentration, and only polylogarithmically in the total molecular count. Thus our asymptotic analysis captures the dramatic speedup when molecular counts are large, and shows that for bounded concentrations the computation time is essentially invariant with molecular count. Finally, by noticing that even robust stochastic chemical reaction networks are capable of embedding complex computational problems, we argue that the linear dependence on simulated time and concentration is likely optimal. PMID:19254187

  3. Towards a unified model of neutrino-nucleus reactions for neutrino oscillation experiments

    NASA Astrophysics Data System (ADS)

    Nakamura, S. X.; Kamano, H.; Hayato, Y.; Hirai, M.; Horiuchi, W.; Kumano, S.; Murata, T.; Saito, K.; Sakuda, M.; Sato, T.; Suzuki, Y.

    2017-05-01

    A precise description of neutrino-nucleus reactions will play a key role in addressing fundamental questions such as the leptonic CP violation and the neutrino mass hierarchy through analyzing data from next-generation neutrino oscillation experiments. The neutrino energy relevant to the neutrino-nucleus reactions spans a broad range and, accordingly, the dominant reaction mechanism varies across the energy region from quasi-elastic scattering through nucleon resonance excitations to deep inelastic scattering. This corresponds to transitions of the effective degree of freedom for theoretical description from nucleons through meson-baryon to quarks. The main purpose of this review is to report our recent efforts towards a unified description of the neutrino-nucleus reactions over the wide energy range; recent overall progress in the field is also sketched. Starting with an overview of the current status of neutrino-nucleus scattering experiments, we formulate the cross section to be commonly used for the reactions over all the energy regions. A description of the neutrino-nucleon reactions follows and, in particular, a dynamical coupled-channels model for meson productions in and beyond the Δ (1232) region is discussed in detail. We then discuss the neutrino-nucleus reactions, putting emphasis on our theoretical approaches. We start the discussion with electroweak processes in few-nucleon systems studied with the correlated Gaussian method. Then we describe quasi-elastic scattering with nuclear spectral functions, and meson productions with a Δ -hole model. Nuclear modifications of the parton distribution functions determined through a global analysis are also discussed. Finally, we discuss issues to be addressed for future developments.

  4. Towards a unified model of neutrino-nucleus reactions for neutrino oscillation experiments.

    PubMed

    Nakamura, S X; Kamano, H; Hayato, Y; Hirai, M; Horiuchi, W; Kumano, S; Murata, T; Saito, K; Sakuda, M; Sato, T; Suzuki, Y

    2017-05-01

    A precise description of neutrino-nucleus reactions will play a key role in addressing fundamental questions such as the leptonic CP violation and the neutrino mass hierarchy through analyzing data from next-generation neutrino oscillation experiments. The neutrino energy relevant to the neutrino-nucleus reactions spans a broad range and, accordingly, the dominant reaction mechanism varies across the energy region from quasi-elastic scattering through nucleon resonance excitations to deep inelastic scattering. This corresponds to transitions of the effective degree of freedom for theoretical description from nucleons through meson-baryon to quarks. The main purpose of this review is to report our recent efforts towards a unified description of the neutrino-nucleus reactions over the wide energy range; recent overall progress in the field is also sketched. Starting with an overview of the current status of neutrino-nucleus scattering experiments, we formulate the cross section to be commonly used for the reactions over all the energy regions. A description of the neutrino-nucleon reactions follows and, in particular, a dynamical coupled-channels model for meson productions in and beyond the [Formula: see text](1232) region is discussed in detail. We then discuss the neutrino-nucleus reactions, putting emphasis on our theoretical approaches. We start the discussion with electroweak processes in few-nucleon systems studied with the correlated Gaussian method. Then we describe quasi-elastic scattering with nuclear spectral functions, and meson productions with a [Formula: see text]-hole model. Nuclear modifications of the parton distribution functions determined through a global analysis are also discussed. Finally, we discuss issues to be addressed for future developments.

  5. Inverse electron demand Diels-Alder reactions in chemical biology.

    PubMed

    Oliveira, B L; Guo, Z; Bernardes, G J L

    2017-08-14

    The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.

  6. Cooperative action of coherent groups in broadly heterogeneous populations of interacting chemical oscillators

    PubMed Central

    Mikhailov, A. S.; Zanette, D. H.; Zhai, Y. M.; Kiss, I. Z.; Hudson, J. L.

    2004-01-01

    We present laboratory experiments on the effects of global coupling in a population of electrochemical oscillators with a multimodal frequency distribution. The experiments show that complex collective signals are generated by this system through spontaneous emergence and joint operation of coherently acting groups representing hierarchically organized resonant clusters. Numerical simulations support these experimental findings. Our results suggest that some forms of internal self-organization, characteristic for complex multiagent systems, are already possible in simple chemical systems. PMID:15263084

  7. Density functional study of chemical reaction equilibrium for dimerization reactions in slit and cylindrical nanopores

    NASA Astrophysics Data System (ADS)

    Malijevský, Alexandr; Lísal, Martin

    2009-04-01

    We present a theoretical study of the effects of confinement on chemical reaction equilibrium in slit and cylindrical nanopores. We use a density functional theory (DFT) to investigate the effects of temperature, pore geometry, bulk pressure, transition layering, and capillary condensation on a dimerization reaction that mimics the nitric oxide dimerization reaction, 2NO⇌(NO)2, in carbonlike slit and cylindrical nanopores in equilibrium with a vapor reservoir. In addition to the DFT calculations, we also utilize the reaction ensemble Monte Carlo method to supplement the DFT results for reaction conversion. This work is an extension of the previous DFT study by Tripathi and Chapman [J. Chem. Phys. 118, 7993 (2003)] on the dimerization reactions confined in the planar slits.

  8. Resonant Excitation of White Dwarf Oscillations in Compact Object Binaries: 1. The No Back Reaction Approximation

    SciTech Connect

    Rathore, Y.

    2004-06-14

    We consider the evolution of white dwarfs with compact object companions (specifically black holes with masses up to {approx} 10{sup 6} M{sub {circle_dot}}, neutron stars, and other white dwarfs). We suppose that the orbits are initially quite elliptical and then shrink and circularize under the action of gravitational radiation. During this evolution, the white dwarfs will pass through resonances when harmonics of the orbital frequency match the stellar oscillation eigenfrequencies. As a star passes through these resonances, the associated modes will be excited and can be driven to amplitudes that are so large that there is a back reaction on the orbit which, in turn, limits the growth of the modes. A formalism is presented for describing this dynamical interaction for a non-rotating star in the linear approximation when the orbit can be treated as non-relativistic. A semi-analytical expression is found for computing the resonant energy transfer as a function of stellar and orbital parameters for the regime where back reaction may be neglected. This is used to calculate the results of passage through a sequence of resonances for several hypothetical systems. It is found that the amplitude of the {ell} = m = 2 f-mode can be driven into the non-linear regime for appropriate initial conditions. We also discuss where the no back reaction approximation is expected to fail, and the qualitative effects of back reaction.

  9. PDF calculation of scalar mixing layer with simple chemical reactions

    NASA Astrophysics Data System (ADS)

    Kanzaki, Takao; Pope, Stephen B.

    1999-11-01

    A joint velocity-composition-turbulent frequency PDF(JPDF) model is used to simulate reactive mixing layer in a grid-generated turbulence with the influence of second-order irreversible chemical reactions. To investigate the effects of molecular mixing, a gas flow and a liquid flow are simulated. For a gas flow, the oxidation reaction (NO+ O3 arrow NO2 +O2 ) between nitricoxide (NO) and ozone (O3 ) is used. For a liquid flow, the saponification reaction(NaOH+HCOOCH3 arrow HCOONa+CH_3OH) between sodiumhydroxide(NaOH) and methylformate(HCOOCH_3) is used. The both cases are moderately fast reactions. Therefore, reactive scalar statistics are affected by turbulent mixing. The results of caliculation are compared with experimental data of Komori et al.(1994) and Bilger et al.(1991)

  10. Chemical research on red pigments after adverse reactions to tattoo.

    PubMed

    Tammaro, A; Toniolo, C; Giulianelli, V; Serafini, M; Persechino, S

    2016-03-01

    Currently, the incidence of tattooing is on the rise compared to the past, especially among adolescents, and it leads to the urgency of monitoring the security status of tattooing centers, as well as to inform people about the risks of tattoo practice. In our clinical experience, 20% of tattooed patients presented adverse reactions, like allergic contact dermatitis, psoriasis with Koebner's phenomena and granulomatous reactions, with the latter most prevalent and most often related to red pigment. Adverse reactions to tattoo pigments, especially the red one, are well known and described in literature. Great attention has to be focused on the pigments used, especially for the presence of new substances, often not well known. For this reason, we decided to perform a study on 12 samples of red tattoo ink, obtained by patients affected by different cutaneous reactions in the site of tattoo, to analyze their chemical composition.

  11. Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase.

    PubMed

    Hopmann, Kathrin H; Himo, Fahmi

    2008-07-01

    The dehalogenation reaction of haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 was investigated theoretically using hybrid density functional theory methods. HheC catalyzes the enantioselective conversion of halohydrins into their corresponding epoxides. The reaction is proposed to be mediated by a catalytic Ser132-Tyr145-Arg149 triad, and a distinct halide binding site is suggested to facilitate halide displacement by stabilizing the free ion. We investigated the HheC-mediated dehalogenation of (R)-2-chloro-1-phenylethanol using three quantum chemical models of various sizes. The calculated barriers and reaction energies give support to the suggested reaction mechanism. The dehalogenation occurs in a single concerted step, in which Tyr145 abstracts a proton from the halohydrin substrate and the substrate oxyanion displaces the chloride ion, forming the epoxide. Characterization of the involved stationary points is provided. Furthermore, by using three different models of the halide binding site, we are able to assess the adopted modeling methodology.

  12. Oscillating chemiluminescence with thiosemicarbazide in a batch reactor.

    PubMed

    Sorouraddin, M H; Iranifam, M

    2008-01-01

    Oscillating chemical reactions are complex systems involving a large number of chemical species. In oscillating chemical reactions, some species, usually reaction intermediates, exhibit fluctuations in their concentration. In this report, a novel slowly-damped oscillating chemiluminescence produced by the addition of thiosemicarbazide (TSC) to the oscillating system H2O2-KSCN-CuSO4-NaOH was investigated. Narrow and slightly asymmetric light pulses of 1.5 s half-width are emitted at 440 nm, with an oscillation period of 22-363 s, an induction period of 9-397 s and an emitted light time of 700-1500 s, depending on reagent concentrations. In this study the dependence of the induction period and the oscillation period on the reagent concentrations was investigated and both parameters were plotted with respect to reagent concentrations. Copper concentration showed a significant effect on the oscillation period. A possible mechanism for the oscillating chemiluminescence reaction is discussed.

  13. A chemical reaction network solver for the astrophysics code NIRVANA

    NASA Astrophysics Data System (ADS)

    Ziegler, U.

    2016-02-01

    Context. Chemistry often plays an important role in astrophysical gases. It regulates thermal properties by changing species abundances and via ionization processes. This way, time-dependent cooling mechanisms and other chemistry-related energy sources can have a profound influence on the dynamical evolution of an astrophysical system. Modeling those effects with the underlying chemical kinetics in realistic magneto-gasdynamical simulations provide the basis for a better link to observations. Aims: The present work describes the implementation of a chemical reaction network solver into the magneto-gasdynamical code NIRVANA. For this purpose a multispecies structure is installed, and a new module for evolving the rate equations of chemical kinetics is developed and coupled to the dynamical part of the code. A small chemical network for a hydrogen-helium plasma was constructed including associated thermal processes which is used in test problems. Methods: Evolving a chemical network within time-dependent simulations requires the additional solution of a set of coupled advection-reaction equations for species and gas temperature. Second-order Strang-splitting is used to separate the advection part from the reaction part. The ordinary differential equation (ODE) system representing the reaction part is solved with a fourth-order generalized Runge-Kutta method applicable for stiff systems inherent to astrochemistry. Results: A series of tests was performed in order to check the correctness of numerical and technical implementation. Tests include well-known stiff ODE problems from the mathematical literature in order to confirm accuracy properties of the solver used as well as problems combining gasdynamics and chemistry. Overall, very satisfactory results are achieved. Conclusions: The NIRVANA code is now ready to handle astrochemical processes in time-dependent simulations. An easy-to-use interface allows implementation of complex networks including thermal processes

  14. Deblocking reaction of chemically amplified ArF positive resists

    NASA Astrophysics Data System (ADS)

    Yamana, Mitsuharu; Itani, Toshiro; Yoshino, Hiroshi; Hashimoto, Shuichi; Tanabe, Hiroyoshi; Kasama, Kunihiko

    1998-06-01

    Deblocking reaction mechanisms and lithographic performance in chemically amplified positive ArF resists were investigated by analyzing acid concentration and blocking level. The resists consisted of triphenylsulfonium triflate as a acid generator and either the copolymer, poly(carboxy- tetracyclododecyl methacrylate70-co- tetrahydropyranylcarboxy-tetracyclododecyl methacrylate30) or the terpolymer, poly(tricyclodecylacrylate60- co-tetrahydropyranylmethacrylate20-co-methacrylic acid20). The deblocking reaction mechanisms were evaluated from Arrhenius plots of the deblocking reaction rate constant. It was found that the deblocking reaction of both resists is ruled by two rate-determining steps, i.e., reaction-controlled in the low-temperature region and acid- diffusion-controlled in the high-temperature region. Furthermore, the copolymer resist had better post-exposure- delay (PED) stability. To clarify this result, acid loss caused by air-born contamination effect on deblocking reaction was investigated. The change of amount of blocking group by acid loss was small for the copolymer. Therefore the copolymer resist had better PED stability. Furthermore, the post-exposure bake (PEB) sensitivity of linewidth of the copolymer resist was smaller than that of the terpolymer resist. Both deblocking reaction rate constant and reverse reaction rate constant of the copolymer resist increased with PEB temperature. As a result, equilibrium constant of the copolymer was not valuable with temperature. This is the reason why the copolymer resist has low PEB sensitivity. It is concluded that small acid loss effect on deblocking reaction induces better PED stability. A resist with reverse reaction has an advantage for PEB temperature sensitivity.

  15. Photo-induced chemical reaction of trans-resveratrol.

    PubMed

    Zhao, Yue; Shi, Meng; Ye, Jian-Hui; Zheng, Xin-Qiang; Lu, Jian-Liang; Liang, Yue-Rong

    2015-03-15

    Photo-induced chemical reaction of trans-resveratrol has been studied. UV B, liquid state and sufficient exposure time are essential conditions to the photochemical change of trans-resveratrol. Three principal compounds, cis-resveratrol, 2,4,6-phenanthrenetriol and 2-(4-hydroxyphenyl)-5,6-benzofurandione, were successively generated in the reaction solution of trans-resveratrol (0.25 mM, 100% ethanol) under 100 μW cm(-2) UV B radiation for 4h. cis-Resveratrol, originated from isomerization of trans-resveratrol, resulted in 2,4,6-phenanthrenetriol through photocyclisation reaction meanwhile loss of 2 H. 2,4,6-Phenanthrenetriol played a role of photosensitizer producing singlet oxygen in the reaction pathway. The singlet oxygen triggered [4+2] cycloaddition reaction of trans-resveratrol, and then resulted in the generation of 2-(4-hydroxyphenyl)-5,6-benzofurandione through photorearrangement and oxidation reaction. The singlet oxygen reaction was closely related to the substrate concentration of trans-resveratrol in solution. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

    We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

  17. Controlling chemical oscillations in heterogeneous Belousov-Zhabotinsky gels via mechanical strain.

    PubMed

    Yashin, Victor V; Van Vliet, Krystyn J; Balazs, Anna C

    2009-04-01

    We performed theoretical and computational studies to determine the effect of an applied mechanical strain on the dynamic behavior of heterogeneous polymer gels undergoing the oscillatory Belousov-Zhabotinsky (BZ) reaction. In these spatially heterogeneous gels, the catalyst for the reaction is localized in specific patches within the polymer network and the BZ reaction only occurs within these catalyst-containing patches, which we refer to as BZ patches. We focused on a model for a one-dimensional system, and further assumed that the BZ reaction did not affect the degree of swelling within the gel. For gels having one and two BZ patches, we found that a tensile or compressive strain could induce transitions between the oscillatory and nonoscillatory, steady-state regimes of the system. For certain values of the BZ stoichiometric parameter f , these transitions could exhibit a hysteresis. In systems having two oscillating BZ patches, an applied strain could cause a switching between the in-phase and out-of-phase synchronization of the oscillations. The ability to controllably alter the dynamic behavior of BZ gels through mechanical deformations opens up the possibility of using these materials in the design of chemo-mechanical sensors.

  18. Laser studies of chemical reaction and collision processes

    SciTech Connect

    Flynn, G.

    1993-12-01

    This work has concentrated on several interrelated projects in the area of laser photochemistry and photophysics which impinge on a variety of questions in combustion chemistry and general chemical kinetics. Infrared diode laser probes of the quenching of molecules with {open_quotes}chemically significant{close_quotes} amounts of energy in which the energy transferred to the quencher has, for the first time, been separated into its vibrational, rotational, and translational components. Probes of quantum state distributions and velocity profiles for atomic fragments produced in photodissociation reactions have been explored for iodine chloride.

  19. Towards chemically accurate simulation of molecule-surface reactions.

    PubMed

    Kroes, Geert-Jan

    2012-11-21

    This perspective addresses four challenges facing theorists whose aim is to make quantitatively accurate predictions for reactions of molecules on metal surfaces, and suggests ways of meeting these challenges, focusing on dissociative chemisorption reactions of H(2), N(2), and CH(4). Addressing these challenges is ultimately of practical importance to a more accurate description of overall heterogeneously catalysed reactions, which play a role in the production of more than 90% of man-made chemicals. One challenge is to describe the interaction of a molecule with a metal surface with chemical accuracy, i.e., with errors in reaction barrier heights less than 1 kcal mol(-1). In this framework, the potential of a new implementation of specific reaction parameter density functional theory (SRP-DFT) will be discussed, with emphasis on applications to reaction of H(2) with metal surfaces. Two additional challenges are to come up with improved descriptions of the effects of phonons and electron-hole pairs on reaction of molecules like N(2) on metal surfaces. Phonons can be tackled using sudden approximations in quantum dynamics, and through Ab Initio Molecular Dynamics (AIMD) calculations using classical dynamics. To additionally achieve an accurate description of the effect of electron-hole pair excitation on dissociative chemisorption within a classical dynamics framework, it may be possible to combine AIMD with electronic friction. The fourth challenge we will consider is how to achieve an accurate quantum mechanical description of the dissociative chemisorption of a polyatomic molecule, like methane, on a metal surface. A method of potential interest is the Multi-Configuration Time-Dependent Hartree (MCTDH) method.

  20. Chemical reaction fouling model for single-phase heat transfer

    SciTech Connect

    Panchal, C.B.; Watkinson, A.P.

    1993-08-01

    A fouling model was developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermalboundary layer, or at the fluid/wall interface, depending upon the interactive effects of flu id dynamics, heat and mass transfer, and the controlling chemical reaction. The analysis was used to examine the experimental data for fouling deposition of polyperoxides produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries were analyzed. The results showed that the relative effects of physical parameters on the fouling rate would differ for the three fouling mechanisms; therefore, it is important to identify the controlling mechanism in applying the closed-flow-loop data to industrial conditions.

  1. Advanced chemical heat pumps using liquid-vapor reactions

    NASA Astrophysics Data System (ADS)

    Kirol, L.

    Chemical heat pumps utilizing liquid-vapor reactions can be configured in forms analogous to electric drive vapor-compression heat pumps and heat activated absorption heat pumps. Basic thermodynamic considerations eliminate some heat pumps and place restrictive working fluid requirements on others, but two thermodynamically feasible systems have significant potential advantage over conventional technology. An electric drive reactive heat pump can use smaller heat exchangers and compressor than a vapor-compression machine, and have more flexible operating characteristics. A waste heat driven heat pump (temperature amplifier) using liquid-vapor chemical reactions can operate with higher coefficient of performance and smaller heat exchangers than an absorption temperature amplifying heat pump. Higher temperatures and larger temperature lifts should also be possible.

  2. Crossed molecular beam studies of atmospheric chemical reaction dynamics

    SciTech Connect

    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 + O3 → ClO + O2 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 + O3 → ClO + O2 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 + O3 reaction. The Br + O3 reaction has a direct reaction mechanism similar to that of the Cl + O3 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 + NO2 → 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 NO2

  3. Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators.

    PubMed

    Ghoshal, Gourab; Muñuzuri, Alberto P; Pérez-Mercader, Juan

    2016-01-12

    Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.

  4. Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators

    PubMed Central

    Ghoshal, Gourab; Muñuzuri, Alberto P.; Pérez-Mercader, Juan

    2016-01-01

    Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers. PMID:26753772

  5. Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators

    NASA Astrophysics Data System (ADS)

    Ghoshal, Gourab; Muñuzuri, Alberto P.; Pérez-Mercader, Juan

    2016-01-01

    Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.

  6. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    SciTech Connect

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  7. Separation of the isotopes of boron by chemical exchange reactions

    DOEpatents

    McCandless, Frank P.; Herbst, Ronald S.

    1995-01-01

    The isotopes of boron, .sup.10 B and .sup.11 B, are separated by means of a gas-liquid chemical exchange reaction involving the isotopic equilibrium between gaseous BF.sub.3 and a liquid BF.sub.3 . donor molecular addition complex formed between BF.sub.3 gas and a donor chosen from the group consisting of: nitromethane, acetone, methyl isobutyl ketone, or diisobutyl ketone.

  8. New Method to Acquire Chemomechanical Parameters of Diverse Chemical Reactions

    DTIC Science & Technology

    2011-01-30

    susceptibility of electrophilic sites in polymers to nucleophilic attack (e.g., by water ), which is thought to be a major initiation mechanism of strain...reactions offers unique attributes, e.g., potentially fast actuation cycles , high chemical and mechanical stability, flexible device design and...a model for reversible and pseudoreversible isothermal photoactuation based on the Carnot -type formalism and used it to estimate the maximum single

  9. Exploring chemical diversity via a modular reaction pairing strategy

    PubMed Central

    Loh, Joanna K; Yoon, Sun Young; Samarakoon, Thiwanka B; Rolfe, Alan; Porubsky, Patrick; Neuenswander, Benjamin; Lushington, Gerald H

    2012-01-01

    Summary The efficient synthesis of an 80-member library of unique benzoxathiazocine 1,1-dioxides by a microwave-assisted, intermolecular nucleophilic aromatic substitution (SNAr) diversification pathway is reported. Eight benzofused sultam cores were generated by means of a sulfonylation/SNAr/Mitsunobu reaction pairing protocol, and subsequently diversified by intermolecular SNAr with ten chiral, non-racemic amine/amino alcohol building blocks. Computational analyses were employed to explore and evaluate the chemical diversity of the library. PMID:23019462

  10. Shock-Induced Chemical Reactions in Condensed Matter.

    DTIC Science & Technology

    1982-08-01

    Technical, 4/1/78 - 6/30/82 Matter 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(s) S. CONTRACT OR GRANT NUMUER(e) George E. Duvall, Principal Investigator...CHEMICAL REACTIONS IN CONDENSED MATTER George E. Duvall, Principal Investigator Stephen A. Sheffield* Kendal M. OgilvieT 4 C. Robert Wilson Paul...Temperture," in Sixth Symposium (International on Detonation (Office of Naval Research, Arlington, 1976), ACR-Z21, p. 36. 24. G. Gamow , "Tentative

  11. A microvascular system for chemical reactions using surface waste heat.

    PubMed

    Nguyen, Du Thai; Esser-Kahn, Aaron P

    2013-12-16

    Coffee-powered chemistry: Low-grade waste heat on surfaces can be used to drive chemical reactions, including the regeneration of a CO2 capture solution. Flowing two-phase heat transfer has been implemented within microvascular systems. This stripping system can be adapted to pre-fabricated surfaces, as demonstrated by a coffee mug containing a 1.2 m long microchannel. MEA=monoethanolamine.

  12. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks.

    PubMed

    Smadbeck, Patrick; Kaznessis, Yiannis N

    2014-08-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized.

  13. Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks

    PubMed Central

    Smadbeck, Patrick; Kaznessis, Yiannis N.

    2014-01-01

    Stochasticity in the dynamics of small reacting systems requires discrete-probabilistic models of reaction kinetics instead of traditional continuous-deterministic ones. The master probability equation is a complete model of randomly evolving molecular populations. Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks. With the first solution of chemical master equations, a wide range of experimental observations of small-system interactions may be mathematically conceptualized. PMID:25215268

  14. Separation of the isotopes of boron by chemical exchange reactions

    DOEpatents

    McCandless, F.P.; Herbst, R.S.

    1995-05-30

    The isotopes of boron, {sup 10}B and {sup 11}B, are separated by means of a gas-liquid chemical exchange reaction involving the isotopic equilibrium between gaseous BF{sub 3} and a liquid BF{sub 3} donor molecular addition complex formed between BF{sub 3} gas and a donor chosen from the group consisting of: nitromethane, acetone, methyl isobutyl ketone, or diisobutyl ketone. 1 Fig.

  15. Nitrosonium cation in chemical and biochemical reactions: achievements and prospects

    NASA Astrophysics Data System (ADS)

    Borodkin, G. I.; Shubin, V. G.

    2017-01-01

    Data on the reactivity of nitrosonium cation in chemical reactions are systematized and integrated. The review demonstrates the structural diversity of nitrosonium complexes resulting from the specific features of the electronic structure of NO+. The use of nitrosonium salts in the synthesis of heterocyclic compounds and for the preparation of modern materials, including nanomaterials, is considered. The participation of NO+ in oxidative, catalytic and biochemical processes is discussed. The bibliography includes 332 references.

  16. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.

    PubMed

    Khavrutskii, Ilja V; Smith, Jason B; Wallqvist, Anders

    2013-10-28

    Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM∕molecular mechanical (QM∕MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP∕6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP∕6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal∕mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM∕MM studies of reaction mechanisms.

  17. Chemical Characterization and Reactivity of Fuel-Oxidizer Reaction Product

    NASA Technical Reports Server (NTRS)

    David, Dennis D.; Dee, Louis A.; Beeson, Harold D.

    1997-01-01

    Fuel-oxidizer reaction product (FORP), the product of incomplete reaction of monomethylhydrazine and nitrogen tetroxide propellants prepared under laboratory conditions and from firings of Shuttle Reaction Control System thrusters, has been characterized by chemical and thermal analysis. The composition of FORP is variable but falls within a limited range of compositions that depend on three factors: the fuel-oxidizer ratio at the time of formation; whether the composition of the post-formation atmosphere is reducing or oxidizing; and the reaction or post-reaction temperature. A typical composition contains methylhydrazinium nitrate, ammonium nitrate, methylammonium nitrate, and trace amounts of hydrazinium nitrate and 1,1-dimethylhydrazinium nitrate. Thermal decomposition reactions of the FORP compositions used in this study were unremarkable. Neither the various compositions of FORP, the pure major components of FORP, nor mixtures of FORP with propellant system corrosion products showed any unusual thermal activity when decomposed under laboratory conditions. Off-limit thruster operations were simulated by rapid mixing of liquid monomethylhydrazine and liquid nitrogen tetroxide in a confined space. These tests demonstrated that monomethylhydrazine, methylhydrazinium nitrate, ammonium nitrate, or Inconel corrosion products can induce a mixture of monomethylhydrazine and nitrogen tetroxide to produce component-damaging energies. Damaging events required FORP or metal salts to be present at the initial mixing of monomethylhydrazine and nitrogen tetroxide.

  18. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization

    NASA Astrophysics Data System (ADS)

    Khavrutskii, Ilja V.; Smith, Jason B.; Wallqvist, Anders

    2013-10-01

    Here, we apply the harmonic Fourier beads (HFB) path optimization method to study chemical reactions involving covalent bond breaking and forming on quantum mechanical (QM) and hybrid QM/molecular mechanical (QM/MM) potential energy surfaces. To improve efficiency of the path optimization on such computationally demanding potentials, we combined HFB with conjugate gradient (CG) optimization. The combined CG-HFB method was used to study two biologically relevant reactions, namely, L- to D-alanine amino acid inversion and alcohol acylation by amides. The optimized paths revealed several unexpected reaction steps in the gas phase. For example, on the B3LYP/6-31G(d,p) potential, we found that alanine inversion proceeded via previously unknown intermediates, 2-iminopropane-1,1-diol and 3-amino-3-methyloxiran-2-ol. The CG-HFB method accurately located transition states, aiding in the interpretation of complex reaction mechanisms. Thus, on the B3LYP/6-31G(d,p) potential, the gas phase activation barriers for the inversion and acylation reactions were 50.5 and 39.9 kcal/mol, respectively. These barriers determine the spontaneous loss of amino acid chirality and cleavage of peptide bonds in proteins. We conclude that the combined CG-HFB method further advances QM and QM/MM studies of reaction mechanisms.

  19. Implementation of a vibrationally linked chemical reaction model for DSMC

    NASA Technical Reports Server (NTRS)

    Carlson, A. B.; Bird, Graeme A.

    1994-01-01

    A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.

  20. Harmonic oscillator representation in the theory of scattering and nuclear reactions

    NASA Technical Reports Server (NTRS)

    Smirnov, Yuri F.; Shirokov, A. M.; Lurie, Yuri, A.; Zaitsev, S. A.

    1995-01-01

    The following questions, concerning the application of the harmonic oscillator representation (HOR) in the theory of scattering and reactions, are discussed: the formulation of the scattering theory in HOR; exact solutions of the free motion Schroedinger equation in HOR; separable expansion of the short range potentials and the calculation of the phase shifts; 'isolated states' as generalization of the Wigner-von Neumann bound states embedded in continuum; a nuclear coupled channel problem in HOR; and the description of true three body scattering in HOR. As an illustration the soft dipole mode in the (11)Li nucleus is considered in a frame of the (9)Li+n+n cluster model taking into account of three body continuum effects.

  1. Nanochemistry - Chemical Reactions of Iron and Benzene Within Molecular Clusters

    NASA Astrophysics Data System (ADS)

    Feigerle, C. S.; Bililign, S.; Miller, John C.

    2000-06-01

    Molecular clusters represent a nanoscale test tube where chemical reactions can be examined in a unique way for the effects of the local environment and the possibility of size-dependent reactions. Previous experiments have shown that the ionization/dissociation of iron pentacarbonyl clusters can lead to the formation of iron ions and iron cluster ions and that these species can further react with dopant molecules to yield chemically rearranged products. The present experiments characterize similar reactions with benzene molecules and clusters. Heteroclusters of the form [Fe(CO)5]m(C6H6)nArp are created in an expanding supersonic jet of the component molecules. Following ionization by a 30 ps, 266 nm laser pulse, extensive dissociation, aggregation, and chemical rearrangement occurs leading to ionic products which are characterized by mass spectrometry. Cluster ions of the type Fem(C6H6)n + are observed as products. The stability of the sandwich form of the ion, Fe(benzene)2 +, is inferred from the data. Evidence for a similar special stability for the double-decker, Fe2(benzene)3 +, is presented.

  2. Self-oscillation of polymer chains with an Fe(bpy)3 catalyst induced by the Belousov-Zhabotinsky reaction.

    PubMed

    Hara, Yusuke; Fujimoto, Kenji; Mayama, Hiroyuki

    2014-01-16

    We successfully synthesized poly(N-isopropylacrylamide) covalently bonded to a Fe(bpy)3 catalyst moiety for the Belousov-Zhabotinsky (BZ) reaction. The lower critical solution temperature (LCST) of the polymer chain in the oxidized state had a slightly greater than that in the reduced state. This resulted in the polymer undergoing soluble-insoluble self-oscillation induced by the BZ reaction at constant temperatures. In addition, the period of the self-oscillation of the polymer chain shows a linear dependence on the temperature.

  3. Phase and chemical equilibria in multicomponent fluid systems with a chemical reaction

    NASA Astrophysics Data System (ADS)

    Toikka, A. M.; Samarov, A. A.; Toikka, M. A.

    2015-04-01

    Studies of the phase and chemical equilibria in the systems with chemical reaction cover a wide range of problems related to both experimental determination of physicochemical characteristics of these systems and various aspects of thermodynamic analysis of the phase and chemical processes occurring there. The main goal of this review consists in systematization and analysis of available experimental data concerning the vapour-liquid and liquid-liquid equilibria in multicomponent systems where chemical reactions occur. The studies considered here have been mainly published in recent years, and they include rather detailed data on physicochemical properties, phase transitions and chemical processes in fluid systems, i.e., the data which are essential for thermodynamic analysis. Available approaches to the thermodynamic analysis of heterogeneous systems with chemical reactions are also discussed. Particular attention is paid to the studies of the simultaneous phase and chemical equilibria. We hope that this review could be useful both for fundamental studies of heterogeneous reactive systems and for solving applied problems on the design of combined reactive and mass-transfer processes. The bibliography includes 79 references.

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

    SciTech Connect

    Gray, S.K.

    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.

  5. Laser-initiated chemical reactions in carbon suspensions.

    SciTech Connect

    McGrath, T. E.; Diebold, G. J.; Bartels, D. M.; Crowell, R. A.; Chemistry; Brown Univ.

    2002-10-31

    We report on laser-initiated chemical reactions in colloidal carbon suspensions. Irradiation of carbon particles ranging in size from 13 to 75 nm in diameter suspended in water, toluene, and benzene with high power nanosecond, picosecond, and femtosecond laser pulses leads to the formation of a number of gaseous hydrocarbons as well as a series of liquid-phase products. In the product gas above irradiated carbon suspensions in water, H{sub 2} and CO, the main reaction products of the carbon-steam reaction, and numerous hydrocarbons ranging from C{sub 1}-C{sub 4} were detected. Irradiation of particulate carbon in toluene and benzene gave H{sub 2} as the main gas product with small amounts of C{sub 1}-C{sub 3} hydrocarbons. Bibenzyl and biphenyl were found as the main liquid products produced in toluene and benzene suspensions, respectively, but with numerous polycyclic aromatic hydrocarbons in smaller concentrations. The amount of products generated by pulsed laser irradiation is shown to depend on particle size and concentration, as well as the laser fluence and pulse width. The chemical reactions reported take place under conditions characterized by extremely high temperatures and pressures of short duration.

  6. Effect of aspect ratio on chemical reactions on microchip.

    PubMed

    Shimizu, Takahiro; Masaki, Hiroyuki; Korenaga, Takashi

    2006-01-01

    Parallel two-phase laminar flow, which is formed when two solutions flow in microchannels, has been developed and has advanced unique research in the area of microchip analysis. In two-phase laminar flow, channel size has a significant effect on the efficiency of chemical reactions. However, the sizes of microchannels vary greatly in many studies. In this paper, we report on the effect of microchannel size on chemical reactions on a microchip. Aspect ratio is defined as the ratio of depth to width of a microchannel. Five microchips with different aspect ratios (from 0.50 to 2.00) were fabricated by mechanical machining. The reaction of nitrous acid and Saltzman reagent was carried out on these microchips and the absorbance was measured on-line in a capillary tube, which was attached to the outlet on the microchip. The results showed that the color reaction occurred more efficiently as the aspect ratio increased. This result is expected to be useful when determining the size of microchannels.

  7. Arbitrarily Complex Chemical Reactions on Particles

    NASA Astrophysics Data System (ADS)

    Benson, D. A.; Bolster, D.

    2016-12-01

    Previous particle-tracking (PT) algorithms for chemical reaction conceptualize each particle being composed of one species. Reactions occur by either complete or partial birth/death processes between interacting particles. Here we extend the method by placing any number of chemical species on each particle, thereby allowing the single-step calculation of arbitrarily complex reactions using standard methods. The algorithm relies on calculating the correct mass transfer of species between particles, which is exactly given by our previous probabilistic algorithm. The various novel components of the new method are verified against analytic solutions where possible. The potential benefits of the method have been discussed elsewhere in the context of simple bimolecular reactions: the PT method does not artificially mix constituents by numerical dispersion, the particles do not have a Courant number criterion for stability, and the number of particles is very often going to be smaller than the number of cells in a typical grid-based simulation, so that the number of numerical geochemical calculations is similarly smaller.

  8. The nature of chemical reaction-driven tip-streaming

    NASA Astrophysics Data System (ADS)

    Mayer, H. C.; Krechetnikov, R.

    2013-05-01

    The discovery of chemical reaction-driven tip-streaming (also known as "an amazing drop") was made about a decade ago during measurements of the dynamic interfacial tension of a water-alkali pendant droplet immersed in oil-linoleic acid. A plausible explanation for this self-sustained ejection of micron sized droplets from the tip of the macroscopic pendant drop was offered at that time and attributed to Marangoni stresses driving the reaction-produced surfactant along the interface. Later, asymptotic theory based on the analysis of a complete fluid dynamical formulation supported this hypothesis. As this discovery promised a way of microdroplet generation without the need for complex microchannel geometries or externally imposed flow or electric fields, we were recently motivated to study the influence of the reagent concentrations and reaction rate on the droplet generation. However, in an attempt to recreate the original experiments, we revealed that the cause for tip-streaming is not what it originally seemed to be. This led to a series of experiments clarifying the role of the Marangoni stresses and the crucial differences from similar phenomena. As the mechanism by which the phenomenon was originally thought to operate was supported by recent theoretical studies, the present work leads to new intriguing questions of existence and conditions under which a chemical reaction alone can drive Marangoni stresses capable of self-sustaining the process of tip-streaming.

  9. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach.

    PubMed

    van Roekel, Hendrik W H; Rosier, Bas J H M; Meijer, Lenny H H; Hilbers, Peter A J; Markvoort, Albert J; Huck, Wilhelm T S; de Greef, Tom F A

    2015-11-07

    Living cells are able to produce a wide variety of biological responses when subjected to biochemical stimuli. It has become apparent that these biological responses are regulated by complex chemical reaction networks (CRNs). Unravelling the function of these circuits is a key topic of both systems biology and synthetic biology. Recent progress at the interface of chemistry and biology together with the realisation that current experimental tools are insufficient to quantitatively understand the molecular logic of pathways inside living cells has triggered renewed interest in the bottom-up development of CRNs. This builds upon earlier work of physical chemists who extensively studied inorganic CRNs and showed how a system of chemical reactions can give rise to complex spatiotemporal responses such as oscillations and pattern formation. Using purified biochemical components, in vitro synthetic biologists have started to engineer simplified model systems with the goal of mimicking biological responses of intracellular circuits. Emulation and reconstruction of system-level properties of intracellular networks using simplified circuits are able to reveal key design principles and molecular programs that underlie the biological function of interest. In this Tutorial Review, we present an accessible overview of this emerging field starting with key studies on inorganic CRNs followed by a discussion of recent work involving purified biochemical components. Finally, we review recent work showing the versatility of programmable biochemical reaction networks (BRNs) in analytical and diagnostic applications.

  10. Oscillations in the stability of consecutive chemical bonds revealed by ion-induced desorption.

    PubMed

    Ossowski, Jakub; Rysz, Jakub; Krawiec, Mariusz; Maciazek, Dawid; Postawa, Zbigniew; Terfort, Andreas; Cyganik, Piotr

    2015-01-19

    While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self-assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary-ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule-metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical-bond stability have a very general nature and break the translational symmetry in molecules.

  11. Physio-chemical reactions in recycle aggregate concrete.

    PubMed

    Tam, Vivian W Y; Gao, X F; Tam, C M; Ng, K M

    2009-04-30

    Concrete waste constitutes the major proportion of construction waste at about 50% of the total waste generated. An effective way to reduce concrete waste is to reuse it as recycled aggregate (RA) for the production of recycled aggregate concrete (RAC). This paper studies the physio-chemical reactions of cement paste around aggregate for normal aggregate concrete (NAC) and RAC mixed with normal mixing approach (NMA) and two-stage mixing approach (TSMA) by differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). Four kinds of physio-chemical reactions have been recorded from the concrete samples, including the dehydration of C(3)S(2)H(3), iron-substituted ettringite, dehydroxylation of CH and development of C(6)S(3)H at about 90 degrees C, 135 degrees C, 441 degrees C and 570 degrees C, respectively. From the DSC results, it is confirmed that the concrete samples with RA substitution have generated less amount of strength enhancement chemical products when compared to those without RA substitution. However, the results from the TSMA are found improving the RAC quality. The pre-mix procedure of the TSMA can effectively develop some strength enhancing chemical products including, C(3)S(2)H(3), ettringite, CH and C(6)S(3)H, which shows that RAC made from the TSMA can improve the hydration processes.

  12. Mesoscale simulations of shockwave energy dissipation via chemical reactions

    NASA Astrophysics Data System (ADS)

    Antillon, Edwin; Strachan, Alejandro

    2015-06-01

    We use a particle-based mesoscale model that incorporates chemical reactions at a coarse-grained level to study the response of materials under shockwave-loading conditions. An additional implicit variable (the particle size) is used to describe volume-reducing chemical reactions using an intra-molecular potential inspired by Transition State Theory, while the dynamics of the center-of-mass motion evolves according to inter-particle forces. The equations of motion are derived from a Hamiltonian and the model captures both: total energy conservation and Galilean invariance. We demonstrate that this model captures complex thermo-mechanical-chemical processes, and we use these features to explore materials with the capabilities to dissipate shocks-wave energy due to ballistic impacts. Our results characterize how the parameters of the chemical model affect shock-wave attenuation, and we elucidate on how the coupling between the different energy-transferring mechanisms influences nucleation of chemistry for conditions away from equilibrium.

  13. Reversible chemical reactions for single-color multiplexing microscopy.

    PubMed

    Brox, Dominik; Schwering, Michael; Engelhardt, Johann; Herten, Dirk-Peter

    2014-08-04

    Recent developments in biology demand an increasing number of simultaneously imaged structures with standard fluorescence microscopy. However, the number of multiplexed channels is limited for most multiplexing modalities, such as spectral multiplexing or fluorescence-lifetime imaging. We propose extending the number of imaging channels by using chemical reactions, controlling the emissive state of fluorescent dyes. As proof of concept, we reversibly switch a fluorescent copper sensor to enable successive imaging of two different structures in the same spectral channel. We also show that this chemical multiplexing is orthogonal to existing methods. By using two different dyes, we combine chemical with spectral multiplexing for the simultaneous imaging of four different structures with only two spectrally different channels. We characterize and discuss the approach and provide perspectives for extending imaging modalities in stimulated emission depletion microscopy, for which spectral multiplexing is technically demanding.

  14. APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

    SciTech Connect

    Nguyen, H.D.

    1991-11-01

    Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.

  15. APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

    SciTech Connect

    Nguyen, H.D.

    1991-11-01

    Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable to other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.

  16. Probing a chemical compass: novel variants of low-frequency reaction yield detected magnetic resonance.

    PubMed

    Maeda, Kiminori; Storey, Jonathan G; Liddell, Paul A; Gust, Devens; Hore, P J; Wedge, C J; Timmel, Christiane R

    2015-02-07

    We present a study of a carotenoid-porphyrin-fullerene triad previously shown to function as a chemical compass: the photogenerated carotenoid-fullerene radical pair recombines at a rate sensitive to the orientation of an applied magnetic field. To characterize the system we develop a time-resolved Low-Frequency Reaction Yield Detected Magnetic Resonance (tr-LF-RYDMR) technique; the effect of varying the relative orientation of applied static and 36 MHz oscillating magnetic fields is shown to be strongly dependent on the strength of the oscillating magnetic field. RYDMR is a diagnostic test for involvement of the radical pair mechanism in the magnetic field sensitivity of reaction rates or yields, and has previously been applied in animal behavioural experiments to verify the involvement of radical-pair-based intermediates in the magnetic compass sense of migratory birds. The spectroscopic selection rules governing RYDMR are well understood at microwave frequencies for which the so-called 'high-field approximation' is valid, but at lower frequencies different models are required. For example, the breakdown of the rotating frame approximation has recently been investigated, but less attention has so far been given to orientation effects. Here we gain physical insights into the interplay of the different magnetic interactions affecting low-frequency RYDMR experiments performed in the challenging regime in which static and oscillating applied magnetic fields as well as internal electron-nuclear hyperfine interactions are of comparable magnitude. Our observations aid the interpretation of existing RYDMR-based animal behavioural studies and will inform future applications of the technique to verify and characterize further the biological receptors involved in avian magnetoreception.

  17. Self-oscillation of polymer chains induced by the Belousov-Zhabotinsky reaction under acid-free conditions.

    PubMed

    Hara, Yusuke; Yoshida, Ryo

    2005-05-19

    A novel self-oscillating polymer was prepared by utilizing the Belousov-Zhabotinsky (BZ) reaction. In this study, a sulfonic acid group was newly introduced as a pH-control site into the copolymer of N-isopropylacrylamide, and the ruthenium complex was introduced as a catalyst site. By introducing the pH-control site, we succeed in causing the soluble-insoluble self-oscillation of the polymer solution under acid-free conditions in which only two BZ substrates, malonic acid and sodium bromate, were present as added agents. The self-oscillating behavior was remarkably influenced by the temperature and polymer concentration, which reflects the intermolecular aggregative capacity of the polymer chains in the reduced state to change the lower critical solution temperature. This achievement of self-oscillation of polymer chains under acid-free conditions may lead to their practical use as novel biomimetic materials under biological conditions.

  18. Oscillatory template exchange in polyoxometalate capsules: a ligand-triggered, redox-powered, chemically damped oscillation.

    PubMed

    Miras, Haralampos N; Sorus, Marjorie; Hawkett, Jonathan; Sells, Daniel O; McInnes, Eric J L; Cronin, Leroy

    2012-04-25

    The redox-controlled driven oscillatory template exchange between phosphate (P) and vanadate (V) anions enclosed in an {X(2)M(18)} cluster is reported. Extensive investigations using a range of techniques, including correlated ESI-MS, EPR, and UV-vis as a function of reaction time, showed that six complete oscillations interconverting the capsule species present in solution from {P(2)M(18)} to {V(2)M(18)} were possible, provided that a sufficient concentration of the TEA reducing agent was present in solution.

  19. Compare and contrast the reaction coordinate diagrams for chemical reactions and cytoskeletal force generators

    PubMed Central

    Scholey, Jonathan M.

    2013-01-01

    Reaction coordinate diagrams are used to relate the free energy changes that occur during the progress of chemical processes to the rate and equilibrium constants of the process. Here I briefly review the application of these diagrams to the thermodynamics and kinetics of the generation of force and motion by cytoskeletal motors and polymer ratchets as they mediate intracellular transport, organelle dynamics, cell locomotion, and cell division. To provide a familiar biochemical context for discussing these subcellular force generators, I first review the application of reaction coordinate diagrams to the mechanisms of simple chemical and enzyme-catalyzed reactions. My description of reaction coordinate diagrams of motors and polymer ratchets is simplified relative to the rigorous biophysical treatment found in many of the references that I use and cite, but I hope that the essay provides a valuable qualitative representation of the physical chemical parameters that underlie the generation of force and motility at molecular scales. In any case, I have found that this approach represents a useful interdisciplinary framework for understanding, researching, and teaching the basic molecular mechanisms by which motors contribute to fundamental cell biological processes. PMID:23408787

  20. Compare and contrast the reaction coordinate diagrams for chemical reactions and cytoskeletal force generators.

    PubMed

    Scholey, Jonathan M

    2013-02-01

    Reaction coordinate diagrams are used to relate the free energy changes that occur during the progress of chemical processes to the rate and equilibrium constants of the process. Here I briefly review the application of these diagrams to the thermodynamics and kinetics of the generation of force and motion by cytoskeletal motors and polymer ratchets as they mediate intracellular transport, organelle dynamics, cell locomotion, and cell division. To provide a familiar biochemical context for discussing these subcellular force generators, I first review the application of reaction coordinate diagrams to the mechanisms of simple chemical and enzyme-catalyzed reactions. My description of reaction coordinate diagrams of motors and polymer ratchets is simplified relative to the rigorous biophysical treatment found in many of the references that I use and cite, but I hope that the essay provides a valuable qualitative representation of the physical chemical parameters that underlie the generation of force and motility at molecular scales. In any case, I have found that this approach represents a useful interdisciplinary framework for understanding, researching, and teaching the basic molecular mechanisms by which motors contribute to fundamental cell biological processes.

  1. Experimental observation of dynamical behaviors of four, five and six oscillators in rings and nine oscillators in a branched network

    NASA Astrophysics Data System (ADS)

    Nishiyama, Nobuaki

    1995-01-01

    Cation-exchange beads loaded with ferroin were immersed in the Belousov-Zabotinsky reaction mixture and used as chemical oscillators. Four, five and six chemical oscillators were spatially distributed in rings. Coupling among the oscillators was due to mass diffusion. Spontaneous switching between two out-of-phase modes was observed in the ring oscillator systems. In the case of ring with three or four oscillators, transient extinction of oscillations was also observed. In addition, dynamical behaviors of a branched network with nine oscillators were reported.

  2. [Anaphylactic reactions to low-molecular weight chemicals].

    PubMed

    Nowak, Daria; Panaszek, Bernard

    2015-02-06

    Low-molecular weight chemicals (haptens) include a large group of chemical compounds occurring in work environment, items of everyday use (cleaning products, clothing, footwear, gloves, furniture), jewelry (earrings, bracelets), drugs, especially in cosmetics. They cause type IV hypersensitive reactions. During the induction phase of delayed-type hypersensitivity, haptens form complexes with skin proteins. After internalization through antigen presenting cells, they are bound to MHC class II molecules. Next, they are exposed against specific T-lymphocytes, what triggers activation of Th1 cells mainly. After repeating exposition to that hapten, during effector phase, Th1 induce production of cytokines affecting non-specific inflammatory cells. Usually, it causes contact dermatitis. However, occasionally incidence of immediate generalized reactions after contact with some kinds of haptens is noticed. A question arises, how the hapten does induce symptoms which are typical for anaphylaxis, and what contributes to amplification of this mechanism. It seems that this phenomenon arises from pathomechanism occurring in contact urticaria syndrome in which an anaphylactic reaction may be caused either by contact of sensitized skin with protein antigens, high-molecular weight allergens, or haptens. One of the hypotheses indicates the leading role of basophiles in this process. Their contact with haptens, may cause to release mediators of immediate allergic reaction (histamine, eicosanoids) and to produce cytokines corresponding to Th2 cells profile. Furthermore, Th17 lymphocytes secreting pro-inflammatory interleukin-17 might be engaged into amplifying hypersensitivity into immediate reactions and regulatory T-cells may play role in the process, due to insufficient control of the activity of effector cells.

  3. Computational analysis of the mechanism of chemical reactions in terms of reaction phases: hidden intermediates and hidden transition States.

    PubMed

    Kraka, Elfi; Cremer, Dieter

    2010-05-18

    Computational approaches to understanding chemical reaction mechanisms generally begin by establishing the relative energies of the starting materials, transition state, and products, that is, the stationary points on the potential energy surface of the reaction complex. Examining the intervening species via the intrinsic reaction coordinate (IRC) offers further insight into the fate of the reactants by delineating, step-by-step, the energetics involved along the reaction path between the stationary states. For a detailed analysis of the mechanism and dynamics of a chemical reaction, the reaction path Hamiltonian (RPH) and the united reaction valley approach (URVA) are an efficient combination. The chemical conversion of the reaction complex is reflected by the changes in the reaction path direction t(s) and reaction path curvature k(s), both expressed as a function of the path length s. This information can be used to partition the reaction path, and by this the reaction mechanism, of a chemical reaction into reaction phases describing chemically relevant changes of the reaction complex: (i) a contact phase characterized by van der Waals interactions, (ii) a preparation phase, in which the reactants prepare for the chemical processes, (iii) one or more transition state phases, in which the chemical processes of bond cleavage and bond formation take place, (iv) a product adjustment phase, and (v) a separation phase. In this Account, we examine mechanistic analysis with URVA in detail, focusing on recent theoretical insights (with a variety of reaction types) from our laboratories. Through the utilization of the concept of localized adiabatic vibrational modes that are associated with the internal coordinates, q(n)(s), of the reaction complex, the chemical character of each reaction phase can be identified via the adiabatic curvature coupling coefficients, A(n,s)(s). These quantities reveal whether a local adiabatic vibrational mode supports (A(n,s) > 0) or resists

  4. Localized stationary and traveling reaction-diffusion patterns in a two-layer A +B → oscillator system

    NASA Astrophysics Data System (ADS)

    Budroni, M. A.; De Wit, A.

    2016-06-01

    When two solutions containing separate reactants A and B of an oscillating reaction are put in contact in a gel, localized spatiotemporal patterns can develop around the contact zone thanks to the interplay of reaction and diffusion processes. Using the Brusselator model, we explore analytically the deployment in space and time of the bifurcation diagram of such an A +B → oscillator system. We provide a parametric classification of possible instabilities as a function of the ratio of the initial reactant concentrations and of the reaction intermediate species diffusion coefficients. Related one-dimensional reaction-diffusion dynamics are studied numerically. We find that the system can spatially localize waves and Turing patterns as well as induce more complex dynamics such as zigzag spatiotemporal waves when Hopf and Turing modes interact.

  5. Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field.

    PubMed

    Boulanger, Eliot; Thiel, Walter

    2014-04-08

    The polarization of the environment can influence the results from hybrid quantum mechanical/molecular mechanical (QM/MM) simulations of enzymatic reactions. In this article, we address several technical aspects in the development of polarizable QM/MM embedding using the Drude Oscillator (DO) force field. We propose a stable and converging update of the DO polarization state for geometry optimizations and a suitable treatment of the QM/MM-DO boundary when the QM and MM regions are separated by cutting through a covalent bond. We assess the performance of our approach by computing binding energies and geometries of three selected complexes relevant to biomolecular modeling, namely the water trimer, the N-methylacetamide dimer, and the cationic bis(benzene)sodium sandwich complex. Using a recently published MM-DO force field for proteins, we evaluate the effect of MM polarization on the QM/MM energy profiles of the enzymatic reactions catalyzed by chorismate mutase and by p-hydroxybenzoate hydroxylase. We find that inclusion of MM polarization affects the computed barriers by about 10%.

  6. Chemical reaction and dust formation studies in laboratory hydrocarbon plasmas.

    NASA Astrophysics Data System (ADS)

    Hippler, Rainer; Majumdar, Abhijit; Thejaswini, H. C.

    Plasma chemical reaction studies with relevance to, e.g., Titan's atmosphere have been per-formed in various laboratory plasmas [1,2]. Chemical reactions in a dielectric barrier discharge at medium pressure of 250-300 mbar have been studied in CH4 /N2 and CH4 /Ar gas mixtures by means of mass spectrometry. The main reaction scheme is production of H2 by fragmenta-tion of CH4 , but also production of larger hydrocarbons like Cn Hm with n up to 10 including formation of different functional CN groups is observed. [1] A. Majumdar and R. Hippler, Development of dielectric barrier discharge plasma processing apparatus for mass spectrometry and thin film deposition, Rev. Sci. Instrum. 78, 075103 (2007) [2] H.T. Do, G. Thieme, M. Frühlich, H. Kersten, and R. Hippler, Ion Molecule and Dust Particle Formation in Ar/CH4 , Ar/C2 H2 and Ar/C3 H6 Radio-frequency Plasmas, Contrib. Plasma Phys. 45, No. 5-6, 378-384 (2005)

  7. Chemical reaction network approaches to Biochemical Systems Theory.

    PubMed

    Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R

    2015-11-01

    This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Chemical reaction optimization for solving shortest common supersequence problem.

    PubMed

    Khaled Saifullah, C M; Rafiqul Islam, Md

    2016-10-01

    Shortest common supersequence (SCS) is a classical NP-hard problem, where a string to be constructed that is the supersequence of a given string set. The SCS problem has an enormous application of data compression, query optimization in the database and different bioinformatics activities. Due to NP-hardness, the exact algorithms fail to compute SCS for larger instances. Many heuristics and meta-heuristics approaches were proposed to solve this problem. In this paper, we propose a meta-heuristics approach based on chemical reaction optimization, CRO_SCS that is designed inspired by the nature of the chemical reactions. For different optimization problems like 0-1 knapsack, quadratic assignment, global numeric optimization problems CRO algorithm shows very good performance. We have redesigned the reaction operators and a new reform function to solve the SCS problem. The outcomes of the proposed CRO_SCS algorithm are compared with those of the enhanced beam search (IBS_SCS), deposition and reduction (DR), ant colony optimization (ACO) and artificial bee colony (ABC) algorithms. The length of supersequence, execution time and standard deviation of all related algorithms show that CRO_SCS gives better results on the average than all other algorithms. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Holistic Metrics for Assessment of the Greenness of Chemical Reactions in the Context of Chemical Education

    ERIC Educational Resources Information Center

    Ribeiro, M. Gabriela T. C.; Machado, Adelio A. S. C.

    2013-01-01

    Two new semiquantitative green chemistry metrics, the green circle and the green matrix, have been developed for quick assessment of the greenness of a chemical reaction or process, even without performing the experiment from a protocol if enough detail is provided in it. The evaluation is based on the 12 principles of green chemistry. The…

  10. Holistic Metrics for Assessment of the Greenness of Chemical Reactions in the Context of Chemical Education

    ERIC Educational Resources Information Center

    Ribeiro, M. Gabriela T. C.; Machado, Adelio A. S. C.

    2013-01-01

    Two new semiquantitative green chemistry metrics, the green circle and the green matrix, have been developed for quick assessment of the greenness of a chemical reaction or process, even without performing the experiment from a protocol if enough detail is provided in it. The evaluation is based on the 12 principles of green chemistry. The…

  11. Nature of the chemical reaction for furfural modified asphalt

    SciTech Connect

    Memon, G.M.; Chollar, B.H.

    1994-12-31

    Three of the most serious problems of asphalt pavements today are rutting, cracking, and susceptibility to moisture damage (stripping). Asphalt manufacturers have been mixing asphalts with polymers to produce polymer-modified asphalts with improved rheological properties. However, the costs for these improved polymer-modified asphalts are almost double that of regular asphalts. FHWA researchers have found that asphalt modified by the chemical, furfural (which is prepared by simple elimination reaction of aldopentoses obtained from oat hulls), exhibited better stripping properties and was less temperature susceptible than the virgin asphalt while costing less than polymer-modified asphalts. This paper discusses the possible structure of the furfural-modified asphalt, data for the virgin and furfural-modified asphalts and their Corbett fractions, data from a model reaction between phenol and furfural, and a possible explanation of this structure based on these data.

  12. Chemical characteristics of mineral trioxide aggregate and its hydration reaction

    PubMed Central

    2012-01-01

    Mineral trioxide aggregate (MTA) was developed in early 1990s and has been successfully used for root perforation repair, root end filling, and one-visit apexification. MTA is composed mainly of tricalcium silicate and dicalcium silicate. When MTA is hydrated, calcium silicate hydrate (CSH) and calcium hydroxide is formed. Formed calcium hydroxide interacts with the phosphate ion in body fluid and form amorphous calcium phosphate (ACP) which finally transforms into calcium deficient hydroxyapatite (CDHA). These mineral precipitate were reported to form the MTA-dentin interfacial layer which enhances the sealing ability of MTA. Clinically, the use of zinc oxide euginol (ZOE) based materials may retard the setting of MTA. Also, the use of acids or contact with excessive blood should be avoided before complete set of MTA, because these conditions could adversely affect the hydration reaction of MTA. Further studies on the chemical nature of MTA hydration reaction are needed. PMID:23429542

  13. Thermal energy storage. [by means of chemical reactions

    NASA Technical Reports Server (NTRS)

    Grodzka, P. G.

    1975-01-01

    The principles involved in thermal energy storage by sensible heat, chemical potential energy, and latent heat of fusion are examined for the purpose of evolving selection criteria for material candidates in the low ( 0 C) and high ( 100 C) temperature ranges. The examination identifies some unresolved theoretical considerations and permits a preliminary formulation of an energy storage theory. A number of candidates in the low and high temperature ranges are presented along with a rating of candidates or potential candidates. A few interesting candidates in the 0 to 100 C region are also included. It is concluded that storage by means of reactions whose reversibility can be controlled either by product removal or by catalytic means appear to offer appreciable advantages over storage with reactions whose reversability cannot be controlled. Among such advantages are listed higher heat storage capacities and more favorable options regarding temperatures of collection, storage, and delivery. Among the disadvantages are lower storage efficiencies.

  14. Modeling the complex bromate-iodine reaction.

    PubMed

    Machado, Priscilla B; Faria, Roberto B

    2009-05-07

    In this article, it is shown that the FLEK model (ref 5 ) is able to model the experimental results of the bromate-iodine clock reaction. Five different complex chemical systems, the bromate-iodide clock and oscillating reactions, the bromite-iodide clock and oscillating reactions, and now the bromate-iodine clock reaction are adequately accounted for by the FLEK model.

  15. Predicting the evolution of fast chemical reactions in chaotic flows.

    PubMed

    Tsang, Yue-Kin

    2009-08-01

    We study the fast irreversible bimolecular reaction in a two-dimensional chaotic flow. The reactants are initially segregated and together fill the whole domain. Simulations show that the reactant concentration decays exponentially with rate lambda and then crosses over to the algebraic law of chemical kinetics in the final stage of the reaction. We estimate the crossover time from the reaction rate constant and the flow parameters. The exponential decay phase of the reaction can be described in terms of an equivalent passive scalar problem, allowing us to predict lambda using the theory of passive scalar advection. Depending on the relative length scale between the velocity and the concentration fields, lambda is either related to the distribution of the finite-time Lyapunov exponent of the flow or given in terms of an effective diffusivity which is independent of the small-scale stretching properties of the flow. For the former case, we suggest an optimal choice of flow parameters at which lambda is maximum.

  16. Confinement effects on chemical reactions in nanostructured carbon materials

    NASA Astrophysics Data System (ADS)

    George, Aaron; Kostov, Milen; Buongiorno Nardelli, Marco

    2005-03-01

    Chemical reactions are frequently carried out in nano-structured media, such as micellar or colloidal solutions, nano-porous media, hydrogels or organogels, or in systems involving nano-particles. Nanostructured environments have been shown to enhance reaction rates through a variety of catalytic effects, such as high surface area, interactions with the nano-structure or confinement. In this work, we have used state-of-the-art electronic structure techniques to study the prototypical example of the hydrogen-producing reaction of formaldehyde dissociation (H2CO -> H2 + CO) within various configurations of a graphitic pore. Using the Nudged Elastic Band (NEB) method for transition states analysis, we have found that the activation energy of the dissociation can be influenced by the presence of a graphitic pore. In particular, while a graphene surface reduces the activation barrier for the reaction, this catalytic effect is enhanced by the presence of two planar sheets, which mimic the geometry of a nano-pore. These findings will be discussed in terms of the charge transfer and/or polarization mechanism associated with the catalytic process.

  17. Chemical Kinetic Reaction Mechanisms for Combustion of Hydrocarbon and Other Types of Chemical Fuels

    DOE Data Explorer

    The central feature of the Combustion Chemistry project at LLNL is the development, validation, and application of detailed chemical kinetic reaction mechanisms for the combustion of hydrocarbon and other types of chemical fuels. For the past 30 years, LLNL's Chemical Sciences Division has built hydrocarbon mechanisms for fuels from hydrogen and methane through much larger fuels including heptanes and octanes. Other classes of fuels for which models have been developed include flame suppressants such as halons and organophosphates, and air pollutants such as soot and oxides of nitrogen and sulfur. Reaction mechanisms have been tested and validated extensively through comparisons between computed results and measured data from laboratory experiments (e.g., shock tubes, laminar flames, rapid compression machines, flow reactors, stirred reactors) and from practical systems (e.g., diesel engines, spark-ignition engines, homogeneous charge, compression ignition (HCCI) engines). These kinetic models are used to examine a wide range of combustion systems.

  18. Spatially resolved chemical reaction monitoring using magnetic resonance imaging.

    PubMed

    Feindel, Kirk W

    2016-06-01

    Over the previous three decades, the use of MRI for studying dynamic physical and chemical processes of materials systems has grown significantly. This mini-review provides a brief introduction to relevant principles of MRI, including methods of spatial localization, factors contributing to image contrast, and chemical shift imaging. A few historical examples of (1) H MRI for reaction monitoring will be presented, followed by a review of recent research including (1) H MRI studies of gelation and biofilms, (1) H, (7) Li, and (11) B MRI studies of electrochemical systems, in vivo glucose metabolism monitored with (19) F MRI, and in situ temperature monitoring with (27) Al MRI. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Scaling Laws for Pulsed Chain-Reaction Chemical Lasers.

    DTIC Science & Technology

    1981-08-07

    HOFLANO, J3 S WHITTIER FOR701-SO-C-OOB1 UCASFE0TR-006i167213 -1 SO-TR-61-57 N MEL LEYELi two Scaling Laws for Pulsed Chain-Reaction Chemical Lasers H...44 CNN u-i LU C=, C= Ca . C= -IN HAND Mil C C" 41 U c-iG- Ca1 ~-J4J -~40) c.Ji C-4- C= G’H Io sifld 83ld A91:3N3 1i7- For small K,te is of the order

  20. Exploring chemical diversity via a modular reaction pairing strategy.

    PubMed

    Loh, Joanna K; Yoon, Sun Young; Samarakoon, Thiwanka B; Rolfe, Alan; Porubsky, Patrick; Neuenswander, Benjamin; Lushington, Gerald H; Hanson, Paul R

    2012-01-01

    The efficient synthesis of an 80-member library of unique benzoxathiazocine 1,1-dioxides by a microwave-assisted, intermolecular nucleophilic aromatic substitution (S(N)Ar) diversification pathway is reported. Eight benzofused sultam cores were generated by means of a sulfonylation/S(N)Ar/Mitsunobu reaction pairing protocol, and subsequently diversified by intermolecular S(N)Ar with ten chiral, non-racemic amine/amino alcohol building blocks. Computational analyses were employed to explore and evaluate the chemical diversity of the library.

  1. Method for detecting pollutants. [through chemical reactions and heat treatment

    NASA Technical Reports Server (NTRS)

    Rogowski, R. S.; Richards, R. R.; Conway, E. J. (Inventor)

    1976-01-01

    A method is described for detecting and measuring trace amounts of pollutants of the group consisting of ozone, nitrogen dioxide, and carbon monoxide in a gaseous environment. A sample organic solid material that will undergo a chemical reaction with the test pollutant is exposed to the test environment and thereafter, when heated in the temperature range of 100-200 C., undergoes chemiluminescence that is measured and recorded as a function of concentration of the test pollutant. The chemiluminescence of the solid organic material is specific to the pollutant being tested.

  2. Peptide Bond Synthesis by a Mechanism Involving an Enzymatic Reaction and a Subsequent Chemical Reaction.

    PubMed

    Abe, Tomoko; Hashimoto, Yoshiteru; Zhuang, Ye; Ge, Yin; Kumano, Takuto; Kobayashi, Michihiko

    2016-01-22

    We recently reported that an amide bond is unexpectedly formed by an acyl-CoA synthetase (which catalyzes the formation of a carbon-sulfur bond) when a suitable acid and l-cysteine are used as substrates. DltA, which is homologous to the adenylation domain of nonribosomal peptide synthetase, belongs to the same superfamily of adenylate-forming enzymes, which includes many kinds of enzymes, including the acyl-CoA synthetases. Here, we demonstrate that DltA synthesizes not only N-(d-alanyl)-l-cysteine (a dipeptide) but also various oligopeptides. We propose that this enzyme catalyzes peptide synthesis by the following unprecedented mechanism: (i) the formation of S-acyl-l-cysteine as an intermediate via its "enzymatic activity" and (ii) subsequent "chemical" S → N acyl transfer in the intermediate, resulting in peptide formation. Step ii is identical to the corresponding reaction in native chemical ligation, a method of chemical peptide synthesis, whereas step i is not. To the best of our knowledge, our discovery of this peptide synthesis mechanism involving an enzymatic reaction and a subsequent chemical reaction is the first such one to be reported. This new process yields peptides without the use of a thioesterified fragment, which is required in native chemical ligation. Together with these findings, the same mechanism-dependent formation of N-acyl compounds by other members of the above-mentioned superfamily demonstrated that all members most likely form peptide/amide compounds by using this novel mechanism. Each member enzyme acts on a specific substrate; thus, not only the corresponding peptides but also new types of amide compounds can be formed. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Exploring the Chemical Reach of the Madden-Julian Oscillation using the A-Train data

    NASA Astrophysics Data System (ADS)

    Tian, B.; Li, K.; Waliser, D. E.; Yung, Y. L.; Fetzer, E.; Worden, J.; Schwartz, M. J.

    2010-12-01

    The Madden-Julian Oscillation (MJO) (aka Intraseasonal Oscillation) is the dominant component of the intraseasonal (30-90 day) variability in the tropical atmosphere. Since its discovery, the MJO has continued to be a topic of significant interest due to its extensive interactions with other components of the climate system and the fact that it represents a connection between the better-understood weather and seasonal-to-interannual climate variations. To date, influences of the MJO on the physical components of global climate system have been well recognized, documented, and in same cases, also well understood (e.g., monsoon, ENSO, hurricane, and extratropical weather). However, the impacts of the MJO on the chemical component of the climate system have been realized only recently and have not been well documented and understood. In the paper, we will present our recent exploration activities on the chemical reach of the MJO using the modern atmospheric composition satellite data. In particular, we will highlight our new findings on the MJO-related variations of water vapor (H2O) using the Aqua AIRS H2O data and the Aura TES HDO data, carbon dioxide (CO2) using the Aqua AIRS CO2 data, ozone using the Aura MLS and Aura TES ozone data, and aerosol from the MODIS AOT data.

  4. From perception to action: phase-locked gamma oscillations correlate with reaction times in a speeded response task

    PubMed Central

    Fründ, Ingo; Busch, Niko A; Schadow, Jeanette; Körner, Ursula; Herrmann, Christoph S

    2007-01-01

    Background Phase-locked gamma oscillations have so far mainly been described in relation to perceptual processes such as sensation, attention or memory matching. Due to its very short latency (≈90 ms) such oscillations are a plausible candidate for very rapid integration of sensory and motor processes. Results We measured EEG in 13 healthy participants in a speeded reaction task. Participants had to press a button as fast as possible whenever a visual stimulus was presented. The stimulus was always identical and did not have to be discriminated from other possible stimuli. In trials in which the participants showed a fast response, a slow negative potential over central electrodes starting approximately 800 ms before the response and highly phase-locked gamma oscillations over central and posterior electrodes between 90 and 140 ms after the stimulus were observed. In trials in which the participants showed a slow response, no slow negative potential was observed and phase-locked gamma oscillations were significantly reduced. Furthermore, for slow response trials the phase-locked gamma oscillations were significantly delayed with respect to fast response trials. Conclusion These results indicate the relevance of phase-locked gamma oscillations for very fast (not necessarily detailed) integration processes. PMID:17439642

  5. Parameter estimation in complex flows with chemical reactions

    NASA Astrophysics Data System (ADS)

    Robinson, Daniel J.

    The estimation of unknown parameters in engineering and scientific models continues to be of great importance in order to validate them to available experimental data. These parameters of concern cannot be known beforehand, but must be measured experimentally, variables such as chemical species concentrations, pressures, or temperatures as examples. Particularly, in chemically reacting flows, the estimation of kinetic rate parameters from experimentally determined values is in great demand and not well understood. New parameter optimization algorithms have been developed from a Gauss-Newton formulation for the estimation of reaction rate parameters in several different complex flow applications. A zero-dimensional parameter estimation methodology was used in conjunction with a parameter sensitivity study and then applied to three-dimensional flow models. This new parameter estimation technique was applied to three-dimensional models for chemical vapor deposition of silicon carbide and gallium arsenide semiconductor materials. The parameter estimation for silicon carbide for several different operating points was in close agreement to experiment. The parameter estimation for gallium arsenide proved to be very accurate, being within four percent of the experimental data. New parameter estimation algorithms were likewise created for a three-dimensional multiphase model for methanol spray combustion. The kinetic rate parameters delivered results in close agreement to experiment for profiles of combustion species products. In addition, a new parameter estimation method for the determination of spray droplet sizes and velocities is presented. The results for methanol combustion chemical species profiles are in good agreement to experiment for several different droplet sizes. Lastly, the parameter estimation method was extended to a bio-kinetic application, namely mitochondrial cells, that are cardiac or respiratory cells found in animals and humans. The results for the

  6. Single-collision studies of energy transfer and chemical reaction

    SciTech Connect

    Valentini, J.J.

    1993-12-01

    The research focus in this group is state-to-state dynamics of reaction and energy transfer in collisions of free radicals such as H, OH, and CH{sub 3} with H{sub 2}, alkanes, alcohols and other hydrogen-containing molecules. The motivation for the work is the desire to provide a detailed understanding of the chemical dynamics of prototype reactions that are important in the production and utilization of energy sources, most importantly in combustion. The work is primarily experimental, but with an important and growing theoretical/computational component. The focus of this research program is now on reactions in which at least one of the reactants and one of the products is polyatomic. The objective is to determine how the high dimensionality of the reactants and products differentiates such reactions from atom + diatom reactions of the same kinematics and energetics. The experiments use highly time-resolved laser spectroscopic methods to prepare reactant states and analyze the states of the products on a single-collision time scale. The primary spectroscopic tool for product state analysis is coherent anti-Stokes Raman scattering (CARS) spectroscopy. CARS is used because of its generality and because the extraction of quantum state populations from CARS spectra is straightforward. The combination of the generality and easy analysis of CARS makes possible absolute cross section measurements (both state-to-state and total), a particularly valuable capability for characterizing reactive and inelastic collisions. Reactant free radicals are produced by laser photolysis of appropriate precursors. For reactant vibrational excitation stimulated Raman techniques are being developed and implemented.

  7. Community Detection Using Dual-Representation Chemical Reaction Optimization.

    PubMed

    Chang, Honghao; Feng, Zuren; Ren, Zhigang

    2016-09-23

    Many complex networks have been shown to have community structures. Detecting those structures is very important for understanding the organization and function of networks. Because this problem is NP-hard, it is appropriate to resort to evolutionary algorithms. Chemical reaction optimization (CRO) is a novel evolutionary algorithm inspired by the interactions among molecules during chemical reactions. In this paper, we propose a CRO variant named dual-representation CRO (DCRO) to address the community detection problem. DCRO encodes a solution in two representations: one is locus-based and the other is vector-based. The former representation can ensure the validity of a solution and fits for diversification search, and the latter is convenient for intensification search. We thus design two operators for CRO based on these two representations. Their cooperation enables DCRO to achieve a good balance between exploration and exploitation. Experimental results on synthetic and real-life networks show that DCRO can find community structures close to the actual ones and is capable of achieving solutions comparable to several state-of-the-art methods.

  8. Community Detection Using Dual-Representation Chemical Reaction Optimization.

    PubMed

    Chang, Honghao; Feng, Zuren; Ren, Zhigang

    2016-09-23

    Many complex networks have been shown to have community structures. Detecting those structures is very important for understanding the organization and function of networks. Because this problem is NP-hard, it is appropriate to resort to evolutionary algorithms. Chemical reaction optimization (CRO) is a novel evolutionary algorithm inspired by the interactions among molecules during chemical reactions. In this paper, we propose a CRO variant named dual-representation CRO (DCRO) to address the community detection problem. DCRO encodes a solution in two representations: one is locus-based and the other is vector-based. The former representation can ensure the validity of a solution and fits for diversification search, and the latter is convenient for intensification search. We thus design two operators for CRO based on these two representations. Their cooperation enables DCRO to achieve a good balance between exploration and exploitation. Experimental results on synthetic and real-life networks show that DCRO can find community structures close to the actual ones and is capable of achieving solutions comparable to several state-of-the-art methods.

  9. Oscillation and reaction board techniques for estimating inertial properties of a below-knee prosthesis.

    PubMed

    Smith, Jeremy D; Ferris, Abbie E; Heise, Gary D; Hinrichs, Richard N; Martin, Philip E

    2014-05-08

    The purpose of this study was two-fold: (1) demonstrate a technique that can be used to directly estimate the inertial properties of a below-knee prosthesis, and (2) contrast the effects of the proposed technique and that of using intact limb inertial properties on joint kinetic estimates during walking in unilateral, transtibial amputees. An oscillation and reaction board system was validated and shown to be reliable when measuring inertial properties of known geometrical solids. When direct measurements of inertial properties of the prosthesis were used in inverse dynamics modeling of the lower extremity compared with inertial estimates based on an intact shank and foot, joint kinetics at the hip and knee were significantly lower during the swing phase of walking. Differences in joint kinetics during stance, however, were smaller than those observed during swing. Therefore, researchers focusing on the swing phase of walking should consider the impact of prosthesis inertia property estimates on study outcomes. For stance, either one of the two inertial models investigated in our study would likely lead to similar outcomes with an inverse dynamics assessment.

  10. Oscillation and Reaction Board Techniques for Estimating Inertial Properties of a Below-knee Prosthesis

    PubMed Central

    Smith, Jeremy D.; Ferris, Abbie E.; Heise, Gary D.; Hinrichs, Richard N.; Martin, Philip E.

    2014-01-01

    The purpose of this study was two-fold: 1) demonstrate a technique that can be used to directly estimate the inertial properties of a below-knee prosthesis, and 2) contrast the effects of the proposed technique and that of using intact limb inertial properties on joint kinetic estimates during walking in unilateral, transtibial amputees. An oscillation and reaction board system was validated and shown to be reliable when measuring inertial properties of known geometrical solids. When direct measurements of inertial properties of the prosthesis were used in inverse dynamics modeling of the lower extremity compared with inertial estimates based on an intact shank and foot, joint kinetics at the hip and knee were significantly lower during the swing phase of walking. Differences in joint kinetics during stance, however, were smaller than those observed during swing. Therefore, researchers focusing on the swing phase of walking should consider the impact of prosthesis inertia property estimates on study outcomes. For stance, either one of the two inertial models investigated in our study would likely lead to similar outcomes with an inverse dynamics assessment. PMID:24837164

  11. Influence of organic acids on oscillations and waves in the ferroin-catalyzed Belousov-Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Krüger, Frank; Nagy-Ungvárai, Zsuzsanna; Müller, Stefan C.

    Experiments of the influence of mesoxalic and tartronic acid on the oscillatory behavior and on the spiral tip motion in a ferroin-catalyzed Belousov-Zhabotinsky (BZ) solution are reported. The oscillations were observed in batch and CSTR systems, and for the investigations of the spiral tip motion an open gel reactor was used. A characteristic shoulder in the oscillations is associated with an additional Br - production phase. The chemical parameters for a transition from a hypocycloidal to a circular tip trajectory are found. The findings are compared with the temporal and spatial dynamic behavior, occurring during the ageing process of the solution.

  12. Reaction Paths and Chemical Activation Reactions of 2-Methyl-5-Furanyl Radical with (3)O2.

    PubMed

    Hudzik, Jason M; Bozzelli, Joseph W

    2017-10-05

    Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol(-1), due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring. The thermochemistry and kinetics of the oxidation of 2-methyfuran radical at position 5 of the furan ring, 2-methyl-5-furanyl radical (2MF5j), is analyzed. The resulting chemically activated species, 2MF5OOj radical, has a well depth of 51 kcal mol(-1) below the 2MF5j + O2 reactants; this is 4-5 kcal mol(-1) deeper than that of phenyl and vinyl radical plus O2, with both of these reactions known to undergo chain branching. Important, low-energy reaction pathways include chain branching dissociations, intramolecular abstractions, group transfers, and radical oxygen additions. Enthalpies of formation, entropies, and heat capacities for the stable molecules, radicals, and transition-state species are analyzed using computational methods. Calculated ΔH(°)f 298 values were determined using an isodesmic work reaction from the CBS-QB3 composite method. Elementary rate parameters are from saddle point transition-state structures and compared to variational transition-state analysis for the barrierless reactions. Temperature- and pressure-dependent rate constants which are calculated using QRRK and master equation analysis is used for falloff and stabilization.

  13. Perturbation of the tris(2,2'-bipyridine) ruthenium(II)-catalyzed Belousov-Zhabotinsky oscillating chemiluminescence reaction by L-cysteine and its application.

    PubMed

    Liu, Huimin; Han, Heyou

    2009-01-01

    Perturbation of the tris(2,2'-bipyridine)ruthenium(II) [Ru(bpy)(3)2+]-catalyzed Belousov-Zhabotinsky (BZ) oscillating chemiluminescence (CL) reaction induced by L-cysteine was observed in the closed system. It was found that the CL intensity was decreased in the presence of L-cysteine. Meanwhile, oscillation period and oscillating induction period were prolonged. The sufficient reproducible induction period was used as parameter for the analytical application of oscillating CL reaction. Under the optimum conditions, the changes in the oscillating CL induction period were linearly proportional to the concentration of L-cysteine in the range from 8.0 x 10(-7) to 5.0 x 10(-5 )mol L(-1) (r = 0.997) with a detection limit of 4.3 x 10(-7) mol L(-1). The possible mechanism of L-cysteine perturbation on the oscillating CL reaction was also discussed.

  14. The quantum dynamics of electronically nonadiabatic chemical reactions

    NASA Technical Reports Server (NTRS)

    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

  15. Ternary phase diagram for the Belousov-Zhabotinsky reaction-induced mechanical oscillation of intelligent PNIPAM colloids.

    PubMed

    Shen, Jingyi; Pullela, Srinivasa; Marquez, Manuel; Cheng, Zhengdong

    2007-12-06

    Belousov-Zhabotinsky (BZ) reaction-induced mechanical oscillation of poly(N-isopropylacrylamide) (PNIPAM) gel particles was investigated by the systematic variation of BZ substrate concentrations. The correlation between the dynamic behavior and substrate concentrations was presented in a ternary phase diagram. Both oscillatory and steady-state regimes exist on the phase diagram and are separated by a high-frequency oscillation band. Dependence of oscillation frequency and induction time on the substrate concentrations was also studied. To achieve size uniformity, these PNIPAM gel particles with covalently bound tris(bipyridyl)ruthenium(II) were synthesized via the coordination chemistry between a ruthenium complex and the monodispersed PNIPAM gel particles bearing bipyridine ligands.

  16. Assessment of reaction-rate predictions of a collision-energy approach for chemical reactions in atmospheric flows.

    SciTech Connect

    Gallis, Michail A.; Bond, Ryan Bomar; Torczynski, John Robert

    2010-06-01

    A recently proposed approach for the Direct Simulation Monte Carlo (DSMC) method to calculate chemical-reaction rates is assessed for high-temperature atmospheric species. The new DSMC model reproduces measured equilibrium reaction rates without using any macroscopic reaction-rate information. Since it uses only molecular properties, the new model is inherently able to predict reaction rates for arbitrary non-equilibrium conditions. DSMC non-equilibrium reaction rates are compared to Park's phenomenological nonequilibrium reaction-rate model, the predominant model for hypersonic-flow-field calculations. For near-equilibrium conditions, Park's model is in good agreement with the DSMC-calculated reaction rates. For far-from-equilibrium conditions, corresponding to a typical shock layer, significant differences can be found. The DSMC predictions are also found to be in very good agreement with measured and calculated non-equilibrium reaction rates, offering strong evidence that this is a viable and reliable technique to predict chemical reaction rates.

  17. Complex dynamic behavior in the bromate-oxalic acid-acetone-Mn(II) oscillating reaction in a continuous stirred tank reactor (CSTR)

    NASA Astrophysics Data System (ADS)

    Silva, Lucyane C.; Faria, Roberto B.

    2007-05-01

    The oscillating reaction bromate-oxalic acid-acetone-Mn(II)-sulfuric acid was observed for the first time in a CSTR at 20 °C. Depending on the bromate concentrations and flow rate, the system showed large amplitude oscillations, two kinds of mixed mode oscillations, quasiperiodicity and bursts of large amplitude oscillations, all mapped in a phase diagram. More complex behavior was favored at low bromate concentrations. The system without acetone was discovered to oscillate too, but the more complex patterns were not seen, indicating that acetone is implied in their formation.

  18. Miscible viscous fingering with a chemical reaction involving precipitation.

    PubMed

    Nagatsu, Yuichiro; Bae, Si-Kyun; Kato, Yoshihito; Tada, Yutaka

    2008-06-01

    We experimentally investigated the effects of a chemical reaction involving precipitation on the miscible viscous fingering pattern formed in a Hele-Shaw cell. The precipitation concentration, the ratio of the reactant concentrations initially included in the more- and less-viscous liquids, and the Péclet number were varied. For a Péclet number at the stoichiometric ratio the precipitation had significant effects on the fingering pattern when its concentration exceeded a threshold value. Interestingly, the type of effect of the precipitation on the pattern depended on its concentration. At moderate concentration, a straight-shaped finger was observed. At high concentration, the finger was bent in an almost perpendicular direction. The effect of precipitation on the pattern also depended on the ratio of reactant concentrations.

  19. Miscible viscous fingering involving production of gel by chemical reactions

    NASA Astrophysics Data System (ADS)

    Nagatsu, Yuichiro; Hoshino, Kenichi

    2015-11-01

    We have experimentally investigated miscible viscous fingering with chemical reactions producing gel. Here, two systems were employed. In one system, sodium polyacrylate (SPA) solution and aluminum ion (Al3 +) solution were used as the more and less viscous liquids, respectively. In another system, SPA solution and ferric ion (Fe3 +) solution were used as the more and less viscous liquids, respectively. In the case of Al3 +, displacement efficiency was smaller than that in the non-reactive case, whereas in the case of Fe3 +, the displacement efficiency was larger. We consider that the difference in change of the patterns in the two systems will be caused by the difference in the properties of the gels. Therefore, we have measured the rheological properties of the gels by means of a rheometer. We discuss relationship between the VF patterns and the rheological measurement.

  20. Chemical Reactions in the Processing of Mosi2 + Carbon Compacts

    NASA Technical Reports Server (NTRS)

    Jacobson, Nathan S.; Lee, Kang N.; Maloy, Stuart A.; Heuer, Arthur H.

    1993-01-01

    Hot-pressing of MoSi2 powders with carbon at high temperatures reduces the siliceous grain boundary phase in the resultant compact. The chemical reactions in this process were examined using the Knudsen cell technique. A 2.3 wt pct oxygen MoSi2 powder and a 0.59 wt pct oxygen MoSi2 powder, both with additions of 2 wt pct carbon, were examined. The reduction of the siliceous grain boundary phase was examined at 1350 K and the resultant P(SiO)/P(CO) ratios interpreted in terms of the SiO(g) and CO(g) isobars on the Si-C-O predominance diagram. The MoSi2 + carbon mixtures were then heated at the hot-pressing temperature of 2100 K. Large weight losses were observed and could be correlated with the formation of a low-melting eutectic and the formation and vaporization of SiC.

  1. Chemical Reactions in the Processing of Mosi2 + Carbon Compacts

    NASA Technical Reports Server (NTRS)

    Jacobson, Nathan S.; Lee, Kang N.; Maloy, Stuart A.; Heuer, Arthur H.

    1993-01-01

    Hot-pressing of MoSi2 powders with carbon at high temperatures reduces the siliceous grain boundary phase in the resultant compact. The chemical reactions in this process were examined using the Knudsen cell technique. A 2.3 wt pct oxygen MoSi2 powder and a 0.59 wt pct oxygen MoSi2 powder, both with additions of 2 wt pct carbon, were examined. The reduction of the siliceous grain boundary phase was examined at 1350 K and the resultant P(SiO)/P(CO) ratios interpreted in terms of the SiO(g) and CO(g) isobars on the Si-C-O predominance diagram. The MoSi2 + carbon mixtures were then heated at the hot-pressing temperature of 2100 K. Large weight losses were observed and could be correlated with the formation of a low-melting eutectic and the formation and vaporization of SiC.

  2. Waste Heat Recovery from Blast Furnace Slag by Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Qin, Yuelin; Lv, Xuewei; Bai, Chenguang; Qiu, Guibao; Chen, Pan

    2012-08-01

    Blast furnace (BF) slag, which is the main byproduct in the ironmaking process, contains large amounts of sensible heat. To recover the heat, a new waste heat-recovery system—granulating molten BF slag by rotary multinozzles cup atomizer and pyrolyzing printed circuited board with obtained hot BF slag particle—was proposed in this study. The feasibility of the waste heat-recovery system was verified by dry granulation and pyrolyzation experiments. The energy of hot BF slag could be converted to chemical energy through the pyrolysis reaction, and a large amount of combustible gas like CO, H2, C m H n , and CH4 can be generated during the process.

  3. Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks

    SciTech Connect

    Ziaul Huque

    2007-08-31

    This is the final technical report for the project titled 'Mathematically Reduced Chemical Reaction Mechanism Using Neural Networks'. The aim of the project was to develop an efficient chemistry model for combustion simulations. The reduced chemistry model was developed mathematically without the need of having extensive knowledge of the chemistry involved. To aid in the development of the model, Neural Networks (NN) was used via a new network topology known as Non-linear Principal Components Analysis (NPCA). A commonly used Multilayer Perceptron Neural Network (MLP-NN) was modified to implement NPCA-NN. The training rate of NPCA-NN was improved with the GEneralized Regression Neural Network (GRNN) based on kernel smoothing techniques. Kernel smoothing provides a simple way of finding structure in data set without the imposition of a parametric model. The trajectory data of the reaction mechanism was generated based on the optimization techniques of genetic algorithm (GA). The NPCA-NN algorithm was then used for the reduction of Dimethyl Ether (DME) mechanism. DME is a recently discovered fuel made from natural gas, (and other feedstock such as coal, biomass, and urban wastes) which can be used in compression ignition engines as a substitute for diesel. An in-house two-dimensional Computational Fluid Dynamics (CFD) code was developed based on Meshfree technique and time marching solution algorithm. The project also provided valuable research experience to two graduate students.

  4. Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics

    NASA Astrophysics Data System (ADS)

    Rao, Riccardo; Esposito, Massimiliano

    2016-10-01

    We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations with mass action kinetics. Our most general framework considers open networks driven by time-dependent chemostats. The energy and entropy balances are established and a nonequilibrium Gibbs free energy is introduced. The difference between this latter and its equilibrium form represents the minimal work done by the chemostats to bring the network to its nonequilibrium state. It is minimized in nondriven detailed-balanced networks (i.e., networks that relax to equilibrium states) and has an interesting information-theoretic interpretation. We further show that the entropy production of complex-balanced networks (i.e., networks that relax to special kinds of nonequilibrium steady states) splits into two non-negative contributions: one characterizing the dissipation of the nonequilibrium steady state and the other the transients due to relaxation and driving. Our theory lays the path to study time-dependent energy and information transduction in biochemical networks.

  5. Electrokinetics for control of on-chip chemical reactions.

    NASA Astrophysics Data System (ADS)

    Erickson, David; Venditti, Roberto

    2005-03-01

    It is well known that electrokinetics affords precise control over flow and species transport in microfluidic systems through simple manipulation of externally applied electric potentials. In this work it is demonstrated how electrokinetic effects can be extended to provide simultaneous control over on-chip chemical reactions through manipulation of the local thermal (ohmic/joule heating), shear (electroosmosis) and electrical (electrophoresis) energies at the reaction site. The coupling of the electrical, flow and ``whole-chip'' thermal effects in both the fluidic and substrate domains are investigated through extensive finite element simulations and experimentally validated using microscale fluorescence thermometry. The simulations reveal changes in viscosity and local conductivity on the order of 50% induced by changes in the fluidic geometry. General chip design guidelines for maximizing or minimizing these effects will also be discussed. The degree of precision available and clinical utility of the technique is demonstrated through the detection of a single base pair mutation (single nucleotide polymorphism) in a DNA microarray integrated into a PDMS/glass microfluidic chip.

  6. Reaction routes leading to CO2 and CO in the Briggs-Rauscher oscillator: analogies between the oscillatory BR and BZ reactions.

    PubMed

    Muntean, Norbert; Szabó, Gabriella; Wittmann, Maria; Lawson, Thuy; Fülöp, János; Noszticzius, Zoltán; Onel, Lavinia

    2009-08-13

    With Fenton-type experiments, it is shown that the intense CO2/CO evolution in the Briggs-Rauscher (BR) reaction is due to decarboxylation/decarbonylation of organic free radicals. The metal ion applied in the Fenton-type experiments was Fe2+ or Ti3+ or Mn2+ combined with H2O2 or S2O(8)(2-) as a peroxide, whereas the organic substrate was malonic acid (MA) or a 1:1 mixture of MA and iodomalonic acid (IMA). Experiments with a complete BR system applying MA or the MA/IMA mixture indicate that practically all CO2 and CO comes from IMA. The decarboxylation/decarbonylation mechanisms of various iodomalonyl radicals can be analogous to that of the bromomalonyl radicals studied already in the Belousov-Zhabotinsky (BZ) reaction. It is found that an intense CO2/CO evolution requires the simultaneous presence of H2O2, IO3-, Mn2+, and IMA. It is suggested that the critical first step of this complex reaction takes place in the coordination sphere of Mn2+. That first step can initiate a chain reaction where organic and hydroperoxyl radicals are the chain carriers. A chain reaction was already found in a BZ oscillator as well. Therefore, the analogies between the BR and BZ oscillators are due to the fact that in both mechanisms, free radicals and, in most cases, also transition-metal complexes play an important role.

  7. Chemically Reversible Reactions of Hydrogen Sulfide with Metal Phthalocyanines

    PubMed Central

    2015-01-01

    Hydrogen sulfide (H2S) is an important signaling molecule that exerts action on various bioinorganic targets. Despite this importance, few studies have investigated the differential reactivity of the physiologically relevant H2S and HS– protonation states with metal complexes. Here we report the distinct reactivity of H2S and HS– with zinc(II) and cobalt(II) phthalocyanine (Pc) complexes and highlight the chemical reversibility and cyclability of each metal. ZnPc reacts with HS–, but not H2S, to generate [ZnPc-SH]−, which can be converted back to ZnPc by protonation. CoPc reacts with HS–, but not H2S, to form [CoIPc]−, which can be reoxidized to CoPc by air. Taken together, these results demonstrate the chemically reversible reaction of HS– with metal phthalocyanine complexes and highlight the importance of H2S protonation state in understanding the reactivity profile of H2S with biologically relevant metal scaffolds. PMID:24785654

  8. Stochastic analysis of Chemical Reaction Networks using Linear Noise Approximation.

    PubMed

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca

    2016-11-01

    Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analyzed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species. We present an approximate model checking algorithm based on the Linear Noise Approximation (LNA) of the CME, whose computational complexity is independent of the population size of each species and polynomial in the number of different species. The algorithm requires the solution of first order polynomial differential equations. We prove that our approach is valid for any CRN close enough to the thermodynamical limit. However, we show on four case studies that it can still provide good approximation even for low molecule counts. Our approach enables rigorous analysis of CRNs that are not analyzable by solving the CME, but are far from the deterministic limit. Moreover, it can be used for a fast approximate stochastic characterization of a CRN.

  9. Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation.

    PubMed

    Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca

    2016-10-28

    Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some molecules occur in low numbers. Unfortunately, both approaches become infeasible if the system is complex and/or it cannot be ensured that initial populations are small. We develop a probabilistic logic for CRNs that enables stochastic analysis of the evolution of populations of molecular species. We present an approximate model checking algorithm based on the Linear Noise Approximation (LNA) of the CME, whose computational complexity is independent of the population size of each species and polynomial in the number of different species. The algorithm requires the solution of first order polynomial differential equations. We prove that our approach is valid for any CRN close enough to the thermodynamical limit. However, we show on four case studies that it can still provide good approximation even for low molecule counts. Our approach enables rigorous analysis of CRNs that are not analyzable by solving the CME, but are far from the deterministic limit. Moreover, it can be used for a fast approximate stochastic characterization of a CRN. Copyright © 2016. Published by Elsevier Ireland Ltd.

  10. From Master-Slave to Peer-to-Peer Coupling in Chemical Reaction Networks.

    PubMed

    Holló, Gábor; Dúzs, Brigitta; Szalai, István; Lagzi, István

    2017-05-04

    Design strategy through linking a driving pH oscillator (master system) to a pH sensitive complexation, precipitation, or protonation equilibrium (slave system) has been widely used to create and control concentration oscillations of chemical entities (e.g., monovalent cations, DNA, nanoparticles) not participating in the pH oscillatory system. No systematic investigation has been carried out on how the components of these equilibria affect the characteristics of the driving pH oscillators, and this feedback effect has been often neglected in previous studies. Here we show that pH sensitive species (hydrogen carbonate, EDTA) through a pH-dependent equilibrium could significantly affect the characteristics (time period and amplitude) of the driving pH oscillators. By varying the concentration of those species we are able to control the strength of the chemical feedback from slave system to master system thus introducing a transition from master-slave coupling to peer-to-peer coupling in linked chemical systems. To illustrate this transition and coupling strategies we investigate two coupled chemical systems, namely, the bromate-sulfite pH oscillator and carbonate-carbon dioxide equilibrium and the hydrogen peroxide-thiosulfate-copper(II) and EDTA complexation equilibrium. As a sign of the peer-to-peer coupling the characteristics of the driving oscillatory systems can be tuned by controlling the feedback strength, and the oscillations can be canceled above a critical value of this parameter.

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

    NASA Astrophysics Data System (ADS)

    Srinivas, Niranjan

    hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways. We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

  12. Chemical Reaction and Flow Modeling in Fullerene and Nanotube Production

    NASA Technical Reports Server (NTRS)

    Scott, Carl D.; Farhat, Samir; Greendyke, Robert B.

    2004-01-01

    The development of processes to produce fullerenes and carbon nanotubes has largely been empirical. Fullerenes were first discovered in the soot produced by laser ablation of graphite [1]and then in the soot of electric arc evaporated carbon. Techniques and conditions for producing larger and larger quantities of fullerenes depended mainly on trial and error empirical variations of these processes, with attempts to scale them up by using larger electrodes and targets and higher power. Various concepts of how fullerenes and carbon nanotubes were formed were put forth, but very little was done based on chemical kinetics of the reactions. This was mainly due to the complex mixture of species and complex nature of conditions in the reactors. Temperatures in the reactors varied from several thousand degrees Kelvin down to near room temperature. There are hundreds of species possible, ranging from atomic carbon to large clusters of carbonaceous soot, and metallic catalyst atoms to metal clusters, to complexes of metals and carbon. Most of the chemical kinetics of the reactions and the thermodynamic properties of clusters and complexes have only been approximated. In addition, flow conditions in the reactors are transient or unsteady, and three dimensional, with steep spatial gradients of temperature and species concentrations. All these factors make computational simulations of reactors very complex and challenging. This article addresses the development of the chemical reaction involved in fullerene production and extends this to production of carbon nanotubes by the laser ablation/oven process and by the electric arc evaporation process. In addition, the high-pressure carbon monoxide (HiPco) process is discussed. The article is in several parts. The first one addresses the thermochemical aspects of modeling; and considers the development of chemical rate equations, estimates of reaction rates, and thermodynamic properties where they are available. The second part

  13. Chemomechanical oscillations in a responsive gel induced by an autocatalytic reaction

    SciTech Connect

    Li, Kai; Wu, Peiyi; Cai, Shengqiang

    2014-07-28

    In this article, we investigate dynamic behaviors of a gel layer attached to a rigid substrate and submerged in a continuous stirred tank reactor. With a continuous feed of fresh reactants in the reactor, the concentrations of reactants stay constant on the surface of the gel layer. However, the concentrations of reactants inside the gel are inhomogeneous and vary with time, which are determined by the diffusion and chemical reactions of the reactants. Additionally, both monotonic and oscillatory swelling-shrinking dynamics are predicted in the gel if the swelling capability of the gel depends on the concentration of a reactant. Based on autocatalytic reaction, kinetic model, and nonequilibrium thermodynamic theory of gels, in this article, we investigate the effect of the thickness of the gel layer, lateral prestretches in the gel and the initial concentrations of reactants in the gel on its dynamic behaviors. We have also calculated the evolution of the swelling force that the gel layer exerts on its constrained substrate. The results of this article may find potential applications in using responsive gels to make chemo-mechanical sensors, actuators, biomimetic devices, and even drug delivery systems.

  14. Computer-controlled system for the study of oxidase reactions: application to the peroxidase-oxidase oscillator.

    PubMed

    McDonald, Andrew G; Tipton, Keith F

    2010-12-16

    An apparatus for the study of bisubstrate oxidase reactions at maintained steady-state substrate concentrations is described, and its specific application to the peroxidase-oxidase biochemical oscillator is reported. Instrument control and data acquisition are provided by custom software written in LabVIEW. The software allows measurement, recording, and control of dissolved oxygen through a Clark-type oxygen electrode, reaction monitoring by a UV/vis spectrophotometer, and controlled substrate delivery by a syringe infusion pump. For peroxidase from horseradish, the optimal pH for oscillatory behavior was found to be in the range 4.5-5.5.

  15. Inorganic chemicals in an effluent-dominated stream as indicators for chemical reactions and streamflows

    NASA Astrophysics Data System (ADS)

    Kim, Kangjoo; Lee, Ji Sun; Oh, Chang-Whan; Hwang, Gab-Soo; Kim, Jinsam; Yeo, Sungku; Kim, Yeongkyoo; Park, Seongmin

    2002-07-01

    The chemical behavior of major inorganic ions in the streams of the Mankyung River area (South Korea) was investigated. Mixing with effluent from the Jeonju STP (a municipal sewage treatment plant in Jeonju City) was the most important process in regulating the water chemistry of the streams. The effluent was chemically distinct relative to the stream waters in inorganic composition. Behavior of various ions was evaluated by comparing their concentrations with the concentration of chloride, a conservative chemical species. It was revealed that concentrations of chloride and sulfate, the total concentration of major cations, and electrical conductivity in the stream were controlled only by mixing, indicating their conservative behavior similar to chloride. Alkalinity and concentration of nitrate, however, were regulated by various reactions such as mixing, photosynthesis, respiration, and decomposition of organic matter. Streamflows were estimated by observing chemical composition of the effluent and those of up/downstream waters. Estimated flows based on the conservative chemical parameters were nearly the same as those directly measured using an area-velocity method, indicating the validity of the chemistry-based method.

  16. Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction.

    PubMed

    Schenk, Gerhard; Mitić, Nataša; Gahan, Lawrence R; Ollis, David L; McGeary, Ross P; Guddat, Luke W

    2012-09-18

    Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-β-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear

  17. Low-energy electron-stimulated chemical reactions of CO in water ice

    NASA Astrophysics Data System (ADS)

    Yamamoto, S.; Beniya, A.; Mukai, K.; Yamashita, Y.; Yoshinobu, J.

    2004-04-01

    We investigated low-energy electron-stimulated chemical reactions between CO and water molecules in low-temperature ice using infrared reflection absorption spectroscopy. Carbon dioxide, the formyl radical, formaldehyde, and methanol were produced by electron irradiation of the water/CO/water layered ice. The electron energy threshold and temperature dependence for the chemical reactions were investigated to elucidate the reaction mechanisms.

  18. CH 1 Introduction to Chemistry. Study Guide to Minicourse I - 13 Chemical Reaction Principles.

    ERIC Educational Resources Information Center

    Schlenker, Richard

    Provided is a study guide for an introductory minicourse to the principles of chemical reactions. This written text is designed to accompany a series of audio tapes and 35mm slides which the student studies at his own pace. The course presents chemical kinetics, reaction mechanisms, reaction rates, and equilibrium. (SL)

  19. Progression in High School Students' (Aged 16-18) Conceptualizations about Chemical Reactions in Solution.

    ERIC Educational Resources Information Center

    Boo, Hong-Kwen; Watson, J. R.

    2001-01-01

    Explores the development over time of students' understandings of the concept of chemical reaction in the context of two familiar reactions in solution. Based on interviews (n=48), results show that students made some progress in their understanding of the concept of chemical reaction but some fundamental misconceptions remained. (Author/MM)

  20. Transport Properties of a Kinetic Model for Chemical Reactions without Barriers

    SciTech Connect

    Alves, Giselle M.; Kremer, Gilberto M.; Soares, Ana Jacinta

    2011-05-20

    A kinetic model of the Boltzmann equation for chemical reactions without energy barrier is considered here with the aim of evaluating the reaction rate and characterizing the transport coefficient of shear viscosity for the reactive system. The Chapman-Enskog solution of the Boltzmann equation is used to compute the chemical reaction effects, in a flow regime for which the reaction process is close to the final equilibrium state. Some numerical results are provided illustrating that the considered chemical reaction without energy barrier can induce an appreciable influence on the reaction rate and on the transport coefficient of shear viscosity.